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<h3>
Liubov Chuprikova pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/q2cli">Debian Med / q2cli</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb">5e908400</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-06-13T17:16:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2019.4.0</pre>
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</ul>
<h4>24 changed files:</h4>
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<li class="file-stats">
<a href="#749265f6511bc4239de81ab66ede284d63282a64">
.github/ISSUE_TEMPLATE/6-where-to-go.md
</a>
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<li class="file-stats">
<a href="#f7478ad2bb1f2fdc99e6d1a022c885c19f82b885">
.github/SUPPORT.md
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<li class="file-stats">
<a href="#bbbaebc3b23edbc86f41413722d48d29eeeb5f58">
q2cli/__init__.py
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<li class="file-stats">
<a href="#ba66450cf2f4739dc96974820c344fd32edb89f0">
q2cli/_version.py
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<li class="file-stats">
<a href="#79ab0b14dff3d9ba5099bcc9a20f5260bd07a8e5">
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q2cli/builtin/__init__.py
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<a href="#4b9183b04ea8b786b7629167ed36b068044653d0">
q2cli/dev.py
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q2cli/builtin/dev.py
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<li class="file-stats">
<a href="#71b88b101d6e0e9e60898a2fdbc162df0c2b301a">
q2cli/info.py
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q2cli/builtin/info.py
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<li class="file-stats">
<a href="#fd958db9213491909191b55c302d3c4274621ebb">
q2cli/tools.py
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q2cli/builtin/tools.py
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q2cli/click/__init__.py
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q2cli/click/command.py
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q2cli/click/licenses/click.LICENSE.rst
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<li class="file-stats">
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q2cli/click/option.py
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q2cli/click/parser.py
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q2cli/click/type.py
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q2cli/commands.py
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<a href="#dfd184050fb528c09218940c2d755dd558c09f9d">
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−
q2cli/core.py
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q2cli/core/__init__.py
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q2cli/cache.py
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q2cli/core/cache.py
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<a href="#eada752a2adf82b343f70a4bedf2ece9781b60f2">
q2cli/completion.py
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q2cli/core/completion.py
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q2cli/handlers.py
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<a href="#dc5f5985a047865b81ba832edeea7666a8a308b7">
q2cli/tests/test_cli.py
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<a href="#69859555882ae5b802d6b617deeaece2a2130265">
q2cli/tests/test_core.py
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<a href="#a118f7a6f38ac6924500fb5556f843fdf73e82fb">
q2cli/tests/test_tools.py
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<a href="#67c0d02b0c1dcfe41eea76bbf17741e56aa00544">
q2cli/util.py
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<h4>Changes:</h4>
<li id="749265f6511bc4239de81ab66ede284d63282a64">
<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#749265f6511bc4239de81ab66ede284d63282a64"><strong>.github/ISSUE_TEMPLATE/6-where-to-go.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,6 +59,9 @@ Sorted alphabetically by repo name.</td>
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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
59
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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
59
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="p">-</span> The q2-diversity plugin</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"> https://github.com/qiime2/q2-diversity/issues</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">-</span> The q2-diversity-lib plugin</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"> https://github.com/qiime2/q2-diversity-lib/issues</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">-</span> The q2-emperor plugin</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"> https://github.com/qiime2/q2-emperor/issues</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>
</pre>
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</tr>
</table>
<br>
</li>
<li id="f7478ad2bb1f2fdc99e6d1a022c885c19f82b885">
<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#f7478ad2bb1f2fdc99e6d1a022c885c19f82b885"><strong>.github/SUPPORT.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,6 +52,8 @@ Sorted alphabetically by repo name.</td>
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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"> | The q2-demux plugin</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
53
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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
53
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">q2-diversity</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/qiime2/q2-diversity/issues</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
54
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"> | The q2-diversity plugin</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">q2-diversity-lib</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/qiime2/q2-diversity-lib/issues</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"> | The q2-diversity-lib plugin</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
55
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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">q2-emperor</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/qiime2/q2-emperor/issues</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"> | The q2-emperor plugin</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">q2-feature-classifier</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/qiime2/q2-feature-classifier/issues</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#bbbaebc3b23edbc86f41413722d48d29eeeb5f58"><strong>q2cli/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,9 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Option</span><span class="p">,</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_versions</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Option'</span><span class="p">,</span> <span class="s" style="color: #d14;">'option'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_versions</span><span class="p">()[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">get_versions</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#ba66450cf2f4739dc96974820c344fd32edb89f0"><strong>q2cli/_version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">1</span>.0)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">bd4936307955a839c754dae505722e53328a124a</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-0<span class="idiff left right">1-29 14:00:34</span> +0000"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">4</span>.0)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">dc80fad32777035091692ce1083088380a6ac509</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-0<span class="idiff left right">5-03 04:14:45</span> +0000"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,11 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.click.command</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ToolCommand</span><span class="p">,</span> <span class="n" style="color: #333;">ToolGroupCommand</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Utilities for developers and advanced users.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Utilities for developers and advanced users.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolGroupCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dev</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +24,8 @@ def dev():</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">"is necessary because package versions do not typically "</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"change each time an update is made to a package's code. "</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"Setting the environment variable Q2CLIDEV to any value "</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"will always refresh the cache when a command is run."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"will always refresh the cache when a command is run."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refresh_cache</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.cache</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">refresh</span><span class="p">()</span></span></pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.c<span class="idiff left right">ore.c</span>ache</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c<span class="idiff left">ore</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">c</span>ache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">refresh</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#71b88b101d6e0e9e60898a2fdbc162df0c2b301a"><strong>q2cli/info.py</strong>
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<strong>q2cli/builtin/info.py</strong>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">q2cli</span></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">q2cli.click.command</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ToolCommand</span></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_echo_version</span><span class="p">():</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,9 +25,9 @@ def _echo_version():</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_echo_plugins</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.cache</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.c<span class="idiff left right">ore.c</span>ache</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">plugins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plugins</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">plugins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c<span class="idiff left">ore</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">c</span>ache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plugins</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">plugins</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">plugin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">plugins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,32 +36,17 @@ def _echo_plugins():</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'the official QIIME 2 plugins at https://qiime2.org'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_echo_installed_packages</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pip</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This code was derived from an example provide here:</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23885252/3424666</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">installed_packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">([</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s==</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pip</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_installed_distributions</span><span class="p">()])</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">installed_packages</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Display information about current deployment.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--py-packages'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Display names and versions of all installed Python '</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'packages.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">info</span><span class="p">(</span><span class="n" style="color: #333;">py_packages</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Display information about current deployment.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">info</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.cache</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This import improves performance for repeated _echo_plugins</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.core.cache</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'System versions'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">_echo_version</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Installed plugins'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">_echo_plugins</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">py_packages</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Installed Python packages'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">_echo_installed_packages</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Application config directory'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_app_dir</span><span class="p">())</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#fd958db9213491909191b55c302d3c4274621ebb"><strong>q2cli/tools.py</strong>
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<strong>q2cli/builtin/tools.py</strong>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,10 +10,15 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.click.command</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ToolCommand</span><span class="p">,</span> <span class="n" style="color: #333;">ToolGroupCommand</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Tools for working with QIIME 2 files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">_COMBO_METAVAR</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ARTIFACT/VISUALIZATION'</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Tools for working with QIIME 2 files.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolGroupCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tools</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,18 +28,18 @@ def tools():</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'or a Visualization'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Exporting extracts (and optionally transforms) data '</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'stored inside an Artifact or Visualization. Note that '</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'Visualizations cannot be transformed with --output-format'</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">option</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--input-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'Visualizations cannot be transformed with --output-format'</span><span class="p"><span class="idiff left right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">cls</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">ToolCommand</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">click</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">option</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--input-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">metavar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">_COMBO_METAVAR</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to file that should be exported'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">writable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to file or directory where '</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'data should be exported to'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-format'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-format'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Format which the data should be exported as. '</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'This option cannot be used with Visualizations'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">export_data</span><span class="p">(</span><span class="n" style="color: #333;">input_path</span><span class="p">,</span> <span class="n" style="color: #333;">output_path</span><span class="p">,</span> <span class="n" style="color: #333;">output_format</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,29 +117,30 @@ def show_importable_formats(ctx, param, value):</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Import data to create a new QIIME 2 Artifact. See "</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"https://docs.qiime2.org/ for usage examples and details "</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"on the file types and associated semantic types that can "</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"be imported."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--type'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"be imported."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--type'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The semantic type of the artifact that will be created '</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">'upon importing. Use --show-importable-types to see what '</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'importable semantic types are available in the current '</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">'deployment.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to file or directory that should be imported.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">option</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--output-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">,</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">click</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">option</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--output-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">metavar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'ARTIFACT'</span></span><span class="p">,</span></span>
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126
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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127
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">writable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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128
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path where output artifact should be written.'</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-format'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-format'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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130
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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The format of the data to be imported. If not provided, '</span></span>
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131
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="s" style="color: #d14;">'data must be in the format expected by the semantic type '</span></span>
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132
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">'provided via --type.'</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--show-importable-types'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--show-importable-types'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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134
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">show_importable_types</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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135
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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show the semantic types that can be supplied to --type '</span></span>
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136
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">'to import data into an artifact.'</span><span class="p">)</span></span>
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137
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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--show-importable-formats'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--show-importable-formats'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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138
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">show_importable_formats</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show formats that can be supplied to --input-format to '</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">'import data into an artifact.'</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,9 +169,11 @@ def import_data(type, input_path, output_path, input_format):</td>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Take a peek at a QIIME 2 Artifact or '</span></span>
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164
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">'Visualization.'</span><span class="p">,</span></span>
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Display basic information about a QIIME 2 Artifact or "</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"Visualization, including its UUID and type."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">"Visualization, including its UUID and type."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'path'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_COMBO_METAVAR</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">peek</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,10 +192,11 @@ def peek(path):</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Inspect columns available in metadata.'</span><span class="p">,</span></span>
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185
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Inspect metadata files or artifacts viewable as metadata.'</span></span>
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186
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">' Providing multiple file paths to this command will merge'</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="s" style="color: #d14;">' the metadata.'</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--tsv/--no-tsv'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">' the metadata.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--tsv/--no-tsv'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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189
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Print as machine-readable TSV instead of text.'</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'paths'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'paths'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">metavar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'METADATA...'</span></span><span class="p"><span class="idiff right">,</span></span></span>
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191
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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192
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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193
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pretty_failure</span><span class="p">(</span><span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -265,11 +274,12 @@ def _load_metadata(path):</td>
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'View a QIIME 2 Visualization.'</span><span class="p">,</span></span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Displays a QIIME 2 Visualization until the command "</span></span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="s" style="color: #d14;">"exits. To open a QIIME 2 Visualization so it can be "</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="s" style="color: #d14;">"used after the command exits, use 'qiime extract'."</span><span class="p">)</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'visualization-path'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="s" style="color: #d14;">"used after the command exits, use 'qiime extract'."</span><span class="p">,</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'visualization-path'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'VISUALIZATION'</span><span class="p">,</span></span>
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270
