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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ctdopts">Debian Med / ctdopts</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5">30fee58c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-03-29T12:37:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3</pre>
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<h4>5 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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+
.travis.yml
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<li class="file-stats">
<a href="#61c5ccb699d3bd1d778dd867ea98e770ede7bc28">
CTDopts/CTDopts.py
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<li class="file-stats">
<a href="#05e0372f8165776bed0a53b989eaffd9e3139848">
example.py
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<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
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+
setup.cfg
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install pycodestyle</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - pip install lxml ruamel.yaml</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd $TRAVIS_BUILD_DIR</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pycodestyle"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pycodestyle"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycodestyle CTDopts</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">run</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">example"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">run</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">example"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">ls -la && python example.py</span></span></pre>
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<li id="61c5ccb699d3bd1d778dd867ea98e770ede7bc28">
<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5#61c5ccb699d3bd1d778dd867ea98e770ede7bc28"><strong>CTDopts/CTDopts.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">@@ -17,6 +17,8 @@ class _ASingleton(type):</td>
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<pre style="margin: 0;"> <span id="LC17" 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="n" style="color: #333;">cls</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="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cls</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;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_instances</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;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_instances</span><span class="p">[</span><span class="n" style="color: #333;">cls</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">_ASingleton</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__call__</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="LC20" 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="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;">_instances</span><span class="p">[</span><span class="n" style="color: #333;">cls</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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<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;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_instances</span><span class="p">[</span><span class="n" style="color: #333;">cls</span><span class="p">]</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +28,9 @@ class _Null(object):</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">__metaclass__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ASingleton</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</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="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_InFile</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"""Dummy class for input-file CTD type. I think most users would want to just get the file path</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">@@ -42,15 +47,26 @@ class _OutFile(str):</td>
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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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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># module globals for some common operations (python types to CTD-types back and forth)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">TYPE_TO_CTDTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="s" style="color: #d14;">'int'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="s" style="color: #d14;">'<span class="idiff left">float'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'string'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">bool</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'boolean</span>'</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;">TYPE_TO_CTDTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="s" style="color: #d14;">'int'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="s" style="color: #d14;">'<span class="idiff left">double'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'string'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">bool</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'bool</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'input-file'</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="s" style="color: #d14;">'output-file'</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;">CTDTYPE_TO_TYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'int'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="s" style="color: #d14;">'float'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'double'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="s" style="color: #d14;">'string'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="s" style="color: #d14;">'boolean'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="s" style="color: #d14;">'bool'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'input-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="s" style="color: #d14;">'output-file'</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">_InFile</span><span class="p">:</span> <span class="n" style="color: #333;">_InFile</span><span class="p">,</span> <span class="n" style="color: #333;">_OutFile</span><span class="p">:</span> <span class="n" style="color: #333;">_OutFile</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;">PARAM_DEFAULTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'advanced'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'restrictions'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</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="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">'supported_formats'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'tags'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'position'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;"># unused. TODO.</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;"># a boolean type caster to circumvent bool('false')==True when we cast CTD 'value' attributes to their correct type</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">CAST_BOOLEAN</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'true'</span><span class="p">,</span> <span class="s" style="color: #d14;">'True'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">CAST_BOOLEAN</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> a boolean type caster to circumvent bool('false')==True when we cast CTD</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> 'value' attributes to their correct type</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> """</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="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">return</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'true'</span><span class="p">,</span> <span class="s" style="color: #d14;">'True'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</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>
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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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54
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># instead of using None or _Null, we define non-present 'position' attribute values as -1</span></span>
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55
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="n" style="color: #333;">NO_POSITION</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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56
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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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<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="114" 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">@@ -98,7 +114,7 @@ def flatten_dict(arg_dict, as_string=False):</td>
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98
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">flattener</span><span class="p">(</span><span class="n" style="color: #333;">subgroup</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="p">):</span></span>
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99
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># recursive closure that accesses and modifies result dict and registers nested elements</span></span>
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100
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># as it encounters them</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;">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;">subgroup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">():</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" 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;">subgroup</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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102
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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="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">Mapping</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># collections.Mapping instead of dict for generality</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">flattener</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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104
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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;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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="122" 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">@@ -106,7 +122,7 @@ def flatten_dict(arg_dict, as_string=False):</td>
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106
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>
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107
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">flattener</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">,</span> <span class="p">[])</span></span>
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108
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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;">if</span> <span class="n" style="color: #333;">as_string</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="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;">keylist</span><span class="p">):</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">keylist</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;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</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="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;">keylist</span><span class="p">):</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">keylist</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;">result</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="k" style="font-weight: 600;">else</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;">return</span> <span class="n" style="color: #333;">result</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" 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">@@ -117,9 +133,9 @@ def override_args(*arg_dicts):</td>
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133
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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="s" style="color: #d14;"> combined_args = override_args(args_from_ctd, args_from_commandline)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">overridden_args</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;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">flatten_dict</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arg_dicts</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">overridden_args</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;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">flatten_dict</span><span class="p">(</span><span class="n" style="color: #333;">d</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 class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arg_dicts</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC137" 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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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">keylist</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;">overridden_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">():</span></span>
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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;">keylist</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;">overridden_args</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="n" style="color: #333;">set_nested_key</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">keylist</span><span class="p">,</span> <span class="n" style="color: #333;">value</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;">return</span> <span class="n" style="color: #333;">result</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" 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">@@ -211,16 +227,30 @@ class ModelError(Exception):</td>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">ModelError</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;">__init__</span><span class="p">()</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>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ModelTypeError</span><span class="p">(</span><span class="n" style="color: #333;">ModelError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">"""Exception if file of wrong type is provided</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">ModelTypeError</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;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC235" 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;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</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="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"An error occurred while parsing the CTD file: </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;">message</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">str</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="LC242" class="line" lang="python"></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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ModelParsingError</span><span class="p">(</span><span class="n" style="color: #333;">ModelError</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">"""Exception for errors related to CTD parsing</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC247" 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;">message</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">ModelParsingError</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;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC249" 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;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"An error occurred while parsing the CTD file: </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;">message</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">str</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="LC256" 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">@@ -298,7 +328,7 @@ class _FileFormat(_Restriction):</td>
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<pre style="margin: 0;"> <span id="LC328" 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;">formats</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">_FileFormat</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;">__init__</span><span class="p">()</span></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;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">formats</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># to handle ['txt', 'csv', 'tsv'] and '*.txt,*.csv,*.tsv'</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">formats</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">replace</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'*.'</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="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">strip</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">formats</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">','</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">formats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">replace</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'*.'</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="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">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">formats</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">','</span></span><span class="p"><span class="idiff right">)]</span></span></span>
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<pre style="margin: 0;"> <span id="LC332" 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;">formats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">formats</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ctd_restriction_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -336,7 +366,25 @@ class _Choices(_Restriction):</td>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Parameter</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC368" 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;">__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;">parent</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="LC369" 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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">parent</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;">node</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;">kwargs</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;">if</span> <span class="n" style="color: #333;">node</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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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</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;">name</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" 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;">_init_from_kwargs</span><span class="p">(</span><span class="n" style="color: #333;">parent</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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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" 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;">_init_from_node</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">node</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>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_from_node</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="n" style="color: #333;">nd</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="n" style="color: #333;">setup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_translate_ctd_to_param</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"ITEM"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ITEMLIST"</span><span class="p">],</span> <span class="s" style="color: #d14;">"Tried to init Parameter from </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;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ITEMLIST'</span><span class="p">:</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" 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;">nd</span><span class="p">)</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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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">setup</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;">listitem</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">listitem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nd</span><span class="p">]</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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;">setup</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>
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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;">setup</span><span class="p">[</span><span class="s" style="color: #d14;">'is_list'</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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385
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<pre style="margin: 0;">+<span id="LC385" 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;">_init_from_kwargs</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">setup</span><span class="p">)</span></span>
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386
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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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_from_kwargs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parent</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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340
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="s" style="color: #d14;">"""Required positional arguments: `name` string and `parent` ParameterGroup object</span></span>
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341
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"><span class="s" style="color: #d14;"> Optional keyword arguments:</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">@@ -353,13 +401,13 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"><span class="s" style="color: #d14;"> `short_name`: string for short name annotation</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"><span class="s" style="color: #d14;"> `position`: index (1-based) of the position on which the parameter appears on the command-line</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC356" 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="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"name"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">,</span> <span class="s" style="color: #d14;">"Parameter initialisation without name"</span></span>
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<pre style="margin: 0;">+<span id="LC405" 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;">kwargs</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="LC406" 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;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span></span>
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<pre style="margin: 0;">-<span id="LC358" 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_name</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'short_name'</span><span class="p">,</span> <span class="n" style="color: #333;">_Null</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC407" 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_name</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'short_name'</span><span class="p">,</span> <span class="n" style="color: #333;">_Null</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC408" 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="LC409" 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;">CTDTYPE_TO_TYPE</span><span class="p">[</span><span class="n" style="color: #333;">kwargs</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;">'type'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</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;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">KeyError</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnsupportedTypeError</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</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;">'type'</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC413" 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;">tags</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'tags'</span><span class="p">,</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">@@ -371,34 +419,34 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC419" 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;">advanced</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CAST_BOOLEAN</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</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;">'advanced'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC420" 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;">position</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</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;">'position'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">NO_POSITION</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">default</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span> <span class="n" style="color: #333;">_Null</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">default</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span> <span class="n" style="color: #333;">_Null</span><span class="p"><span class="idiff left right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC424" 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;">_validate_numerical_defaults</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="LC377" class="line" lang="python"><span class="idiff left right"> </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 class="c1" style="color: #998; font-style: italic;"># TODO 1_6_3: right now the CTD schema requires the 'value' attribute to be present for every parameter.</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># So every time we build a model from a CTD file, we find at least a default='' or default=[]</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for every parameter. This should change soon, but for the time being, we have to get around this</span></span>
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381
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># and disregard such default attributes. The below two lines will be deleted after fixing 1_6_3.</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span> <span class="ow" style="font-weight: 600;">or</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;">is_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]):</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_Null</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_Null</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># enforce that default is the correct type if exists. Elementwise for lists</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">default</span></span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">_Null</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC387" 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;">_Null</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" 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="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="p"><span class="idiff right">)</span></span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">_Null</span><span class="p">:</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" 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;">_Null</span><span class="p"><span class="idiff left right">()</span></span></span>
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388
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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="LC437" 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="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC438" 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="LC439" 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_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC392" 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="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">default</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC440" 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="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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442
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<pre style="margin: 0;"> <span id="LC442" 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="bp" style="color: #999;">self</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;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># same for choices. I'm starting to think it's really unpythonic and we should trust input. TODO</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC397" 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="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC446" 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;"><span class="idiff left right">is</span></span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"Boolean flag can't be a list type"</span></span>
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<pre style="margin: 0;"> <span id="LC448" 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;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># override whatever we found. Boolean flags can't be required...</span></span>
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<pre style="margin: 0;"> <span id="LC449" 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;">CAST_BOOLEAN</span><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Default value should exist IFF argument is not required.</span></span>
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: if we can have optional list arguments they don't have to have a default? (empty list)</span></span>
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: CTD Params 1.6.3 have a required value attrib. That's very wrong for parameters that are required.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" 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="471" 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">@@ -423,14 +471,14 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ModelParsingError</span><span class="p">(</span><span class="s" style="color: #d14;">"Provided range [</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] is not of type </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="LC472" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">num_range</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">num_range</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">type</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'choices'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC426" 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;">restrictions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_Choices</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kwargs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'choices'</span></span><span class="p"><span class="idiff right">]</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC474" 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;">restrictions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_Choices</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kwargs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'choices'</span></span><span class="p"><span class="idiff right">])</span>))</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'file_formats'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC476" 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;">restrictions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_FileFormat</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'file_formats'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># perform some basic validation on the provided default values...</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># an empty string IS NOT a float/int!<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># an empty string IS NOT a float/int!</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_numerical_defaults</span><span class="p">(</span><span class="bp" style="color: #999;">self</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 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="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff left right">default</span></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;">_Null</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;">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="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">type</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="p"><span class="idiff right">)</span></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;">_Null</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC482" 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;">int</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="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">defaults_to_validate</span> <span class="o" style="font-weight: 600;">=</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;">errors_so_far</span> <span class="o" style="font-weight: 600;">=</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">@@ -460,14 +508,21 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"><span class="s" style="color: #d14;"> ie. the nesting lineage of the Parameter object. With `name_only` setting on, it only returns</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"><span class="s" style="color: #d14;"> the names of said objects. For top level parameters, it's a list with a single element.</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent</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="LC466" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Exclude ParameterGroup here, since they do not have a short_name attribute (lzimmermann)</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">lineage</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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">short_name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">short_name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">ParameterGroup</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name_only</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reverse</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lineage</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name_only</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">n</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="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">short_name</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">n</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;">short_name</span></span>
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<pre style="margin: 0;">+<span id="LC515" 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="LC516" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;">+<span id="LC517" 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;">parent</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="LC518" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC519" 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="LC520" 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;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">n</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;">get_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</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="LC523" class="line" lang="python"> <span class="s" style="color: #d14;">"""return an iterator over all parameters</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC528" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="547" 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">@@ -492,7 +547,6 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC547" 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;">default</span></span>
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<pre style="margin: 0;"> <span id="LC548" 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;"># otherwise take the parameter default</span></span>
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<pre style="margin: 0;"> <span id="LC549" 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;">default</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># XML attributes to be created (depending on whether they are needed or not):</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># name, value, type, description, tags, restrictions, supported_formats</span></span>
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<pre style="margin: 0;"> <span id="LC552" 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">@@ -501,14 +555,16 @@ class Parameter(object):</td>
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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="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># we'll deal with list parameters later, now only normal:</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: once Param_1_6_3.xsd gets fixed, we won't have to set an empty value='' attrib.</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># but right now value is a required attribute.</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">''</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_Null</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">str</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="LC505" 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 class="c1" style="color: #998; font-style: italic;"># for booleans str(True) returns 'True' but the XS standard is lowercase</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</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="LC559" 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="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">type</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">bool</span></span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># for booleans str(True) returns 'True' but the XS standard is lowercase</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'value'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'true'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'false'</span></span>
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">attribs</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;">TYPE_TO_CTDTYPE</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;">type</span><span class="p">]</span></span>
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508
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562
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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="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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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</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;">description</span></span>
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564
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<pre style="margin: 0;"> <span id="LC564" 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;">tags</span><span class="p">:</span></span>
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'tags'</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="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;">tags</span><span class="p">)</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">attribs</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="nb" style="color: #0086b3;">str</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;">required</span><span class="p">)</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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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'advanced'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</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;">advanced</span><span class="p">)</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="LC568" class="line" lang="python"></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;"># Choices and NumericRange restrictions go in the 'restrictions' attrib, FileFormat has</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;"># its own attribute 'supported_formats' for whatever historic reason.</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">@@ -519,9 +575,10 @@ class Parameter(object):</td>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"></span>