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--index-extension'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'html'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--index-extension'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'html'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The extension of the index file that should be opened. '</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="s" style="color: #d14;">'[default: html]'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">view</span><span class="p">(</span><span class="n" style="color: #333;">visualization_path</span><span class="p">,</span> <span class="n" style="color: #333;">index_extension</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -337,12 +347,13 @@ def view(visualization_path, index_extension):</td>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="s" style="color: #d14;">"Visualization's archive, including provenance, metadata, "</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="s" style="color: #d14;">"and actual data. Use 'qiime tools export' to export only "</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">"the data stored in an Artifact or Visualization, with "</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="s" style="color: #d14;">"the choice of exporting to different formats."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="s" style="color: #d14;">"the choice of exporting to different formats."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--input-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_COMBO_METAVAR</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to file that should be extracted'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">q2cli</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left right">click</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--output-path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">writable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Directory where archive should be extracted to '</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -370,10 +381,12 @@ def extract(input_path, output_path):</td>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="s" style="color: #d14;">'and/or more thorough validation of your data (e.g. when '</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="s" style="color: #d14;">'debugging issues with your data or analyses).</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Note: '</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="s" style="color: #d14;">'validation can take some time to complete, depending on '</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="s" style="color: #d14;">'the size and type of your data.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="s" style="color: #d14;">'the size and type of your data.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'path'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--level'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Choice</span><span class="p">([</span><span class="s" style="color: #d14;">'min'</span><span class="p">,</span> <span class="s" style="color: #d14;">'max'</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_COMBO_METAVAR</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--level'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Choice</span><span class="p">([</span><span class="s" style="color: #d14;">'min'</span><span class="p">,</span> <span class="s" style="color: #d14;">'max'</span><span class="p">]),</span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Desired level of validation. "min" will perform minimal '</span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="s" style="color: #d14;">'validation, and "max" will perform maximal validation (at '</span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="s" style="color: #d14;">'the potential cost of runtime).'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -404,9 +417,11 @@ def validate(path, level):</td>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Print citations for a QIIME 2 result.'</span><span class="p">,</span></span>
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406
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Print citations as a BibTex file (.bib) for a QIIME 2'</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="s" style="color: #d14;">' result.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="s" style="color: #d14;">' result.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ToolCommand</span><span class="p">)</span></span>
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argument</span><span class="p">(</span><span class="s" style="color: #d14;">'path'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_COMBO_METAVAR</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">citations</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#2670690bb5fc3e71b0d71bad6dea0577a5b0a717"><strong>q2cli/click/__init__.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#00a3610cef01cb0a07b0017655f3d8587b7eb372"><strong>q2cli/click/command.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Some of the source code in this file is derived from original work:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># To see the license for the original work, see licenses/click.LICENSE.rst</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Specific reproduction and derivation of original work is marked below.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click.core</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BaseCommandMixin</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Modified from original:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L867 ></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_parser</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"""Creates the underlying option parser for this command."""</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.parser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Q2Parser</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q2Parser</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_params</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_to_parser</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Modified from original:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L934 ></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_parser</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">skip_rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># surely this is enough attempts</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">param_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ClickException</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">skip_rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">skip_rest</span><span class="p">:</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iter_params_for_processing</span><span class="p">(</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">param_order</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_params</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)):</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_parse_result</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ClickException</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allow_extra_args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resilient_parsing</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">UsageError</span><span class="p">(</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'Got unexpected extra argument</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)'</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'s'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_str</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)))))</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">errors</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_help</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">errors</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">problems</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'There were some problems with the command:'</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">problems</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'There was a problem with the command:'</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="n" style="color: #333;">problems</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">(</span><span class="mi" style="color: #099;">78</span><span class="p">,</span> <span class="s" style="color: #d14;">' '</span><span class="p">),</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'yellow'</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">errors</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">formatting</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrap_text</span><span class="p">(</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format_message</span><span class="p">(),</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">initial_indent</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s) '</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">errors</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">'?'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">skip_rest</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">''</span><span class="p">),</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">subsequent_indent</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">args</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_option_names</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">'__option_names'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_params</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="s" style="color: #d14;">'q2_name'</span><span class="p">):</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_name</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__option_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">names</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__option_names</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">list_commands</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">super</span><span class="p">(),</span> <span class="s" style="color: #d14;">'list_commands'</span><span class="p">):</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">list_commands</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_opt_groups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">'Options'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_params</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">))}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_help_text</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">):</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format_help_text</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_paragraph</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Modified from original:</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># /c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L830 ></span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_usage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"""Writes the usage line into the formatter."""</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">pieces</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collect_usage_pieces</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_usage</span><span class="p">(</span><span class="n" style="color: #333;">_style_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command_path</span><span class="p">),</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">pieces</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">,</span> <span class="n" style="color: #333;">COL_MAX</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">23</span><span class="p">,</span> <span class="n" style="color: #333;">COL_MIN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># write options</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">opt_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">options</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_opt_groups</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">opt_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">options</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_help_record</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">opt_records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">))</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">opt_groups</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_records</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">first_columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">COL_MAX</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">COL_MIN</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">first_columns</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">COL_MAX</span><span class="p">)))</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt_group</span><span class="p">,</span> <span class="n" style="color: #333;">opt_records</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opt_groups</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opt_records</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_heading</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="n" style="color: #333;">opt_group</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indent</span><span class="p">()</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">padded_border</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">current_indent</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opt_records</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_option</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="n" style="color: #333;">padded_border</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dedent</span><span class="p">()</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Modified from original:</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># https://github.com/pallets/click/blob</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># /c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L1056</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">commands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">subcommand</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">list_commands</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_command</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">subcommand</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># What is this, the tool lied about a command. Ignore it</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmd</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hidden</span><span class="p">:</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">commands</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">subcommand</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">))</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># allow for 3 times the default spacing</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">commands</span><span class="p">):</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cmd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">commands</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">subcommand</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">commands</span><span class="p">:</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_short_help_str</span><span class="p">(</span><span class="n" style="color: #333;">limit</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">rows</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">_style_command</span><span class="p">(</span><span class="n" style="color: #333;">subcommand</span><span class="p">),</span> <span class="n" style="color: #333;">help</span><span class="p">))</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">section</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="s" style="color: #d14;">'Commands'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)):</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_dl</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="p">,</span> <span class="n" style="color: #333;">COL_SPACING</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">):</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">full_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">current_indent</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">indent_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">current_indent</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">opt_text</span><span class="p">,</span> <span class="n" style="color: #333;">help_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">opt_text_secondary</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">opt_text</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">:</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">opt_text</span><span class="p">,</span> <span class="n" style="color: #333;">opt_text_secondary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_text</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span><span class="p">,</span> <span class="n" style="color: #333;">requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_clean_help</span><span class="p">(</span><span class="n" style="color: #333;">help_text</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">type_placement</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">type_indent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">indent_text</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="s" style="color: #d14;">'get_type_repr'</span><span class="p">):</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_type_repr</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">type_repr</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_repr</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_indent</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">type_placement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'under'</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">type_placement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'beside'</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">opt_text</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">border</span><span class="p">:</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simple_wrap</span><span class="p">(</span><span class="n" style="color: #333;">opt_text</span><span class="p">,</span> <span class="n" style="color: #333;">full_width</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">opt_text</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)]</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt_text_secondary</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">opt_text_secondary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">))</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tokens</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">current_indent</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">styled</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tokens</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'--'</span><span class="p">):</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_style_option</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">required</span><span class="p">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">styled</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indent_text</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">styled</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">to_write</span><span class="p">))</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">type_placement</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'beside'</span><span class="p">:</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simple_wrap</span><span class="p">(</span><span class="n" style="color: #333;">type_repr</span><span class="p">,</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_indent</span><span class="p">),</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">start_col</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">first_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tokens</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first_iter</span><span class="p">:</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_style_type</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">first_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_indent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_indent</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_style_type</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">to_write</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COL_SPACING</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">left_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">padding</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COL_SPACING</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dangling_edge</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">padding</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">padding</span><span class="p">)</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">left_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># jagged start</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">type_placement</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'under'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">padding</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COL_SPACING</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_repr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_indent</span><span class="p">))</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">type_indent</span><span class="p">,</span> <span class="n" style="color: #333;">_style_type</span><span class="p">(</span><span class="n" style="color: #333;">type_repr</span><span class="p">),</span> <span class="n" style="color: #333;">padding</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">left_col</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="s" style="color: #d14;">'meta_help'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">meta_help</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">meta_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simple_wrap</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">meta_help</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">type_indent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">([</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">meta_help</span><span class="p">]):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_indent</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'('</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_indent</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">meta_help</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">')'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COL_SPACING</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">left_col</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">right_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simple_wrap</span><span class="p">(</span><span class="n" style="color: #333;">help_text</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">COL_SPACING</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">right_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_color_important</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tokens</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">right_col</span><span class="p">]</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zip_longest</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">left_col</span><span class="p">,</span> <span class="n" style="color: #333;">right_col</span><span class="p">,</span> <span class="n" style="color: #333;">fillvalue</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">border</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COL_SPACING</span><span class="p">)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">to_write</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">right</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">to_write</span><span class="p">))</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">requirements</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">to_write</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">to_write</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">((</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">left_col</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">left_col</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">''</span><span