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520
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<pre style="margin: 0;"> <span id="LC576" 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_list</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># and now list parameters</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">top</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">'ITEMLIST'</span><span class="p">,</span> <span class="n" style="color: #333;">attribs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># (lzimmermann) I guess _Null has to be exluded here, too</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" 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="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;">value</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;">_Null</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC579" 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="ow" style="font-weight: 600;">or</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="n" style="color: #333;">_Null</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</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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526
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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;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">,</span> <span class="s" style="color: #d14;">'LISTITEM'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'value'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)})</span></span>
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527
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">top</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="587" 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">@@ -530,8 +587,8 @@ class Parameter(object):</td>
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530
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"></span>
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_cli_node</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parent_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>
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532
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">lineage</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_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">top_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">'clielement'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"optionIdentifier"</span><span class="p">:</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+</span></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;">lineage</span><span class="p">)})</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">top_node</span><span class="p">,</span> <span class="s" style="color: #d14;">'mapping'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"referenceName"</span><span class="p">:</span> <span class="n" style="color: #333;">parent_name</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"."</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></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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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">top_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">'clielement'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"optionIdentifier"</span><span class="p">:</span> <span class="n" style="color: #333;">prefix</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </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;">lineage</span><span class="p">)})</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">top_node</span><span class="p">,</span> <span class="s" style="color: #d14;">'mapping'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"referenceName"</span><span class="p">:</span> <span class="n" style="color: #333;">parent_name</span><span class="idiff left"> </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">"."</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </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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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">top_node</span></span>
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593
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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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_positional</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -539,11 +596,23 @@ class Parameter(object):</td>
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"></span>
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ParameterGroup</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC542" 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;">parent</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="LC599" 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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">parent</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;">node</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;">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="LC600" 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;">parameters</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="LC601" 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="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;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span></span>
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<pre style="margin: 0;"> <span id="LC603" 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="LC546" 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;">parameters</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="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</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="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"></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;">validate_contains_keys</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="s" style="color: #d14;">'NODE'</span><span class="p">)</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" 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;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"description"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">:</span></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;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</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 class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'NODE'</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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;">ParameterGroup</span><span class="p">(</span><span class="n" style="color: #333;">parent</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;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"ITEMLIST"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ITEM"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC615" 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;">parameters</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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;">Parameter</span><span class="p">(</span><span class="n" style="color: #333;">parent</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;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">c</span><span class="p">)</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</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="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="LC618" class="line" lang="python"> <span class="s" style="color: #d14;">"""Registers a parameter in a ParameterGroup. Required: `name` string.</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">@@ -568,12 +637,12 @@ class ParameterGroup(object):</td>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"> <span class="s" style="color: #d14;">"""Registers a child parameter group under a ParameterGroup. Required: `name` string. Optional: `description`</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO assertion if name already exists? It just overrides now, but I'm not sure if allowing this behavior is OK</span></span>
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<pre style="margin: 0;">-<span id="LC571" 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;">parameters</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;">ParameterGroup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" 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;">parameters</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;">ParameterGroup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">parent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">description</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC641" 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;">parameters</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="LC642" class="line" lang="python"></span>
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_children</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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575
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</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;">for</span> <span class="n" style="color: #333;">child</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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">iter</span>values</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</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;">parameters</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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646
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<pre style="margin: 0;"> <span id="LC646" 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;">child</span><span class="p">,</span> <span class="n" style="color: #333;">Parameter</span><span class="p">):</span></span>
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578
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">children</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;">child</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="n" style="color: #333;">ParameterGroup</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">@@ -590,7 +659,7 @@ class ParameterGroup(object):</td>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Of course this should never happen if the argument tree is built properly but it would be</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># nice to take care of it if a user happens to randomly define his arguments and groups.</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># So first we could sort self.parameters (Items first, Groups after them).</span></span>
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<pre style="margin: 0;">-<span id="LC593" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">iter</span>values</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC662" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</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="LC663" class="line" lang="python"> <span class="n" style="color: #333;">top</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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_xml_node</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">top</span></span>
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<pre style="margin: 0;"> <span id="LC665" 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">@@ -600,17 +669,41 @@ class ParameterGroup(object):</td>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"><span class="s" style="color: #d14;"> :param arg_dict: dafualt values for elements</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"><span class="s" style="color: #d14;"> :return: list of clielements</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC603" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">iter</span>values</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_cli_node</span><span class="p">(</span><span class="n" style="color: #333;">parent_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_name</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"."</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></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;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC672" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</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="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_cli_node</span><span class="p">(</span><span class="n" style="color: #333;">parent_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_name</span><span class="idiff left"> </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">"."</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> </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;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC676" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'PARAMETER GROUP </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;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">subparam</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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">iter</span>values</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">subparam</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;">parameters</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="LC679" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">subparam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__repr__</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</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="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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;">info</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_lineage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name_only</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;">short_name</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="LC684" class="line" lang="python"> <span class="s" style="color: #d14;">"""Returns a list of zero or more ParameterGroup objects plus this one object at the end,</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"><span class="s" style="color: #d14;"> ie. the nesting lineage of the ParameterGroup object. With `name_only` setting on, it only returns</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"><span class="s" style="color: #d14;"> the names of said objects. For top level parameters, it's a list with a single element.</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name_only</span><span class="p">:</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">n</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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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">short_name</span><span class="p">:</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">n</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;">short_name</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;">+<span id="LC694" 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;">parent</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="LC695" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC696" 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="LC697" 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;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</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="LC700" class="line" lang="python"> <span class="s" style="color: #d14;">"""return an iterator over all parameters</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nodes</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</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;">parameters</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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705
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<pre style="margin: 0;">+<span id="LC705" 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;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_parameters</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">)</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"></span>
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"></span>
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Mapping</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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616
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709
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<pre style="margin: 0;"> <span id="LC709" 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;">reference_name</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">@@ -628,6 +721,190 @@ class CLI(object):</td>
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<pre style="margin: 0;"> <span id="LC721" 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_elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cli_elements</span></span>
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629
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Parameters</span><span class="p">(</span><span class="n" style="color: #333;">ParameterGroup</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC725" 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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">version</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;">from_file</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;">from_node</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;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC726" 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="bp" style="color: #999;">None</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" 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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" 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="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC729" 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_attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># little helper to have similar access as to CTDModel;</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">from_file</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;">or</span> <span class="n" style="color: #333;">from_node</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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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">from_file</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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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getroot</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from_node</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'PARAMETERS'</span><span class="p">:</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ModelTypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Invalid PARAMETERS file root is not <PARAMETERS>"</span><span class="p">)</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># tool_element.attrib['version'] == '1.6.2' # check whether the schema matches the one CTDOpts uses?</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">params_container_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'NODE'</span><span class="p">)</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'./NODE/NODE[@name="1"]'</span><span class="p">)</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" 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;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'./NODE/ITEM[@name="version"]'</span><span class="p">)</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">one</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;">version</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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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">Parameters</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;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</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;">parent</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;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">one</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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<td class="diff-line-num new new_line" data-linenumber="746" 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">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">Parameters</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;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">name</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;">parent</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;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">params_container_node</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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748
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<pre style="margin: 0;">+<span id="LC748" 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;">params_container_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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;">"description"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" 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;">params_container_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</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;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">version</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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751
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<pre style="margin: 0;">+<span id="LC751" 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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">[</span><span class="s" style="color: #d14;">"value"</span><span class="p">]</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" 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="LC753" 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="LC754" 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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">Parameters</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;">__init__</span><span class="p">(</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 class="p">,</span> <span class="n" style="color: #333;">parent</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;">node</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;">description</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"description"</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="LC756" class="line" lang="python"></span>
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757
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<pre style="margin: 0;">+<span id="LC757" 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_attribs</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</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;">description</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_xml_node</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</span><span class="p">):</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">'PARAMETERS'</span><span class="p">,</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">"1.7.0"</span><span class="p">,</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="python"> <span class="s" style="color: #d14;">'xmlns:xsi'</span><span class="p">:</span> <span class="s" style="color: #d14;">"http://www.w3.org/2001/XMLSchema-instance"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="python"> <span class="s" style="color: #d14;">'xsi:noNamespaceSchemaLocation'</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/genericworkflownodes/CTDopts/raw/master/schemas/Param_1_7_0.xsd"</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="python"> <span class="p">})</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">"NODE"</span><span class="p">,</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;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</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="LC766" class="line" lang="python"> <span class="n" style="color: #333;">params</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;">node</span><span class="p">)</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python"></span>
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768
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<pre style="margin: 0;">+<span id="LC768" 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;">version</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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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python"> <span class="n" style="color: #333;">node</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;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">"ITEM"</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">:</span> <span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="s" style="color: #d14;">'value'</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;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'type'</span><span class="p">:</span> <span class="s" style="color: #d14;">"string"</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="s" style="color: #d14;">"Version of the tool that generated this parameters file."</span><span class="p">,</span> <span class="s" style="color: #d14;">"required"</span><span class="p">:</span> <span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="s" style="color: #d14;">"advanced"</span><span class="p">:</span> <span class="s" style="color: #d14;">"true"</span><span class="p">}))</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">one_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Element</span><span class="p">(</span><span class="s" style="color: #d14;">"NODE"</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">:</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="s" style="color: #d14;">"Instance '1' section for '</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;">name</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python"> <span class="n" style="color: #333;">node</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;">one_node</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC773" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</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="LC774" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_xml_node</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"> <span class="n" style="color: #333;">one_node</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;">n</span><span class="p">)</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span></span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_lineage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name_only</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;">short_name</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="LC780" class="line" lang="python"> <span class="s" style="color: #d14;">"""Returns a list of zero or more ParameterGroup objects plus this one object at the end,</span></span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"><span class="s" style="color: #d14;"> ie. the nesting lineage of the ParameterGroup object. With `name_only` setting on, it only returns</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"><span class="s" style="color: #d14;"> the names of said objects. For top level parameters, it's a list with a single element.</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC784" 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="LC785" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</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="LC787" class="line" lang="python"> <span class="s" style="color: #d14;">"""return an iterator over all parameters</span></span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</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;">parameters</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="LC790" 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;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_parameters</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_cl_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cl_args</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;">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;">short_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;">get_remaining</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;">ignore_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="LC793" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parses command line arguments `cl_args` (either a string or a list like sys.argv[1:])</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="python"><span class="s" style="color: #d14;"> assuming that parameter names are prefixed by `prefix` (default '--').</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"><span class="s" style="color: #d14;"> Returns a nested dictionary with found arguments. Note that parameters have to be registered</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python"><span class="s" style="color: #d14;"> in the model to be parsed and returned.</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python"><span class="s" style="color: #d14;"> Remaining (unmatchable) command line arguments can be accessed if the method is called with</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python"><span class="s" style="color: #d14;"> `get_remaining`. In this case, the method returns a tuple, whose first element is the</span></span>
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="python"><span class="s" style="color: #d14;"> argument dictionary, the second a list of unmatchable command line options.</span></span>
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">StoreFirst</span><span class="p">(</span><span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StoreAction</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="python"><span class="s" style="color: #d14;"> OpenMS command line parser uses the value of the first</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python"><span class="s" style="color: #d14;"> occurence of an argument. This action does the same</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python"><span class="s" style="color: #d14;"> (contrary to the default behaviour of the store action)</span></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="python"><span class="s" style="color: #d14;"> see also https://github.com/OpenMS/OpenMS/issues/4545</span></span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC811" 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;">option_strings</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</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;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC812" 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;">_seen_args</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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<pre style="margin: 0;">+<span id="LC813" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">StoreFirst</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;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">option_strings</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</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="LC814" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC815" 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="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">namespace</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">option_strings</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="diff-line-num new new_line" data-linenumber="816" 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">
816
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<pre style="margin: 0;">+<span id="LC816" 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;">dest</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;">_seen_args</span><span class="p">:</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" 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;">_seen_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</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>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">namespace</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="n" style="color: #333;">values</span><span class="p">)</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python"></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span> <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;">cl_args</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cl_args</span></span>
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<td class="diff-line-num new new_line" data-linenumber="821" 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">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if no arguments are given print help</span></span>
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<td class="diff-line-num new new_line" data-linenumber="822" 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">
822
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<pre style="margin: 0;">+<span id="LC822" 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;">cl_arg_list</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="823" 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">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-h"</span><span class="p">)</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" 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_parameters</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" 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">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">lineage</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;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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="828" 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">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">short_lineage</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;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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;">short_name</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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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">cli_param</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;">':'</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;">lineage</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">cli_short_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">short_prefix</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;">short_lineage</span><span class="p">)</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cli_param</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cl_arg_list</span><span class="p">:</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_arg_list</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;">cli_param</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cli_short_param</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cl_arg_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_arg_list</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;">cli_short_param</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># argument processing info passed to argparse in keyword arguments, we build them here</span></span>
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<pre style="margin: 0;">+<span id="LC838" 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="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">idx</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;">cl_arg_list</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cl_arg_list</span><span class="p">[</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'true'</span><span class="p">,</span> <span class="s" style="color: #d14;">'false'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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="nb" style="color: #0086b3;">str</span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'action'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StoreFirst</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">param</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="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">param</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;">str</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">type</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;">restrictions</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">_Choices</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">set</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;">restrictions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">choices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">"true"</span><span class="p">,</span> <span class="s" style="color: #d14;">"false"</span><span class="p">])):</span> <span class="c1" style="color: #998; font-style: italic;"># boolean flags are not followed by a value, only their presence is required</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'action'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'store_true'</span></span>
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<pre style="margin: 0;">+<span id="LC843" 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="LC844" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we take every argument as string and cast them only later in validate_args() if</span></span>
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># explicitly asked for. This is because we don't want to deal with type exceptions</span></span>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># at this stage, and prefer the multi-leveled strictness settings in validate_args()</span></span>
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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="nb" style="color: #0086b3;">str</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'action'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StoreFirst</span></span>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># or '+' rather? Should we allow empty lists here? If default is a proper list with elements</span></span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that we want to clear, this would be the only way to do it so I'm inclined to use '*'</span></span>
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'nargs'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'*'</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="python"></span>
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855