class="p">):</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">formatting</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">term_len</span><span class="p">(</span><span class="n" style="color: #333;">to_write</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># dangling_edge is still correct</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dangling_edge</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">requirements</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span><span class="p">:</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">pad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">requirements</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">pad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">requirements</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dangling_edge</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">((</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pad</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_style_reqs</span><span class="p">(</span><span class="n" style="color: #333;">requirements</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_color_important</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tokens</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tokens</span><span class="p">:</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'_'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">t</span><span class="p">:</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_option_names</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">r'[^\w]'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">r'(\w+)'</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">():</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">()]</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_style_emphasis</span><span class="p">(</span><span class="n" style="color: #333;">word</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="p">[:</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">():]</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">token</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">t</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_clean_help</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">reqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'[required]'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[optional]'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[default: '</span><span class="p">]</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">req</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reqs</span><span class="p">:</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">req</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">text</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">req</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">req_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">requirement</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">text</span><span class="p">[:</span><span class="n" style="color: #333;">req_idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),</span> <span class="n" style="color: #333;">text</span><span class="p">[</span><span class="n" style="color: #333;">req_idx</span><span class="p">:]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ToolCommand</span><span class="p">(</span><span class="n" style="color: #333;">BaseCommandMixin</span><span class="p">,</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">):</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ToolGroupCommand</span><span class="p">(</span><span class="n" style="color: #333;">BaseCommandMixin</span><span class="p">,</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Group</span><span class="p">):</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">simple_wrap</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">start_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[]]</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">current_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">current_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_col</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">tokens</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">text</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">target</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">tokens</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">),</span> <span class="n" style="color: #333;">target</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">tokens</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">target</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tokens</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">token_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">current_width</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">token_len</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">target</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">current_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">current_line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">current_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_len</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">current_width</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">token_len</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_style_option</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'blue'</span><span class="p">,</span> <span class="n" style="color: #333;">underline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_style_type</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_style_reqs</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'magenta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_style_command</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_style_option</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">)</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"></span>
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373
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_style_emphasis</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">underline</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Copyright © 2014 by the Pallets team.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Some rights reserved.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Redistribution and use in source and binary forms of the software as</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">well as documentation, with or without modification, are permitted</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">provided that the following conditions are met:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">- Redistributions of source code must retain the above copyright</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">- Redistributions in binary form must reproduce the above copyright</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in the</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> documentation and/or other materials provided with the distribution.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Neither the name of the copyright holder nor the names of its</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> contributors may be used to endorse or promote products derived from</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> this software without specific prior written permission.</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">THIS SOFTWARE AND DOCUMENTATION IS PROVIDED BY THE COPYRIGHT HOLDERS AND</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE</span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">THIS SOFTWARE AND DOCUMENTATION, EVEN IF ADVISED OF THE POSSIBILITY OF</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">SUCH DAMAGE.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">----</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Click uses parts of optparse written by Gregory P. Ward and maintained</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">by the Python Software Foundation. This is limited to code in parser.py.</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Copyright © 2001-2006 Gregory P. Ward. All rights reserved.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Copyright © 2002-2006 Python Software Foundation. All rights reserved.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#34c31663d5050120ebf76a215b52500c49fb233e"><strong>q2cli/click/option.py</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.type</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">QIIME2Type</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Sentinel to avoid the situation where `None` *is* the default value.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">NoDefault</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GeneratedOption</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">multiple</span><span class="p">,</span> <span class="n" style="color: #333;">is_bool_flag</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'m'</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiple</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'list'</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">set</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_bool_flag</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">no</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="s" style="color: #d14;">'no_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'--{prefix}-{yes}/--{prefix}-{no}'</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">metadata</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">cli_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'--{prefix}-{cli_name}-file'</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'column'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_dest</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_opts</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_decls</span><span class="p">([</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'--{prefix}-{cli_name}-column'</span><span class="p">],</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">cli_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'--{prefix}-{cli_name}'</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">click_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QIIME2Type</span><span class="p">(</span><span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">is_output</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'o'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'metavar'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metavar</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'multiple'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multiple</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'param_decls'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">opt</span><span class="p">]</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'required'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">NoDefault</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'help'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_default</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">NoDefault</span><span class="p">:</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'default'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This is to evade clicks __DEBUG__ check</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_bool_flag</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click_type</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># put things back the way they _should_ be after evading __DEBUG__</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_bool_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_bool_flag</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click_type</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># attrs we will use elsewhere</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multiple</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_ast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ast</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">meta_help</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'file'</span><span class="p">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'multiple arguments will be merged'</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_default</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">desc</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="p">):</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">desc</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">' '</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">NoDefault</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'[optional]'</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'[default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r]'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">,)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">desc</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">consume_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'column'</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_consume_metadata</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">consume_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_consume_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># double consume</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">md_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">consume_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># consume uses self.name, so mutate but backup for after</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">backup</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_dest</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">md_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">consume_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">backup</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">md_col</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">md_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># missing one or the other</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">md_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MissingParameter</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MissingParameter</span><span class="p">(</span><span class="n" style="color: #333;">param_hint</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_opts</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">md_col</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">md_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">md_file</span><span class="p">,</span> <span class="n" style="color: #333;">md_col</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_help_record</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_help_record</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_bool_flag</span><span class="p">:</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_metavar</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metavar</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_metavar</span><span class="p">(),</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'column'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_opts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' COLUMN '</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">record</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Override</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_to_parser</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'column'</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_opts</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_dest</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_bool_flag</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multiple</span><span class="p">:</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'append_maybe'</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'store_maybe'</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">shared</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secondary_opts</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">shared</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multiple</span><span class="p">:</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'append_greedy'</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'append_greedy'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">shared</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_to_parser</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">full_process_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">full_process_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MissingParameter</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'o'</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'output_dir'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)):</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">type_cast_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multiple</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">()</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'i'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_cast_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_multiple</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_check_length</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_multiple</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">type_expr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_from_ast</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_ast</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">)))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">type_expr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BadParameter</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'recieved <</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s> as an argument, which is incompatible'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">' with parameter type: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">type_expr</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_metadata</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'file'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_cast_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with merging "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">"QIIME 2 Metadata:"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'stderr'</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--verbose'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'p'</span><span class="p">:</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_multiple</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_check_length</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_primitive</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_ast</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_from_ast</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_ast</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BadParameter</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">'recieved <</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s> as an argument, which is incompatible'</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">' with parameter type: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">expr</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_cast_value</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">dups</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dups</span><span class="p">:</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BadParameter</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">'recieved <</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s> as an argument, which contains duplicates'</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="s" style="color: #d14;">' of the following: <</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s>'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">dups</span><span class="p">),</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#515b09fdcee7316575e8e96ae9e326544ba615bc"><strong>q2cli/click/parser.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Some of the source code in this file is derived from original work:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># To see the license for the original work, see licenses/click.LICENSE.rst</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Specific reproduction and derivation of original work is marked below.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click.parser</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">parser</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click.exceptions</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">exceptions</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Q2Option</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">takes_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># store_maybe should take a value so that we hit the right branch</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># in OptionParser._match_long_opt</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">takes_value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'store_maybe'</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'append_greedy'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_maybe_take</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rargs</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In a more perfect world, we would have access to all long opts</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># and could verify against those instead of just the prefix '--'</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rargs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'--'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Specific technique derived from original:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># c6042bf2607c5be22b1efef2e42a94ffd281434c/click/core.py#L867 ></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">):</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># actions should update state.opts and state.order</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'append'</span><span class="p">,</span> <span class="s" style="color: #d14;">'append_const'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">'append_maybe'</span><span class="p">,</span> <span class="s" style="color: #d14;">'append_greedy'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'count'</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">exceptions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">UsageError</span><span class="p">(</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'Option </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r was specified multiple times in the command.'</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_opt_name</span><span class="p">())</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'store_maybe'</span><span class="p">:</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maybe_take</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">const</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># can't forget this</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'append_maybe'</span><span class="p">:</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maybe_take</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="p">[])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">const</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="p">[])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maybe_take</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># can't forget this</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'append_greedy'</span><span class="p">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maybe_take</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="p">[])</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maybe_take</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># can't forget this</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">takes_value</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'--'</span><span class="p">):</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Error early instead of cascading the parse error to a "missing"</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parameter, which they ironically did provide</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BadOptionUsage</span><span class="p">(</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s option requires an argument'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_opt_name</span><span class="p">())</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_opt_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="s" style="color: #d14;">'secondary_opts'</span><span class="p">):</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">' / '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secondary_opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="s" style="color: #d14;">'get_error_hint'</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_error_hint</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">' / '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_long_opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Q2Parser</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OptionParser</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Modified from original:</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ic6042bf2607c5be22b1efef2e42a94ffd281434c/click/parser.py#L228 ></span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014 by the Pallets team.