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<pre style="margin: 0;">+<span id="LC855" 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;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="n" style="color: #333;">_Null</span><span class="p">():</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">required</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;">ignore_required</span><span class="p">:</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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="bp" style="color: #999;">True</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python"></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># hardcoded 'group:subgroup:param'</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">a</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="n" style="color: #333;">_Null</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">short_lineage</span><span class="p">):</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">cli_short_param</span><span class="p">,</span> <span class="n" style="color: #333;">cli_param</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cl_arg_kws</span><span class="p">)</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">cli_param</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cl_arg_kws</span><span class="p">)</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python"></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="n" style="color: #333;">parsed_args</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">(</span><span class="n" style="color: #333;">cl_arg_list</span><span class="p">)</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">res_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># OrderedDict()</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param_name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">parsed_args</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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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># None values are created by argparse if it didn't find the argument or default=None, we skip params</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that dont have a default value</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" 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="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="n" style="color: #333;">param_name</span><span class="p">]</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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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="python"> <span class="n" style="color: #333;">set_nested_key</span><span class="p">(</span><span class="n" style="color: #333;">res_args</span><span class="p">,</span> <span class="n" style="color: #333;">param_name</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 class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res_args</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">get_remaining</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="n" style="color: #333;">res_args</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_ctd_tree</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</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;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generates an XML ElementTree from the parameters model and returns</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"><span class="s" style="color: #d14;"> the top <parameters> Element object, that can be output to a file</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"><span class="s" style="color: #d14;"> (Parameters.write_ctd() does everything needed if the user</span></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"><span class="s" style="color: #d14;"> doesn't need access to the actual element-tree).</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"><span class="s" style="color: #d14;"> Calling this function without any arguments generates the tool-describing CTD with default</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"><span class="s" style="color: #d14;"> values. For parameter-storing and logging optional arguments can be passed:</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;"> `arg_dict`: nested dictionary with values to be used instead of defaults.</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python"><span class="s" style="color: #d14;"> other arguments are irnored</span></span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC887" 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;">_xml_node</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_ctd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</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;">log</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;">cli</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="LC890" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generates a CTD XML from the model and writes it to `out_file`, which is either a string</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"><span class="s" style="color: #d14;"> to a file path or a stream with a write() method.</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"><span class="s" style="color: #d14;"> Calling this function without any arguments besides `out_file` generates the tool-describing</span></span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="python"><span class="s" style="color: #d14;"> CTD with default values. For parameter-storing and logging optional arguments can be passed:</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"><span class="s" style="color: #d14;"> `arg_dict`: nested dictionary with values to be used instead of defaults.</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"><span class="s" style="color: #d14;"> `log`: dictionary with the following optional keys:</span></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"><span class="s" style="color: #d14;"> 'time_start' and 'time_finish': proper XML date strings (eg. datetime.datetime.now(pytz.utc).isoformat())</span></span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"><span class="s" style="color: #d14;"> 'status': exit status</span></span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="python"><span class="s" style="color: #d14;"> 'output': standard output or whatever output the user intends to log</span></span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"><span class="s" style="color: #d14;"> 'warning': warning logs</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"><span class="s" style="color: #d14;"> 'error': standard error or whatever error log the user wants to store</span></span>
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="python"><span class="s" style="color: #d14;"> `cli`: boolean whether or not cli elements should be generated (needed for GenericKNIMENode for example)</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="python"> <span class="n" style="color: #333;">write_ctd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">cli</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CTDModel</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC909" 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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">version</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;">from_file</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;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="python"> <span class="s" style="color: #d14;">"""The parameter model of a tool.</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">@@ -646,14 +923,15 @@ class CTDModel(object):</td>
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<pre style="margin: 0;"> <span id="LC923" 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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: check whether optional attributes in kwargs are all allowed or just ignore the rest?</span></span>
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925
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<pre style="margin: 0;"> <span id="LC925" 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_attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span> <span class="c1" style="color: #998; font-style: italic;"># description, manual, docurl, category (+executable stuff).</span></span>
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649
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<pre style="margin: 0;">-<span id="LC649" 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;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Parameter<span class="idiff left">Group</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'1'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'Parameters of </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># openMS legacy, top group named "1"</span></span></span>
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<pre style="margin: 0;">+<span id="LC926" 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;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Parameter<span class="idiff left">s</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">version</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="n" style="color: #333;"><span class="idiff">kwargs</span></span><span class="p"><span class="idiff right">)</span></span></span>
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650
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927
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<pre style="margin: 0;"> <span id="LC927" 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</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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651
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="python"></span>
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652
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_load_from_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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653
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="python"> <span class="s" style="color: #d14;">"""Builds a CTDModel from a CTD XML file.</span></span>
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654
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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655
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getroot</span><span class="p">()</span></span>
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656
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'tool'</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid CTD file, root is not <tool>"</span> <span class="c1" style="color: #998; font-style: italic;"># TODO: own exception</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'tool'</span><span class="p">:</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ModelTypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Invalid CTD file, root is not <tool>"</span><span class="p">)</span></span>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="python"></span>
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936
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<pre style="margin: 0;"> <span id="LC936" 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_attribs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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937
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<pre style="margin: 0;"> <span id="LC937" 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</span> <span class="o" style="font-weight: 600;">=</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">@@ -667,28 +945,15 @@ class CTDModel(object):</td>
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945
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<pre style="margin: 0;"> <span id="LC945" 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_attribs</span><span class="p">[</span><span class="n" style="color: #333;">tool_opt_attrib</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrib</span><span class="p">[</span><span class="n" style="color: #333;">tool_opt_attrib</span><span class="p">]</span></span>
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668
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python"></span>
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669
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tool_element</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root</span><span class="p">:</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ignoring: cli, logs, relocators. cli and relocators might be useful later.</span></span>
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670
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'manual'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">,</span> <span class="s" style="color: #d14;">'executableName'</span><span class="p">,</span> <span class="s" style="color: #d14;">'executablePath'</span><span class="p">]:</span></span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ignoring: cli, logs, relocators. cli and relocators might be useful later.</span></span>
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672
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950
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<pre style="margin: 0;"> <span id="LC950" 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_attribs</span><span class="p">[</span><span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span></span>
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'cli'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC953" 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_cli</span><span class="p">(</span><span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">findall</span><span class="p">(</span><span class="s" style="color: #d14;">'clielement'</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tag</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'PARAMETERS'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># tool_element.attrib['version'] == '1.6.2' # check whether the schema matches the one CTDOpts uses?</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">params_container_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tool_element</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'NODE'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we have to check the case in which the parent node contains </span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># item/itemlist elements AND node element children</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">params_container_node_contains_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params_container_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'ITEM'</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="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">params_container_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'ITEMLIST'</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assert params_container_node.attrib['name'] == self.name</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check params_container_node's first ITEM child's tool version information again? (OpenMS legacy?)</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params_container_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">'NODE'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># OpenMS legacy again, NODE with name="1" on top</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for the case when we have PARAMETERS/NODE/ITEM</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">params</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;">or</span> <span class="n" style="color: #333;">params_container_node_contains_items</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC688" 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;">parameters</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_param_model</span><span class="p">(</span><span class="n" style="color: #333;">params_container_node</span><span class="p">,</span> <span class="n" style="color: #333;">base</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="LC689" 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="LC690" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># OpenMS legacy again, PARAMETERS/NODE/NODE/ITEM</span></span>
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<pre style="margin: 0;">-<span id="LC691" 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;">parameters</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_param_model</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">base</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="LC956" 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;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Parameters</span><span class="p">(</span><span class="n" style="color: #333;">from_node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tool_element</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_build_cli</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">xml_cli_elements</span><span class="p">):</span></span>
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">xml_cli_element</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">xml_cli_elements</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">@@ -750,7 +1015,7 @@ class CTDModel(object):</td>
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_defaults</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="LC1016" class="line" lang="python"> <span class="s" style="color: #d14;">"""Returns a nested dictionary with all parameters of the model having default values.</span></span>
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">params_w_default</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</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_parameters</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">default</span></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;">_Null</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="python"> <span class="n" style="color: #333;">params_w_default</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</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_parameters</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">type</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="p"><span class="idiff right">)</span></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;">_Null</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="python"> <span class="n" style="color: #333;">defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC1020" 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;">params_w_default</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="python"> <span class="n" style="color: #333;">set_nested_key</span><span class="p">(</span><span class="n" style="color: #333;">defaults</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;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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;">param</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -775,7 +1040,7 @@ class CTDModel(object):</td>
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># boolean values are the only ones that don't get casted correctly with, say, bool('false')</span></span>
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="python"> <span class="n" style="color: #333;">typecast</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="nb" style="color: #0086b3;">type</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</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="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">CAST_BOOLEAN</span></span>
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1042
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<pre style="margin: 0;"> <span id="LC1042" 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="LC778" class="line" lang="python"> <span class="n" style="color: #333;">validated_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">typecast</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">arg</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">typecast</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="LC1043" class="line" lang="python"> <span class="n" style="color: #333;">validated_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">typecast</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">arg</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">typecast</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="LC1044" 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 class="c1" style="color: #998; font-style: italic;"># type casting failed</span></span>
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="python"> <span class="n" style="color: #333;">validated_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span> <span class="c1" style="color: #998; font-style: italic;"># just keep it as a string (or list of strings)</span></span>
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">enforce_type</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># but raise a warning or exception depending on enforcement level</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">@@ -805,60 +1070,10 @@ class CTDModel(object):</td>
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="python"> <span class="n" style="color: #333;">set_nested_key</span><span class="p">(</span><span class="n" style="color: #333;">validated_args</span><span class="p">,</span> <span class="n" style="color: #333;">lineage</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;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">validated_args</span></span>
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_cl_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cl_args</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;">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;">short_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;">get_remaining</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="LC809" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parses command line arguments `cl_args` (either a string or a list like sys.argv[1:])</span></span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python"><span class="s" style="color: #d14;"> assuming that parameter names are prefixed by `prefix` (default '--').</span></span>
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"><span class="s" style="color: #d14;"> Returns a nested dictionary with found arguments. Note that parameters have to be registered</span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"><span class="s" style="color: #d14;"> in the model to be parsed and returned.</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="python"><span class="s" style="color: #d14;"> Remaining (unmatchable) command line arguments can be accessed if the method is called with</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;"> `get_remaining`. In this case, the method returns a tuple, whose first element is the</span></span>
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;"> argument dictionary, the second a list of unmatchable command line options.</span></span>
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC820" 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;">list_parameters</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">lineage</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;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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="LC822" class="line" lang="python"> <span class="n" style="color: #333;">short_lineage</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;">get_lineage</span><span class="p">(</span><span class="n" style="color: #333;">name_only</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;">short_name</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="LC823" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># argument processing info passed to argparse in keyword arguments, we build them here</span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</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 class="c1" style="color: #998; font-style: italic;"># boolean flags are not followed by a value, only their presence is required</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'action'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'store_true'</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we take every argument as string and cast them only later in validate_args() if</span></span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># explicitly asked for. This is because we don't want to deal with type exceptions</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># at this stage, and prefer the multi-leveled strictness settings in validate_args()</span></span>
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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="nb" style="color: #0086b3;">str</span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"></span>
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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_list</span><span class="p">:</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># or '+' rather? Should we allow empty lists here? If default is a proper list with elements</span></span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that we want to clear, this would be the only way to do it so I'm inclined to use '*'</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</span><span class="p">[</span><span class="s" style="color: #d14;">'nargs'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'*'</span></span>
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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="python"></span>
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837
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</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;">_Null</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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;">param</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default</span></span>
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839
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="python"></span>
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840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">param</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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841
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_kws</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="bp" style="color: #999;">True</span></span>
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842
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python"></span>
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843
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># hardcoded 'group:subgroup:param1'</span></span>
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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">a</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;">_Null</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">short_lineage</span><span class="p">):</span></span>
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845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">short_prefix</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;">short_lineage</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lineage</span><span class="p">),</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cl_arg_kws</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC846" 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="LC847" class="line" lang="python"> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lineage</span><span class="p">),</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cl_arg_kws</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span> <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;">cl_args</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cl_args</span></span>
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if no arguments are given print help</span></span>
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<pre style="margin: 0;">-<span id="LC852" 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;">cl_arg_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">cl_arg_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-h"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">parsed_args</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl_parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">(</span><span class="n" style="color: #333;">cl_arg_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">res_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># OrderedDict()</span></span>
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">param_name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">parsed_args</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># None values are created by argparse if it didn't find the argument or default=None, we skip params</span></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that dont have a default value</span></span>
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<pre style="margin: 0;">-<span id="LC859" 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="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="n" style="color: #333;">param_name</span><span class="p">]</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="LC860" class="line" lang="python"> <span class="n" style="color: #333;">set_nested_key</span><span class="p">(</span><span class="n" style="color: #333;">res_args</span><span class="p">,</span> <span class="n" style="color: #333;">param_name</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 class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res_args</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">get_remaining</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="n" style="color: #333;">res_args</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_cl_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cl_args</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;">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;">short_prefix</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="LC1074" class="line" lang="python"> <span class="n" style="color: #333;">get_remaining</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;">ignore_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="LC1075" 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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_cl_args</span><span class="p">(</span><span class="n" style="color: #333;">cl_args</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">short_prefix</span><span class="p">,</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="python"> <span class="n" style="color: #333;">get_remaining</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_required</span><span class="p">)</span></span>
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1077
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="python"></span>
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863
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1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_ctd_tree</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</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;">log</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;">cli</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;">prefix</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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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generates an XML ElementTree from the model and returns the top <tool> Element object,</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">@@ -913,27 +1128,8 @@ class CTDModel(object):</td>
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913
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'error'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">log</span><span class="p">:</span></span>
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914
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">log_node</span><span class="p">,</span> <span class="s" style="color: #d14;">'executionError'</span><span class="p">)</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;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'error'</span><span class="p">]</span></span>
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1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># XML.ETREE SYNTAX</span></span>
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917
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">tool</span><span class="p">,</span> <span class="s" style="color: #d14;">'PARAMETERS'</span><span class="p">,</span> <span class="p">{</span></span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'1.6.2'</span><span class="p">,</span></span>
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919
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="python"> <span class="s" style="color: #d14;">'xmlns:xsi'</span><span class="p">:</span> <span class="s" style="color: #d14;">"http://www.w3.org/2001/XMLSchema-instance"</span><span class="p">,</span></span>
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920
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="python"> <span class="s" style="color: #d14;">'xsi:noNamespaceSchemaLocation'</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/genericworkflownodes/CTDopts/raw/master/schemas/Param_1_6_2.xsd"</span></span>
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="python"> <span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This seems to be some OpenMS hack (defining name, description, version for the second time)</span></span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># but I'll stick to it for consistency</span></span>
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925
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="python"> <span class="n" style="color: #333;">top_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="s" style="color: #d14;">'NODE'</span><span class="p">,</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="n" style="color: #333;">description</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;">opt_attribs</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;">'description'</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="LC926" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">top_node</span><span class="p">,</span> <span class="s" style="color: #d14;">'ITEM'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC928" 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;">'version'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC929" 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;">version</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'string'</span><span class="p">,</span></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Version of the tool that generated this parameters file.'</span><span class="p">,</span></span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="python"> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'advanced'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="python"></span>
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934
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># all the above was boilerplate, now comes the actual parameter tree generation</span></span>
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="python"> <span class="n" style="color: #333;">args_top_node</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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_xml_node</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">)</span></span>
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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="python"> <span class="n" style="color: #333;">top_node</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;">args_top_node</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="python"> <span class="n" style="color: #333;">tool</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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_xml_node</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">))</span></span>
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937
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cli</span><span class="p">:</span></span>
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="python"> <span class="n" style="color: #333;">cli_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">tool</span><span class="p">,</span> <span class="s" style="color: #d14;">"cli"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="946" 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">@@ -946,6 +1142,11 @@ class CTDModel(object):</td>
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># xml.etree syntax (no pretty print available, so we use xml.dom.minidom stuff)</span></span>
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tool</span></span>
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</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="LC1146" class="line" lang="python"> <span class="s" style="color: #d14;">"""return an iterator over all parameters</span></span>
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" 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;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_parameters</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="python"></span>
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_ctd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</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;">log</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;">cli</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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950
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generates a CTD XML from the model and writes it to `out_file`, which is either a string</span></span>
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951
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="python"><span class="s" style="color: #d14;"> to a file path or a stream with a write() method.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="962" 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">@@ -962,13 +1163,17 @@ class CTDModel(object):</td>
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962
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1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="python"><span class="s" style="color: #d14;"> 'error': standard error or whatever error log the user wants to store</span></span>
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963
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1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="python"><span class="s" style="color: #d14;"> `cli`: boolean whether or not cli elements should be generated (needed for GenericKNIMENode for example)</span></span>
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964
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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965
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<td class="diff-line-num new_line old" data-linenumber="1166" 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="LC965" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">xml_content</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">parseString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tostring</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">generate_ctd_tree</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">arg_dict</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cli</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">encoding</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"UTF-8"</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">toprettyxml</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">write_ctd</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">out_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">arg_dict</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cli</span></span><span class="p">)</span></span>
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966
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="python"></span>
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967
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<pre style="margin: 0;">-<span id="LC967" 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;">out_file</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># if out_file is a string, we create and write the file</span></span>
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968
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<pre style="margin: 0;">-<span id="LC968" 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;">out_file</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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969
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<pre style="margin: 0;">-<span id="LC969" 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="n" style="color: #333;">xml_content</span><span class="p">)</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" 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;"># otherwise we assume it's a writable stream and write into that.</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="python"> <span class="n" style="color: #333;">out_file</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;">xml_content</span><span class="p">)</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="python"></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_ctd</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">arg_dict</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;">log</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;">cli</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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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="python"> <span class="n" style="color: #333;">xml_content</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseString</span><span class="p">(</span><span class="n" style="color: #333;">tostring</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">generate_ctd_tree</span><span class="p">(</span><span class="n" style="color: #333;">arg_dict</span><span class="p">,</span> <span class="n" style="color: #333;">log</span><span class="p">,</span> <span class="n" style="color: #333;">cli</span><span class="p">),</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"UTF-8"</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toprettyxml</span><span class="p">(</span><span class="n" style="color: #333;">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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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="python"></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" 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;">out_file</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># if out_file is a string, we create and write the file</span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" 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;">out_file</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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1174