</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"""Adds a new option named `dest` to the parser. The destination</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> is not inferred (unlike with optparse) and needs to be explicitly</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> provided. Action can be any of ``store``, ``store_const``,</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> ``append``, ``appnd_const`` or ``count``.</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> The `obj` can be used to identify the option in the order list</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> that is returned from the parser.</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">obj</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dest</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normalize_opt</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opts</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BEGIN MODIFICATIONS</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'store_maybe'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'append_maybe'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Specifically target this branch:</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># c6042bf2607c5be22b1efef2e42a94ffd281434c/click/parser.py#L341 ></span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this happens to prevents click from reading any arguments itself</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># because it will only "pop" off rargs[:0], which is nothing</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">const</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"A 'const' must be provided when action is "</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"'store_maybe' or 'append_maybe'"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'append_greedy'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q2Option</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nargs</span><span class="p">,</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">const</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">obj</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># END MODIFICATIONS</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_opt_prefixes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefixes</span><span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_short_opts</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_short_opt</span><span class="p">[</span><span class="n" style="color: #333;">opt</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_long_opts</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_long_opt</span><span class="p">[</span><span class="n" style="color: #333;">opt</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">option</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">backup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># args will be mutated by super()</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">exceptions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">UsageError</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--help'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">backup</span><span class="p">:</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># all is forgiven</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">'help'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">},</span> <span class="p">[],</span> <span class="p">[</span><span class="s" style="color: #d14;">'help'</span><span class="p">]</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Override of private member:</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># < https://github.com/pallets/click/blob/</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ic6042bf2607c5be22b1efef2e42a94ffd281434c/click/parser.py#L321 ></span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_match_long_opt</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">explicit_value</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">):</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_long_opt</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_close_matches</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This is way better than substring matching</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">possibilities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_close_matches</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_long_opt</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">exceptions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NoSuchOption</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">possibilities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">possibilities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_match_long_opt</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">explicit_value</span><span class="p">,</span> <span class="n" style="color: #333;">state</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#eecee2226af62de28bd22bef07e8b1dae7cd739a"><strong>q2cli/click/type.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_writable_dir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'do-while'</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normpath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">head</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">W_OK</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">X_OK</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">OutDirType</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Click path fails to validate writability on new paths</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is already a file.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r already exists, will not overwrite.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,),</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_writable_dir</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is not a writable directory, cannot write output'</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">' to it.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">QIIME2Type</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ParamType</span><span class="p">):</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">type_ast</span><span class="p">,</span> <span class="n" style="color: #333;">type_repr</span><span class="p">,</span> <span class="n" style="color: #333;">is_output</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_repr</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_ast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type_ast</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_output</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_type_expr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">type_expr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_type_expr</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_type_expr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_from_ast</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_ast</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_type_expr</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># Them's the rules</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_output</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_convert_output</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_semantic_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_convert_input</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_metadata_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_convert_metadata</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_convert_primitive</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_convert_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Click path fails to validate writability on new paths</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is already a directory.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_writable_dir</span><span class="p">(</span><span class="n" style="color: #333;">directory</span><span class="p">):</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is not a writable directory, cannot write output'</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">' to it.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">directory</span><span class="p">,),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_convert_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is not a QIIME 2 Artifact (.qza)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Visualization</span><span class="p">):</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">maybe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'a'</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">maybe</span><span class="p">):</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">' (There is an artifact with the same name:'</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="s" style="color: #d14;">' </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, did you mean that?)'</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">maybe</span><span class="p">))</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is a QIIME 2 visualization (.qzv), not an '</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">' Artifact (.qza)</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">hint</span><span class="p">),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interrogate_collection_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">:</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># collections need to be handled above this</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected an artifact of at least type </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r."</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">" An artifact of type </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r was provided."</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">),</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_convert_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn'</span><span class="p">:</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">artifact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with loading the file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s as "</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">"metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'stderr'</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--verbose'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with viewing the artifact "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s as QIIME 2 Metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'stderr'</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--verbose'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'MetadataColumn'</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metadata</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">metadata_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_column</span><span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with retrieving column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r from "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="s" style="color: #d14;">"the metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">column</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata_column</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="s" style="color: #d14;">"Metadata column is of type </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, but expected </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r."</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">metadata_column</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metadata_column</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_convert_primitive</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_primitive</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_expr</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_metavar</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_type_repr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">):</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">type_repr</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_missing_message</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">):</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_output</span><span class="p">:</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'("--output-dir" may also be used)'</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,22 +6,22 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.dev</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.info</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.tools</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.builtin.dev</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.builtin.info</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.builtin.tools</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.click.command</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BaseCommandMixin</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RootCommand</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RootCommand</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">BaseCommandMixin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"""This class defers to either the PluginCommand or the builtin cmds"""</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">_builtin_commands</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">collections</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">OrderedDict</span></span><span class="p"><span class="idiff right">([</span></span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'info'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'tools'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tools</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'dev'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">dev</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">dev</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="p"><span class="idiff left right">])</span></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">_builtin_commands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">'info'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">'tools'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tools</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">'dev'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">dev</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dev</span></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="p"><span class="idiff left right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,8 +72,8 @@ class RootCommand(click.MultiCommand):</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `self._plugins` will not always be obtained from</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `q2cli.cache.CACHE.plugins`.</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugins</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.cache</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plugins</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.c<span class="idiff left right">ore.c</span>ache</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c<span class="idiff left">ore</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">c</span>ache</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CACHE</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plugins</span></span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">name_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">plugin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugins</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,12 +98,25 @@ class RootCommand(click.MultiCommand):</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">plugin</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin_lookup</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_close_matches</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">possibilities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_close_matches</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin_lookup</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">possibilities</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' Did you mean </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r?'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">possibilities</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">possibilities</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' (Possible commands: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">possibilities</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: QIIME 2 has no plugin/command named </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r."</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hint</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Match exit code of `return None`</span></span>
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102
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"></span>
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103
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PluginCommand</span><span class="p">(</span><span class="n" style="color: #333;">plugin</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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104
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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105
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PluginCommand</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PluginCommand</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">BaseCommandMixin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"""Provides ActionCommands based on available Actions"""</span></span>
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108
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">plugin</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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109
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,8 +146,21 @@ class PluginCommand(click.MultiCommand):</td>
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133
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resilient_parsing</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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135
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]))</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entrypoint</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PluginManager</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iter_entry_points</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">plugin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entrypoint</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">pkg_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entrypoint</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">project_name</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">pkg_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entrypoint</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">pkg_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pkg_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[UNKNOWN]"</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="s" style="color: #d14;">"QIIME 2 Plugin '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (from package '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">],</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">pkg_name</span><span class="p">,</span> <span class="n" style="color: #333;">pkg_version</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="p">)</span></span>
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138
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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139
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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140
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_citation_records</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,82 +175,84 @@ class PluginCommand(click.MultiCommand):</td>
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149
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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150
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_action_lookup</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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151
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: QIIME 2 plugin </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r has no action </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r."</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_close_matches</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">possibilities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_close_matches</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_action_lookup</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">possibilities</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' Did you mean </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r?'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">possibilities</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">possibilities</span><span class="p">:</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' (Possible commands: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">possibilities</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">hint</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: QIIME 2 plugin </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r has no action </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r."</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hint</span><span class="p">,</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">)</span></span>
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154
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Match exit code of `return None`</span></span>
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155
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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156
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ActionCommand</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_plugin</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">)</span></span>
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157
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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158
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ActionCommand</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">):</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ActionCommand</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">BaseCommandMixin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">):</span></span>
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160
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">"""A click manifestation of a QIIME 2 API Action (Method/Visualizer)</span></span>
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161
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> The ActionCommand generates Handlers which map from 1 Action API parameter</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> to one or more Click.Options.</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> MetaHandlers are handlers which are not mapped to an API parameter, they</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> are handled explicitly and generally return a `fallback` function which</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> can be used to supplement value lookup in the regular handlers.</span></span>