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<pre style="margin: 0;">+<span id="LC1174" 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="n" style="color: #333;">xml_content</span><span class="p">)</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" 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;"># otherwise we assume it's a writable stream and write into that.</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="python"> <span class="n" style="color: #333;">out_file</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;">xml_content</span><span class="p">)</span></span>
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972
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1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="python"></span>
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973
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="python"></span>
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">args_from_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1011" 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="1216" 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">@@ -1011,7 +1216,7 @@ def args_from_file(filename):</td>
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1011
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="python"></span>
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1012
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1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="python"></span>
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1013
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_cl_directives</span><span class="p">(</span><span class="n" style="color: #333;">cl_args</span><span class="p">,</span> <span class="n" style="color: #333;">write_tool_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'write_tool_ctd'</span><span class="p">,</span> <span class="n" style="color: #333;">write_param_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'write_param_ctd'</span><span class="p">,</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="python"> <span class="n" style="color: #333;">input_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'input_ctd'</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>
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1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">input_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'input_ctd'</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>
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1015
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="python"> <span class="s" style="color: #d14;">'''Parses command line CTD processing directives. `write_tool_ctd`, `write_param_ctd` and `input_ctd`</span></span>
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1016
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="python"><span class="s" style="color: #d14;"> string are customizable, and will be parsed for in command line. `prefix` should be one or two dashes,</span></span>
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1017
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="python"><span class="s" style="color: #d14;"> default is '--'.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1021" 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="1226" 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">@@ -1021,6 +1226,14 @@ def parse_cl_directives(cl_args, write_tool_ctd='write_tool_ctd', write_param_ct</td>
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1021
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1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="python"><span class="s" style="color: #d14;"> 'write_param_ctd': if flag set, either True or the filename provided in command line. Otherwise None.</span></span>
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1022
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1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="python"><span class="s" style="color: #d14;"> 'input_ctd': filename if found, otherwise None</span></span>
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1023
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transform</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">):</span></span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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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1231
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<pre style="margin: 0;">+<span id="LC1231" 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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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]:</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" 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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<td class="diff-line-num new new_line" data-linenumber="1234" 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">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</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="1236" 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">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="python"></span>
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1024
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1237
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<pre style="margin: 0;"> <span id="LC1237" 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;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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1025
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1238
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<pre style="margin: 0;"> <span id="LC1238" 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_argument</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">write_tool_ctd</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</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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<td class="diff-line-num old_line" data-linenumber="1026" 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">
1026
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1239
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<pre style="margin: 0;"> <span id="LC1239" 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_argument</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">write_param_ctd</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1030" 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="1243" 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">@@ -1030,8 +1243,6 @@ def parse_cl_directives(cl_args, write_tool_ctd='write_tool_ctd', write_param_ct</td>
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1030
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1243
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="python"> <span class="n" style="color: #333;">directives</span><span class="p">,</span> <span class="n" style="color: #333;">rest</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_known_args</span><span class="p">(</span><span class="n" style="color: #333;">cl_arg_list</span><span class="p">)</span></span>
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1031
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="python"> <span class="n" style="color: #333;">directives</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">directives</span><span class="p">)</span></span>
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1032
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="python"></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="python"> <span class="n" style="color: #333;">transform</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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1034
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<td class="diff-line-num new_line old" data-linenumber="1246" 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="LC1034" class="line" lang="python"></span>
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1035
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="python"> <span class="n" style="color: #333;">parsed_directives</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1036
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1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="python"> <span class="n" style="color: #333;">parsed_directives</span><span class="p">[</span><span class="s" style="color: #d14;">'write_tool_ctd'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">directives</span><span class="p">[</span><span class="n" style="color: #333;">write_tool_ctd</span><span class="p">])</span></span>
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1037
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<td class="diff-line-num new_line" data-linenumber="1248" 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">
1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="python"> <span class="n" style="color: #333;">parsed_directives</span><span class="p">[</span><span class="s" style="color: #d14;">'write_param_ctd'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">directives</span><span class="p">[</span><span class="n" style="color: #333;">write_param_ctd</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1045" 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="1256" 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">@@ -1045,4 +1256,4 @@ def validate_contains_keys(dictionary, keys, element_tag):</td>
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1045
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1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dictionary</span><span class="p">,</span> <span class="s" style="color: #d14;">"Missing required attribute '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s element. Present attributes: </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="LC1258" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">element_tag</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1048" 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="s" style="color: #d14;">'{0}="{1}"'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dictionary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">()]))</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1259" 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="s" style="color: #d14;">'{0}="{1}"'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dictionary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()]))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5#05e0372f8165776bed0a53b989eaffd9e3139848"><strong>example.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;"># or for easier access of certain commonly used module methods</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pprint</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytz</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">CTDopts.CTDopts</span> <span class="c1" style="color: #998; font-style: italic;"># once you installed it, it's just CTDopts</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">CTDopts.CTDopts</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CTDModel</span><span class="p">,</span> <span class="n" style="color: #333;">args_from_file</span><span class="p">,</span> <span class="n" style="color: #333;">parse_cl_directives</span><span class="p">,</span> <span class="n" style="color: #333;">flatten_dict</span><span class="p">,</span> <span class="n" style="color: #333;">override_args</span><span class="p">,</span> <span class="n" style="color: #333;">ArgumentRestrictionError</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">@@ -25,7 +24,7 @@ model = CTDModel(</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">category</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'testing'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">executableName</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'exampletool'</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;">executablePath</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'/path/to/exec/exampletool-1.0/exampletool'</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</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>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The parameters of the tool have to be registered the following way:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</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">@@ -35,7 +34,7 @@ model.add(</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">default</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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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'advanced'</span><span class="p">,</span> <span class="s" style="color: #d14;">'magic'</span><span class="p">],</span> <span class="c1" style="color: #998; font-style: italic;"># for certain workflow engines that make use of parameter tags</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A positive integer parameter'</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><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="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'input_files'</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">@@ -44,7 +43,7 @@ model.add(</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">is_list</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># for list parameters with an arbitrary number of values</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">file_formats</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fastq.gz'</span><span class="p">],</span> <span class="c1" style="color: #998; font-style: italic;"># filename restrictions</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A list of filenames to feed this dummy tool with'</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="p">)</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 class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</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;">'this_that'</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">@@ -52,7 +51,7 @@ model.add(</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'this'</span><span class="p">,</span> <span class="s" style="color: #d14;">'that'</span><span class="p">],</span> <span class="c1" style="color: #998; font-style: italic;"># controlled vocabulary</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'this'</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A controlled vocabulary parameter. Allowed values `this` or `that`.'</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Certain tools may want to group parameters together. One can define them like this:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">subparams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_group</span><span class="p">(</span><span class="s" style="color: #d14;">'subparams'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Grouped settings'</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">@@ -63,7 +62,7 @@ subparams.add(</td>
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<pre style="margin: 0;"> <span id="LC62" 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;">float</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.5</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Some floating point setting.'</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="p">)</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="n" style="color: #333;">subparams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">'param_2'</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">@@ -72,7 +71,7 @@ subparams.add(</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'advanced'</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.5</span><span class="p">,</span> <span class="mf" style="color: #099;">5.0</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A list of floating point settings'</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="p">)</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="n" style="color: #333;">subsubparams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subparams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_group</span><span class="p">(</span><span class="s" style="color: #d14;">'subsubparam'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A group of sub-subsettings'</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;">subsubparams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</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">@@ -80,137 +79,137 @@ subsubparams.add(</td>