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168
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">plugin</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.handlers</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.click.type</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plugin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plugin</span></span>
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174
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">action</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">generated_handlers</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_generated_handlers</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">VerboseHandler</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">QuietHandler</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Meta-Handlers:</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_dir_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OutputDirHandler</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CommandConfigHandler</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">plugin</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_parameters</span><span class="p">()),</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_generated_handlers</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.handlers</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_inputs</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_params</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outputs</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_build_generated_options</span><span class="p">()</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_misc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--output-dir'</span><span class="p">],</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OutDirType</span><span class="p">(),</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Output unspecified results to a directory'</span><span class="p">),</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--verbose / --quiet'</span><span class="p">],</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Display verbose output to stdout and/or stderr '</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">'during execution of this action. Or silence '</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">'output if execution is successful (silence is '</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">'golden).'</span><span class="p">),</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">citations_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_citation_records</span><span class="p">)</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="p">]</span></span>
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190
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">handler_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="s" style="color: #d14;">'input'</span><span class="p">:</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArtifactHandler</span><span class="p">,</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">'parameter'</span><span class="p">:</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameter_handler_factory</span><span class="p">,</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">'output'</span><span class="p">:</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ResultHandler</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">options</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_inputs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_params</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outputs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_misc</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">,</span> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">short_help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_build_generated_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.click.option</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">handlers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'signature'</span><span class="p">]:</span></span>
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199
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">item</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'type'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">item</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'ast'</span></span><span class="p"><span class="idiff">][</span></span><span class="s" style="color: #d14;"><span class="idiff">'type'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'collection</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">inner_handler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">handler_map</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">type</span></span><span class="p"><span class="idiff">](</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">item</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">handler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">q2cli</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">handlers</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">CollectionHandler</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inner_handler</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">item</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">type</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'input</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">storage</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">inputs</span></span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">type</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'parameter'</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">storage</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">params</span></span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handler_map</span><span class="p">[</span><span class="nb" style="color: #0086b3;">type</span><span class="p">](</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">handlers</span><span class="p">[</span><span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handler</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">handlers</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Handlers may provide more than one click.Option</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">handler</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">generated_handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">storage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputs</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Meta-Handlers' Options:</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_dir_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GeneratedOption</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inputs</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">citations_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_citation_records</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_opt_groups</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'Inputs'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_inputs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="s" style="color: #d14;">'Parameters'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_params</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="s" style="color: #d14;">'Outputs'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outputs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">'Miscellaneous'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_misc</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_help_option</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_citation_records</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_action</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">citations</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -237,26 +265,35 @@ class ActionCommand(click.Command):</td>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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239
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="s" style="color: #d14;">"""Called when user hits return, **kwargs are Dict[click_names, Obj]"""</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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241
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.util</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">missing_in</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_in_params</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="p">,</span> <span class="n" style="color: #333;">missing_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_out_params</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_in</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">missing_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># A new context is generated for a callback, which will result in</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the ctx.command_path duplicating the action, so just use the</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parent so we can print the help *within* a callback.</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_help</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">option</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">missing_in</span><span class="p">,</span> <span class="n" style="color: #333;">missing_out</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Missing option: --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">_OUTPUT_OPTION_ERR_MSG</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'output_dir'</span><span class="p">)</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'verbose'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">init_outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'_'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'o'</span><span class="p">:</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">init_outputs</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'m'</span><span class="p">:</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="s" style="color: #d14;">'_file'</span><span class="p">)]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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259
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_order_outputs</span><span class="p">(</span><span class="n" style="color: #333;">init_outputs</span><span class="p">)</span></span>
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260
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_action</span><span class="p">()</span></span>
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261
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `qiime2.util.redirected_stdio` defaults to stdout/stderr when</span></span>
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262
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># supplied `None`.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,77 +327,18 @@ class ActionCommand(click.Command):</td>
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290
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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291
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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292
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">output_dir</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">)</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"></span>
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293
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">output</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span><span class="p">):</span></span>
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294
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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295
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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296
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'Saved </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s to: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">),</span></span>
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297
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'green'</span><span class="p">)</span></span>
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298
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_in_params</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.handlers</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">cmd_fallback</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd_fallback</span><span class="p">)</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd_fallback</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'Unsure of how to be quiet and verbose at the '</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="s" style="color: #d14;">'same time.'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'signature'</span><span class="p">]:</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'input'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'parameter'</span><span class="p">:</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">generated_handlers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">handler</span><span class="p">,</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MetadataHandler</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MetadataColumnHandler</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd_fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd_fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">missing</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_out_params</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.handlers</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">cmd_fallback</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">out_fallback</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_dir_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmd_fallback</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fallback</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cmd_fallback</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_fallback</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_order_outputs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outputs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">ordered</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span><span class="p">[</span><span class="s" style="color: #d14;">'signature'</span><span class="p">]:</span></span>
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349
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'output'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">generated_handlers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fallback</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outputs</span><span class="p">,</span> <span class="n" style="color: #333;">missing</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"><span class="n" style="color: #333;">_OUTPUT_OPTION_ERR_MSG</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;">Note: When only providing names for a subset of the output Artifacts or</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;">Visualizations, you must specify an output directory through use of the</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;">--output-dir DIRECTORY flag.</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span></pre>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">ordered</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">outputs</span><span class="p">[</span><span class="n" style="color: #333;">item</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]])</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ordered</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#dfd184050fb528c09218940c2d755dd558c09f9d"><strong>q2cli/core.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Option</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">"""``click.Option`` with customized behavior for q2cli.</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;"> Note to q2cli developers: you'll generally want to use this class and its</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> corresponding decorator (``@q2cli.option``) over ``click.Option`` and</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> ``@click.option`` to keep a consistent CLI behavior across commands. This</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> class and decorator are designed to be drop-in replacements for their Click</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> counterparts.</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param_decls</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'multiple'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'count'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_disallow_repeated_options</span><span class="p">(</span><span class="n" style="color: #333;">attrs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">param_decls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">param_decls</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_disallow_repeated_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">attrs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"""Prevent option from being repeated on the command line.</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> Click allows options to be repeated on the command line and stores the</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> value of the last specified option (this is to support overriding</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> options set in shell aliases). While this is common behavior in CLI</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> tools, it is prevented in q2cli to avoid confusion with options that</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> are intended to be supplied multiple times (``multiple=True``; Click</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> calls these "multiple options"). QIIME 2 metadata is an example of a</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> "multiple option" in q2cli.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> .. [1] http://click.pocoo.org/6/options/#multiple-options</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># General strategy:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make this option a "multiple option" (``multiple=True``) and use a</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># callback to unpack the stored values and assert that only a single</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># value was supplied.</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use the user-supplied callback or define a passthrough callback if</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># one wasn't supplied.</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'callback'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">callback</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'callback'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">callback</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Wrap the callback to intercept stored values so that they can be</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># unpacked and validated.</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">callback_wrapper</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># When `multiple=True` Click will use an empty tuple to represent</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the absence of the option instead of `None`.</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resilient_parsing</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Empty/null case is handled above, so attempt to unpack the value.</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_usage</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"Error: Option --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s was specified multiple times in the "</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"command."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Promote this option to a "multiple option" and use the callback</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># wrapper to make it behave like a regular "single" option.</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'callback'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">callback_wrapper</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'multiple'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the user set a default, promote it to a "multiple option" default</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># by putting it in a list. A default of `None` is a special case that</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># can't be promoted.</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'default'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'default'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'default'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'default'</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Modeled after `click.option` decorator.</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">option</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">param_decls</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"""``@click.option`` decorator with customized behavior for q2cli.</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> See docstring on ``q2cli.Option`` (above) for details.</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'cls'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot override `cls=q2cli.Option` in `attrs`."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'cls'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Option</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">decorator</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">param_decls</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">attrs</span><span class="p">)(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">decorator</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultipleType</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ParamType</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">"""This is just a wrapper, it doesn't do anything on its own"""</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">param_type</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"MULTIPLE "</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't convert anything yet.</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fail</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fail</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_missing_message</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_missing_message</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_metavar</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_metavar</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metavar</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"MULTIPLE "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">metavar</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ResultPath</span><span class="p">(</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_metavar</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">param</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'Visualization'</span><span class="p">:</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"ARTIFACT PATH "</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"VISUALIZATION PATH"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#874e9f895446a24ce25c1483df0fb7d11dad5f50"><strong>q2cli/cache.py</strong>
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<strong>q2cli/core/cache.py</strong>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -188,7 +188,7 @@ class DeploymentCache:</td>
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.completion</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.co<span class="idiff left right">re.co</span>mpletion</span></span>
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192
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -203,7 +203,7 @@ class DeploymentCache:</td>
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203
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">state</span><span class="p">,</span> <span class="n" style="color: #333;">fh</span><span class="p">)</span></span>
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205
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">completion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_bash_completion_script</span><span class="p">(</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">co<span class="idiff left">re</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">co</span>mpletion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_bash_completion_script</span><span class="p">(</span></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="p">[</span><span class="s" style="color: #d14;">'plugins'</span><span class="p">],</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_completion_path</span><span class="p">())</span></span>
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208
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write requirements file last because the above steps may raise errors</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -276,7 +276,7 @@ class DeploymentCache:</td>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">sig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signature</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">sig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signature_order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">sig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'repr'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'repr'</span><span class="p">:</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_get_type_</span>repr</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="s" style="color: #d14;">'ast'</span><span class="p">:</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qiime_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_ast</span><span class="p">()}</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputs</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -292,10 +292,109 @@ class DeploymentCache:</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_default</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'default'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'metavar'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_metavar</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'multiple'</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'is_bool_flag'</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'metadata'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_special_option_flags</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qiime_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">state</span><span class="p">[</span><span class="s" style="color: #d14;">'signature'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">state</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_special_option_flags</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">is_bool_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interrogate_collection_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'simple'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'complex'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_iterable</span><span class="p">(</span><span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span><span class="p">)}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># composite or monomorphic</span></span>
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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span><span class="p">}</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'Bool'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">is_bool_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># not collection</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expr</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Metadata'</span><span class="p">:</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'list'</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'file'</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn'</span><span class="p">:</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'column'</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Bool'</span><span class="p">:</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">is_bool_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">multiple</span><span class="p">,</span> <span class="n" style="color: #333;">is_bool_flag</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_type_repr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interrogate_collection_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_semantic_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span><span class="p">:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'simple'</span><span class="p">:</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">type_repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span><span class="p">)</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">type_repr</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_metavar</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk.util</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">name_to_var</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">'Visualization'</span><span class="p">:</span> <span class="s" style="color: #d14;">'VISUALIZATION'</span><span class="p">,</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="s" style="color: #d14;">'Int'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INTEGER'</span><span class="p">,</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="s" style="color: #d14;">'Str'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="s" style="color: #d14;">'Float'</span><span class="p">:</span> <span class="s" style="color: #d14;">'NUMBER'</span><span class="p">,</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="s" style="color: #d14;">'Bool'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="p">}</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interrogate_collection_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'simple'</span><span class="p">:</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">inner_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">members</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">multiple</span><span class="p">:</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">inner_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">inner_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_semantic_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ARTIFACT'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_metadata_type</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'METADATA'</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">style</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'simple'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'VALUE'</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_to_var</span><span class="p">[</span><span class="n" style="color: #333;">inner_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'NUMBER'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inner_type</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inner_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inner_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">inner_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">predicate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'PROPORTION'</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiple</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Metadata'</span><span class="p">:</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'TEXT'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">''</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'METADATA'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'S'</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'...'</span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metavar</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"></span>
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"></span>
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Singleton. Import and use this instance as necessary.</span></span>
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301
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"><span class="n" style="color: #333;">CACHE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DeploymentCache</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#eada752a2adf82b343f70a4bedf2ece9781b60f2"><strong>q2cli/completion.py</strong>
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<strong>q2cli/core/completion.py</strong>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,6 +73,8 @@ def _generate_command_reply(cmd):</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">):</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secondary_opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">,</span> <span class="s" style="color: #d14;">'q2_extra_opts'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q2_extra_opts</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">subcmd_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiCommand</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#cafae4275a55b843f527028ae328ae9bf9026259"><strong>q2cli/handlers.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Sentinel to avoid the situation where `None` *is* the default value.</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">NoDefault</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'NoDefault'</span><span class="p">,</span> <span class="p">[])()</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ValueNotFoundException</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"""Raised when a value cannot be found. Used for control-flow only."""</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Handler</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># e.g. my_option_name</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># e.g. p_my_option_name</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">description</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cli_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># e.g. p-my-option-name</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"""Should yield 1 or more click.Options"""</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"""Should find 1 or more arguments and convert to a single API value"""</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_locate_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">,</span> <span class="n" style="color: #333;">multiple</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"""Default lookup procedure to find a click.Option provided by user"""</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO revisit this interaction between _locate_value, single vs.</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># multiple options, and fallbacks. Perhaps handlers should always</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use tuples to store values, even for single options, in order to</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># normalize single-vs-multiple option handling. Probably not worth</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># revisiting until there are more unit + integration tests of q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># since there's the potential to break things.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Is it in args?</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click_name</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">missing_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiple</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">missing_value</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">v</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Does our fallback know about it?</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fallback</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">fallback_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fallback</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO fallbacks don't know whether they're handling a single</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># vs. multiple option, so the current expectation is that</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fallbacks will always return a single value. Revisit this</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expectation in the future; perhaps fallbacks should be aware</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of single-vs-multiple options, or perhaps they could always</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return a tuple.</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiple</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">fallback_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fallback_value</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fallback_value</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Do we have a default?</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">NoDefault</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Give up</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_boolean</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse string representing a boolean into Python bool type.</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> Supported values match `configparser.ConfigParser.getboolean`.</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">trues</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'yes'</span><span class="p">,</span> <span class="s" style="color: #d14;">'true'</span><span class="p">,</span> <span class="s" style="color: #d14;">'on'</span><span class="p">]</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">falses</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'no'</span><span class="p">,</span> <span class="s" style="color: #d14;">'false'</span><span class="p">,</span> <span class="s" style="color: #d14;">'off'</span><span class="p">]</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">string_lower</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">string_lower</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">trues</span><span class="p">:</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">string_lower</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">falses</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">"Error: unrecognized value for --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s flag: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"Supported values (case-insensitive): </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">trues</span><span class="p">,</span> <span class="n" style="color: #333;">falses</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_description</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">):</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pretty_cat</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">space</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">space</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pretty_cat</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">help</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pretty_cat</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">help</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">,</span> <span class="n" style="color: #333;">space</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VerboseHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"""Handler for verbose output (--verbose flag)."""</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `is_flag` will set the default to `False`, but `self._locate_value`</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># needs to distinguish between the presence or absence of the flag</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># provided by the user.</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Display verbose output to stdout and/or stderr during '</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">'execution of this action. [default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s]'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Value may have been specified in --cmd-config (or another source in</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the future). If we don't have a bool type yet, attempt to interpret a</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># string representing a boolean.</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_boolean</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">QuietHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">"""Handler for quiet output (--quiet flag)."""</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `is_flag` will set the default to `False`, but `self._locate_value`</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># needs to distinguish between the presence or absence of the flag</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># provided by the user.</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Silence output if execution is successful '</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">'(silence is golden). [default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s]'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Value may have been specified in --cmd-config (or another source in</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the future). If we don't have a bool type yet, attempt to interpret a</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># string representing a boolean.</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_boolean</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">OutputDirHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"""Meta handler which returns a fallback function as its value."""</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="s" style="color: #d14;">'output_dir'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">writable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Output unspecified results to a directory'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: do we want a --force like flag?</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s directory already exists, won't "</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">"overwrite."</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fallback_</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cli_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fallback_</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Always fail to find a value as this handler doesn't exist.</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fail</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fail</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CommandConfigHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">"""Meta handler which returns a fallback function as its value."""</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cli_plugin</span><span class="p">,</span> <span class="n" style="color: #333;">cli_action</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_plugin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cli_plugin</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cli_action</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="s" style="color: #d14;">'cmd_config'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Use config file for command options'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">configparser</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">configparser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ConfigParser</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">config_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'.'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span></span>
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<td class="diff-line-num old old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_plugin</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_action</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="p">])]</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Config file does not contain a section"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="s" style="color: #d14;">" for </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">'.'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_plugin</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_action</span><span class="p">]),</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fallback_</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cli_name</span><span class="p">):</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">config_section</span><span class="p">[</span><span class="n" style="color: #333;">cli_name</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fallback_</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Always fail to find a value as this handler doesn't exist.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fail</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fail</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GeneratedHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ast</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CollectionHandler</span><span class="p">(</span><span class="n" style="color: #333;">GeneratedHandler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">view_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">'List'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">'Set'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">set</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inner_handler</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inner_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inner_handler</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># inner_handler needs to be set first so the prefix lookup works</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view_map</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">prefix</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inner_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefix</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.core</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">option</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inner_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multiple</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># validation happens on a callback for q2cli.core.Option, so unset</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it because we need standard click behavior for multi-options</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># without this, the result of not-passing a value is `None` instead</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of `()` which confuses ._locate_value</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">callback</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultipleType</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">,</span> <span class="n" style="color: #333;">multiple</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">decoded_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use an empty dict because we don't need the inner handler to</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># look for anything; that's our job. We just need it to decode</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># whatever it was we found.</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">decoded</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inner_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span><span class="n" style="color: #333;">empty</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">decoded_values</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">decoded</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view_type</span><span class="p">(</span><span class="n" style="color: #333;">decoded_values</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">decoded_values</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_error_with_duplicate_in_set</span><span class="p">(</span><span class="n" style="color: #333;">decoded_values</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_error_with_duplicate_in_set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">elements</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="n" style="color: #333;">elements</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">dups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_usage</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Option --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s was given these values: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r more than "</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="s" style="color: #d14;">"one time, values passed should be unique."</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">,</span> <span class="n" style="color: #333;">dups</span><span class="p">),</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ArtifactHandler</span><span class="p">(</span><span class="n" style="color: #333;">GeneratedHandler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'i_'</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.core</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ResultPath</span><span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[optional]'</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[required]'</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_description</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">)</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">artifact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">artifact</span><span class="p">,</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Visualization</span><span class="p">):</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_usage</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Option --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s was given a visualization "</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="s" style="color: #d14;">"(.qzv), expected an artifact (.qza)."</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">artifact</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ResultHandler</span><span class="p">(</span><span class="n" style="color: #333;">GeneratedHandler</span><span class="p">):</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'o_'</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ResultPath</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">writable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_description</span><span class="p">(</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="s" style="color: #d14;">'[required if not passing --output-dir]'</span><span class="p">)</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parameter_handler_factory</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Metadata'</span><span class="p">:</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MetadataHandler</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn'</span><span class="p">:</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn[Categorical]'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">column_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'categorical'</span><span class="p">,)</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn[Numeric]'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">column_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'numeric'</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn[Categorical | Numeric]'</span> <span class="ow" style="font-weight: 600;">or</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'MetadataColumn[Numeric | Categorical]'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">column_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'categorical'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numeric'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">(</span></span>
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418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="s" style="color: #d14;">"Parameter </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is type </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, which is not currently supported by "</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="s" style="color: #d14;">"this interface."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">))</span></span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MetadataColumnHandler</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">column_types</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">RegularParameterHandler</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MetadataHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">NoDefault</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="s" style="color: #d14;">"The only supported default value for Metadata is `None`. "</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="python"> <span class="s" style="color: #d14;">"Found this default value: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">,))</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'m_'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click_name</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'_file'</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.core</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">file_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dir_okay</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">readable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultipleType</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Metadata file or artifact viewable as metadata. This '</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="s" style="color: #d14;">'option may be supplied multiple times to merge metadata.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[optional]'</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[required]'</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help</span><span class="p">,</span> <span class="n" style="color: #333;">multiple</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_description</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">,</span> <span class="n" style="color: #333;">multiple</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paths</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">paths</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">path</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paths</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check to see if path is an artifact</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">artifact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with loading the file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s as "</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="s" style="color: #d14;">"metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'stderr'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with viewing the artifact "</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s as QIIME 2 Metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'stderr'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MetadataColumnHandler</span><span class="p">(</span><span class="n" style="color: #333;">Handler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">column_types</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">NoDefault</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="s" style="color: #d14;">"The only supported default value for MetadataColumn "</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"> <span class="s" style="color: #d14;">"subclasses is `None`. Found this default value: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">,))</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'m_'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">click_name</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'_column'</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">repr</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">column_types</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Not passing `description` to metadata handler because `description`</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># applies to the metadata column (`self`).</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MetadataHandler</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Column from metadata file or artifact viewable as metadata.'</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[optional]'</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[required]'</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_click_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_description</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Attempt to find all options before erroring so that all handlers'</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># missing options can be displayed to the user.</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">metadata_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_value</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">column_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If metadata column is optional, there is a chance for metadata to be</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># provided without a metadata column, or vice versa.</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">column_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_handler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">metadata_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">column_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValueNotFoundException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">column_value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">metadata_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata_value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_column</span><span class="p">(</span><span class="n" style="color: #333;">column_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata_column</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_types</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This exception, and any exceptions raised by</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `.get_column()` above, will be handled below in the</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># `except` block.</span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_types</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_types</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'one of the following types: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="python"> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_types</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="python"> <span class="s" style="color: #d14;">"Metadata column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s. Option --</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s expects the "</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="s" style="color: #d14;">"column to be </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">column_value</span><span class="p">,</span> <span class="n" style="color: #333;">metadata_column</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span><span class="p">,</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"There was an issue with retrieving column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r from "</span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="s" style="color: #d14;">"the metadata:"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">column_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_with_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">metadata_column</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RegularParameterHandler</span><span class="p">(</span><span class="n" style="color: #333;">GeneratedHandler</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'p_'</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NoDefault</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: just create custom click.ParamType to avoid this silliness</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'collection'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">ast</span><span class="p">,</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'fields'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">convert_primitive</span><span class="p">(</span><span class="n" style="color: #333;">ast</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_click_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.util</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">no_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'no_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">cli_no_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_cli_name</span><span class="p">(</span><span class="n" style="color: #333;">no_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cli_no_name</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># click.Option type is determined implicitly for flags with</span></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># secondary options, and explicitly passing type=bool results in a</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TypeError, so we pass type=None (the default).</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">option_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cli_name</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">option_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">NoDefault</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[required]'</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[optional]'</span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[default: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s]'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Pass `default=None` and `show_default=False` to `click.Option`</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># because the handlers are responsible for resolving missing values and</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># supplying defaults. Telling Click about the default value here makes</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it impossible to determine whether the user supplied or omitted a</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># value once the handlers are invoked.</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">([</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">option_type</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">show_default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_add_description</span><span class="p">(</span><span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">requirement</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_locate_value</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">,</span> <span class="n" style="color: #333;">fallback</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: should we defer to the Bool primitive? It only allows</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 'true' and 'false'.</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_boolean</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.sdk</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">primitive</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sdk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">,</span> <span class="n" style="color: #333;">expect</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'primitive'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO/HACK: the repr is the primitive used, but since there's a</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># collection handler managing the set/list this get_value should</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># handle only the pieces. This is super gross, but would be</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># unecessary if click.ParamTypes were implemented for each</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># kind of QIIME 2 input.</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'collection'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">primitive</span><span class="p">,</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">primitive</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fields</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">primitive</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +16,8 @@ from qiime2 import Artifact, Visualization</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.type</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IntSequence1</span><span class="p">,</span> <span class="n" style="color: #333;">IntSequence2</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_dummy_plugin</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.info</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.<span class="idiff left right">builtin.</span>info</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.<span class="idiff left right">builtin.</span>tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.commands</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RootCommand</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -312,7 +312,7 @@ class TestOptionalArtifactSupport(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_optional_artifacts_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="s" style="color: #d14;">'optional-artifacts-method'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">42</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--o-output'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'42'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--o-output'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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316
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,7 +321,7 @@ class TestOptionalArtifactSupport(unittest.TestCase):</td>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_one_optional_artifact_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="s" style="color: #d14;">'optional-artifacts-method'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">42</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'42'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="s" style="color: #d14;">'--o-output'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -331,8 +331,8 @@ class TestOptionalArtifactSupport(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_optional_artifacts_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="s" style="color: #d14;">'optional-artifacts-method'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">42</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="s" style="color: #d14;">'--i-optional2'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints3</span><span class="p">,</span> <span class="s" style="color: #d14;">'--p-num2'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">111</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'42'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="s" style="color: #d14;">'--i-optional2'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints3</span><span class="p">,</span> <span class="s" style="color: #d14;">'--p-num2'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'111'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="s" style="color: #d14;">'--o-output'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"></span>
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -342,12 +342,12 @@ class TestOptionalArtifactSupport(unittest.TestCase):</td>
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342
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_artifact_type_mismatch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"> <span class="s" style="color: #d14;">'optional-artifacts-method'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">42</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints3</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="s" style="color: #d14;">'--p-num1'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'42'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-optional1'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ints3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="s" style="color: #d14;">'--o-output'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="s" style="color: #d14;">'type IntSequence<span class="idiff left right">2.*subtype IntSequence1</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="s" style="color: #d14;">'type IntSequence<span class="idiff left right">1.*type IntSequence2.*</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MetadataTestsBase</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -385,19 +385,6 @@ class MetadataTestsBase(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">import_data</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="s" style="color: #d14;">'Mapping'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="s" style="color: #d14;">'dog'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">:</span> <span class="s" style="color: #d14;">'cat'</span><span class="p">})</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_artifact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tempdir</span><span class="p">,</span> <span class="s" style="color: #d14;">'conf.ini'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'[dummy-plugin.identity-with-metadata]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-file=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'[dummy-plugin.identity-with-optional-metadata]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-file=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'[dummy-plugin.identity-with-metadata-column]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-file=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-column=col1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'[dummy-plugin.identity-with-optional-metadata-column]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-file=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="s" style="color: #d14;">'m-metadata-column=col1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tempdir</span><span class="p">)</span></span>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -428,7 +415,7 @@ class TestMetadataSupport(MetadataTestsBase):</td>
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"></span>
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429
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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430
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left right">: --m-metadata-file</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left"> </span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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432
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"></span>
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_metadata_missing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -501,20 +488,7 @@ class TestMetadataSupport(MetadataTestsBase):</td>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-file'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertNotEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'overlapping columns'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exception</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_cmd_config_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">command</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'identity-with-metadata'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-optional-metadata'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">input_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--o-out'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cmd-config'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">exp_tsv</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">col1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#q2:types</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">categorical</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">foo</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">id1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bar</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertMetadataOutput</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">exp_tsv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_tsv</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">exp_yaml</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"metadata: !metadata 'metadata.tsv'"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'overlapping columns'</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestMetadataColumnSupport</span><span class="p">(</span><span class="n" style="color: #333;">MetadataTestsBase</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -525,8 +499,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option: --m-metadata-file"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option: --m-metadata-column"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--m-metadata-file</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_metadata_missing</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -544,7 +517,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left right">: --m-metadata-column</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left"> </span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-column</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optional_column_without_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -554,7 +527,7 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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554
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"></span>
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555
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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556
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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557
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left right">: --m-metadata-file</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing option<span class="idiff left"> </span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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558
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"></span>
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559
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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560
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">command</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'identity-with-metadata-column'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -579,11 +552,9 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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579
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--m-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'col2'</span><span class="p">,</span></span>
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580
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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581
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">exp_tsv</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">col2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#q2:types</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">categorical</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">baz</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">exp_yaml</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"metadata: !metadata '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:metadata.tsv'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_artifact</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uuid</span><span class="p">)</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertMetadataOutput</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">exp_tsv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_tsv</span><span class="p">,</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"> <span class="n" style="color: #333;">exp_yaml</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_yaml</span><span class="p">)</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">--m-metadata-file</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> was specified multiple times'</span><span class="p">,</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multiple_metadata_column</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -595,41 +566,17 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"></span>
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596
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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597
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">--m-metadata-column</span> was specified multiple times'</span><span class="p">,</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;"><span class="idiff left">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">--m-metadata-file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\'</span></span><span class="s" style="color: #d14;"> was specified multiple times'</span><span class="p">,</span></span>
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599
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid_metadata_merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">command</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'identity-with-metadata-column'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-optional-metadata-column'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">input_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--o-out'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--m-metadata-file'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-file'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata_file1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'col1'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertNotEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'overlapping columns'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exception</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_cmd_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">command</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'identity-with-metadata-column'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-optional-metadata-column'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">input_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--o-out'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_artifact</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cmd-config'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd_config</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">exp_tsv</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">col1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#q2:types</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">categorical</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">foo</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">id1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bar</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertMetadataOutput</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">exp_tsv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">exp_tsv</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python"> <span class="n" style="color: #333;">exp_yaml</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"metadata: !metadata 'metadata.tsv'"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_categorical_metadata_column</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-categorical-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--help'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'--m-metadata-column MetadataColumn[Categorical]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-column COLUMN MetadataColumn[Categorical]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-categorical-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -650,16 +597,17 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numbers'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">err_msg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Metadata column 'numbers' is numeric. Option "</span></span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--m-metadata-column expects the column to be categorical."</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">err_msg</span></span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assertIn</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Metadata column"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assertIn</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"numeric"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">output</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"expected Categorical"</span></span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_numeric_metadata_column</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-numeric-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--help'</span><span class="p">)</span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span></span>
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"></span>
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662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'--m-metadata-column MetadataColumn[Numeric]'</span><span class="p">,</span> <span class="n" style="color: #333;">help_text</span><span class="p">)</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;">'--m-metadata-column COLUMN MetadataColumn[Numeric]'</span><span class="p">,</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">help_text</span><span class="p">)</span></span>
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"></span>
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_run_command</span><span class="p">(</span></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="s" style="color: #d14;">'identity-with-numeric-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--i-ints'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -680,9 +628,9 @@ class TestMetadataColumnSupport(MetadataTestsBase):</td>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"> <span class="s" style="color: #d14;">'--m-metadata-column'</span><span class="p">,</span> <span class="s" style="color: #d14;">'strings'</span><span class="p">)</span></span>
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681
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"></span>
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">err_msg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Metadata column 'strings' is categorical. Option "</span></span></span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--m-metadata-column expects the column to be numeric."</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">err_msg</span></span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assertIn</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Metadata column"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assertIn</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"categorical"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">output</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIn</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"expected Numeric"</span></span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<li id="69859555882ae5b802d6b617deeaece2a2130265">
<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#69859555882ae5b802d6b617deeaece2a2130265"><strong>q2cli/tests/test_core.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,15 +11,14 @@ import shutil</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">click.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CliRunner</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Artifact</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.type</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IntSequence1</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_dummy_plugin</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.info</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.tools</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.<span class="idiff left right">builtin.</span>info</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2cli.<span class="idiff left right">builtin.</span>tools</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.commands</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RootCommand</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,22 +34,22 @@ class TestOption(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assertRepeatedOptionError</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">option</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit_code</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'Usage:'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">In</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s was specified multiple times'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">option</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">output</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">Regex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'.*</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s.* was specified multiple times'</span></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">option</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_repeated_eager_option_with_callback</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'import'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--show-importable-types'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--show-importable-types'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertRepeatedOptionError</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">'--show-importable-types'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_repeated_builtin_flag</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">info</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'i<span class="idiff left">nfo'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'--py-packages'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'--py-packages</span>'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">tools</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'i<span class="idiff left">mport'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'--input-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'a'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'--input-path'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'b</span>'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertRepeatedOptionError</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">'--<span class="idiff left right">py-packages</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assertRepeatedOptionError</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">'--<span class="idiff left right">input-path</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_repeated_action_flag</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">qiime_cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RootCommand</span><span class="p">()</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +69,7 @@ class TestOption(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">output_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tempdir</span><span class="p">,</span> <span class="s" style="color: #d14;">'out.qza'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">invoke</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">builtin</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tools</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'import'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--input-path'</span><span class="p">,</span> <span class="n" style="color: #333;">input_path</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'--output-path'</span><span class="p">,</span> <span class="n" style="color: #333;">output_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'--type'</span><span class="p">,</span> <span class="s" style="color: #d14;">'IntSequence1'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'--type'</span><span class="p">,</span> <span class="s" style="color: #d14;">'IntSequence1'</span><span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,11 +115,5 @@ class TestOption(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">Artifact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">output_path</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">),</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">,</span> <span class="mi" style="color: #099;">43</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestOptionDecorator</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_cls_override</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'override `cls=q2cli.Option`'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">q2cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--bar'</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#a118f7a6f38ac6924500fb5556f843fdf73e82fb"><strong>q2cli/tests/test_tools.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ from click.testing import CliRunner</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Artifact</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.core.testing.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_dummy_plugin</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.<span class="idiff left right">builtin.</span>tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tools</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2cli.commands</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RootCommand</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2cli/commit/5e9084009852bf779a99a228c21b0b848c6566bb#67c0d02b0c1dcfe41eea76bbf17741e56aa00544"><strong>q2cli/util.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,13 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_app_dir</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_app_dir</span><span class="p">(</span><span class="s" style="color: #d14;">'q2cli'</span><span class="p">,</span> <span class="n" style="color: #333;">roaming</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">conda_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'CONDA_PREFIX'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">conda_prefix</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">conda_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">W_OK</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">X_OK</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">conda_prefix</span><span class="p">,</span> <span class="s" style="color: #d14;">'var'</span><span class="p">,</span> <span class="s" style="color: #d14;">'q2cli'</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_app_dir</span><span class="p">(</span><span class="s" style="color: #d14;">'q2cli'</span><span class="p">,</span> <span class="n" style="color: #333;">roaming</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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13
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># NOTE: `get_cache_dir` and `get_completion_path` live here instead of</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,6 +57,7 @@ def exit_with_error(e, header='An error has been encountered:',</td>
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52
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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53
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">traceback</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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54
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">tb</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_exception</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">),</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__traceback__</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tb_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">tb_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">segments</span><span class="p">),</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'red'</span><span class="p">,</span> <span class="n" style="color: #333;">bold</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +68,25 @@ def exit_with_error(e, header='An error has been encountered:',</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_current_context</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">status</span><span class="p">)</span></span>
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63
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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64
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_close_matches</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">possibilities</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">difflib</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># bash completion makes an incomplete arg most likely</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">m</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">possibilities</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># otherwise, it may be misspelled</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">difflib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_close_matches</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">possibilities</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.8</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this is probably a good time to look at --help</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">'...'</span><span class="p">]</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matches</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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65
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">pretty_failure</span><span class="p">:</span></span>
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66
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'An error has been encountered:'</span><span class="p">,</span></span>
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67
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'stderr'</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,12 +130,12 @@ def convert_primitive(ast):</td>
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105
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Choices'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Str'</span><span class="p">:</span></span>
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106
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Choice</span><span class="p">(</span><span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'choices'</span><span class="p">])</span></span>
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107
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Range'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Int'</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">start'</span></span><span class="p">]</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">end'</span></span><span class="p">]</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left">range'</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left">range'</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">]</span></span>
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110
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># click.IntRange is always inclusive</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'inclusive<span class="idiff left right">-start'</span></span><span class="p">]:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'inclusive<span class="idiff left">'</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">]:</span></span>
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112
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'inclusive<span class="idiff left right">-end'</span></span><span class="p">]:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'inclusive<span class="idiff left">'</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">]:</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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115
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IntRange</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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116
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predicate</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Range'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ast</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Float'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -147,6 +172,6 @@ def citations_option(get_citation_records):</td>
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147
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">secho</span><span class="p">(</span><span class="s" style="color: #d14;">'No citations found.'</span><span class="p">,</span> <span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'yellow'</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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149
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(<span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'--citations'</span></span><span class="p"><span class="idiff right">,)</span>,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Option</span><span class="p">(<span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'--citations'</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">is_flag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">expose_value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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151
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">is_eager</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">callback</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show citations and exit.'</span><span class="p">)</span></span></pre>
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