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<pre style="margin: 0;"> <span id="LC79" 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;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">default</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="LC81" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"A subsetting's subsetting"</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><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="c1" style="color: #998; font-style: italic;"># Now we have a CTDModel. To write the model to a CTD (xml) file:</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'Model being written to exampleTool.ctd...</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Model being written to exampleTool.ctd...</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_ctd</span><span class="p">(</span><span class="s" style="color: #d14;">'exampleTool.ctd'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></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;"># However, if we already have a CTD model for a tool, we can spare the pain of defining it like above, we can just</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;"># load it from a file directly. Like this:</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'Model loaded from exampleTool.ctd...</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Model loaded from exampleTool.ctd...</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="n" style="color: #333;">model_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CTDModel</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'exampleTool.ctd'</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 class="c1" style="color: #998; font-style: italic;"># We can list all the model's parameters. The below call will get a list of all Parameter objects registered in the model.</span></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;"># These objects store name, type, default, restriction, parent group etc. information we set above.</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"><span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">list_parameters</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"For debugging purposes we can output a human readable representation of Parameter objects. Here's the first one:"</span></span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"For debugging purposes we can output a human readable representation of Parameter objects. Here's the first one:"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Let's print out the name attributes of these parameters.</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'The following parameters were registered in the model:'</span></span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'The following parameters were registered in the model:'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">([</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># In the above model, certain parameters were registered under parameter groups. We can access their 'lineage' and see</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># their nesting levels. Let's display nesting levels separated by colons:</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'The same parameters with subgroup information, if they were registered under parameter groups:'</span></span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><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">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_lineage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name_only</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="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'The same parameters with subgroup information, if they were registered under parameter groups:'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">([</span></span><span class="s" style="color: #d14;"><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">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_lineage</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name_only</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="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></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;"># (Parameter.get_lineage() returns a list of ParameterGroups down to the leaf Parameter. `name_only` setting returns</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;"># only the names of the objects, instead of the actual Parameter objects.</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></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;"># Some of the parameters had default values in the model. We can get those:</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'A dictionary of parameters with default values, returned by CTDModel.get_defaults():'</span></span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'A dictionary of parameters with default values, returned by CTDModel.get_defaults():'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"><span class="n" style="color: #333;">defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_defaults</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">defaults</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;">print</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></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="LC121" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">'As you can see, parameter values are usually stored in nested dictionaries. If you want a flat dictionary, you can'</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">'get that using CTDopts.flatten_dict(). Flat keys can be either tuples of tree node (subgroup) names down to the parameter...'</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;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'As you can see, parameter values are usually stored in nested dictionaries. If you want a flat dictionary, you can'</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">'get that using CTDopts.flatten_dict(). Flat keys can be either tuples of tree node (subgroup) names down to the parameter...'</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;">flat_defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flatten_dict</span><span class="p">(</span><span class="n" style="color: #333;">defaults</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;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">flat_defaults</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;">print</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></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="LC127" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'...or they can be strings where nesing levels are separated by colons:'</span></span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'...or they can be strings where nesing levels are separated by colons:'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"><span class="n" style="color: #333;">flat_defaults_colon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flatten_dict</span><span class="p">(</span><span class="n" style="color: #333;">defaults</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</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="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">flat_defaults_colon</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;">print</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></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="LC132" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">'We can create dictionaries of arguments on our own that we want to validate against the model.'</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;">'CTDopts can read them from argument-storing CTD files or from the command line, but we can just define them in a '</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;">'nested dictionary on our own as well. We start with defining them explicitly.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'We can create dictionaries of arguments on our own that we want to validate against the model.'</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'CTDopts can read them from argument-storing CTD files or from the command line, but we can just define them in a '</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'nested dictionary on our own as well. We start with defining them explicitly.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="n" style="color: #333;">new_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="LC136" class="line" lang="python"><span class="s" style="color: #d14;">'positive_int'</span><span class="p">:</span> <span class="mi" style="color: #099;">111</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;">'input_files'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'file1.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'file2.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'file3.fastq'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;">'subparams'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'param_1'</span><span class="p">:</span> <span class="s" style="color: #d14;">'999.0'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'positive_int'</span><span class="p">:</span> <span class="mi" style="color: #099;">111</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'input_files'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'file1.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'file2.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'file3.fastq'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'subparams'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'param_1'</span><span class="p">:</span> <span class="s" style="color: #d14;">'999.0'</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>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">new_values</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></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="LC143" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"We can validate these arguments against the model, and get a dictionary with parameter types correctly casted "</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;">"and defaults set. Note that subparams:param_1 was casted from string to a floating point number because that's how it "</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;">"was defined in the model."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"We can validate these arguments against the model, and get a dictionary with parameter types correctly casted "</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">"and defaults set. Note that subparams:param_1 was casted from string to a floating point number because that's how it "</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">"was defined in the model."</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;">validated</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate_args</span><span class="p">(</span><span class="n" style="color: #333;">new_values</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">validated</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">'We can write a CTD file containing these validated argument values. Just call CTDModel.write_ctd() with an extra '</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">'parameter: the nested argument dictionary containing the actual values.'</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;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'We can write a CTD file containing these validated argument values. Just call CTDModel.write_ctd() with an extra '</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">'parameter: the nested argument dictionary containing the actual values.'</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;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_ctd</span><span class="p">(</span><span class="s" style="color: #d14;">'exampleTool_preset_params.ctd'</span><span class="p">,</span> <span class="n" style="color: #333;">validated</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC153" 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;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">'As mentioned earlier, CTDopts can load argument values from CTD files. Feel free to change some values in '</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"exampleTool_preset_params.ctd you've just written, and load it back."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'As mentioned earlier, CTDopts can load argument values from CTD files. Feel free to change some values in '</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"exampleTool_preset_params.ctd you've just written, and load it back."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"><span class="n" style="color: #333;">args_from_ctd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args_from_file</span><span class="p">(</span><span class="s" style="color: #d14;">'exampleTool_preset_params.ctd'</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;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">args_from_ctd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"Notice that all the argument values are strings now. This is because we didn't validate them against the model, "</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="s" style="color: #d14;">"just loaded some stuff from a file into a dictionary. If you want to cast them, call CTDModel.validate_args():"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Notice that all the argument values are strings now. This is because we didn't validate them against the model, "</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"just loaded some stuff from a file into a dictionary. If you want to cast them, call CTDModel.validate_args():"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"><span class="n" style="color: #333;">validated_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate_args</span><span class="p">(</span><span class="n" style="color: #333;">args_from_ctd</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">validated_2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"Now certain parameters may have restrictions that we might want to validate for as well. Let's set the parameter "</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">"positive_int to a negative value, and try to validate it with a strictness level enforce_restrictions=1. This "</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">"will register a warning, but still accept the value."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Now certain parameters may have restrictions that we might want to validate for as well. Let's set the parameter "</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"positive_int to a negative value, and try to validate it with a strictness level enforce_restrictions=1. This "</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"will register a warning, but still accept the value."</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;">validated_2</span><span class="p">[</span><span class="s" style="color: #d14;">'positive_int'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"><span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate_args</span><span class="p">(</span><span class="n" style="color: #333;">validated_2</span><span class="p">,</span> <span class="n" style="color: #333;">enforce_restrictions</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="LC171" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"Validation enforcement levels can be 0, 1 or 2 for type-casting, restriction-checking and required argument presence. "</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"They can be set with the keywords enforce_type, enforce_restrictions and enforce_required respectively. Let's increase "</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">"strictness for restriction checking. CTDModel.validate_args() will now raise an exception that we'll catch:</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="LC172" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Validation enforcement levels can be 0, 1 or 2 for type-casting, restriction-checking and required argument presence. "</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"They can be set with the keywords enforce_type, enforce_restrictions and enforce_required respectively. Let's increase "</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"strictness for restriction checking. CTDModel.validate_args() will now raise an exception that we'll catch:</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="LC175" 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="LC176" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate_args</span><span class="p">(</span><span class="n" style="color: #333;">validated_2</span><span class="p">,</span> <span class="n" style="color: #333;">enforce_restrictions</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># , enforce_type=0, enforce_required=0</span></span>
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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="n" style="color: #333;">ArgumentRestrictionError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ee</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;"># other exceptions: ArgumentTypeError, ArgumentMissingError, all subclasses of Argumenterror</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">ee</span></span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">ee</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC180" 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;">print</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"One might want to combine arguments loaded from a CTD file with arguments coming from elsewhere, like the command line."</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="s" style="color: #d14;">"In that case, the method CTDopts.override_args(*arg_dicts) creates a combined argument dictionary where argument values "</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">"are always taken from the rightmost (last) dictionary that has them. Let's override a few parameters:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"One might want to combine arguments loaded from a CTD file with arguments coming from elsewhere, like the command line."</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"In that case, the method CTDopts.override_args(*arg_dicts) creates a combined argument dictionary where argument values "</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"are always taken from the rightmost (last) dictionary that has them. Let's override a few 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;">override</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">'this_that'</span><span class="p">:</span> <span class="s" style="color: #d14;">'that'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="s" style="color: #d14;">'positive_int'</span><span class="p">:</span> <span class="mi" style="color: #099;">777</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"><span class="idiff left right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="n" style="color: #333;">overridden</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">override_args</span><span class="p">(</span><span class="n" style="color: #333;">validated</span><span class="p">,</span> <span class="n" style="color: #333;">override</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">overridden</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"So how to deal with command line arguments? If we have a model, we can look for its arguments. "</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">"Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. "</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="s" style="color: #d14;">"By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'."</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">"Grouped parameters are expected in --group:subgroup:param_x format."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"So how to deal with command line arguments? If we have a model, we can look for its arguments. "</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. "</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'."</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"Grouped parameters are expected in --group:subgroup:param_x format."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="n" style="color: #333;">cl_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_cl_args</span><span class="p">(</span><span class="s" style="color: #d14;">'--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --input_files a.fastq b.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">cl_args</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># # you can get unmatchable command line arguments with get_remaining=True like:</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># cl_args, unparsed = model.parse_cl_args('--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --unrelated_stuff abc', get_remaining=True)</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="LC204" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"Override other parameters with them, and validate it against the model:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Override other parameters with them, and validate it against the model:"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"><span class="n" style="color: #333;">overridden_with_cl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">override_args</span><span class="p">(</span><span class="n" style="color: #333;">validated</span><span class="p">,</span> <span class="n" style="color: #333;">cl_args</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;">validated_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate_args</span><span class="p">(</span><span class="n" style="color: #333;">overridden_with_cl</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="n" style="color: #333;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">validated_3</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"><span class="k" style="font-weight: 600;">print</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="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"One last thing: certain command line directives that are specific to CTD functionality can be parsed for, "</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">"to help your script performing common tasks. These are CTD argument input, CTD model file writing and CTD argument "</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">"file writing. CTDopts.parse_cl_directives() can also be customized as to what directives to look for if the defaults "</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">"--input_ctd, --write_tool_ctd and --write_param_ctd respectively don't satisfy you."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"One last thing: certain command line directives that are specific to CTD functionality can be parsed for, "</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"to help your script performing common tasks. These are CTD argument input, CTD model file writing and CTD argument "</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"file writing. CTDopts.parse_cl_directives() can also be customized as to what directives to look for if the defaults "</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"--input_ctd, --write_tool_ctd and --write_param_ctd respectively don't satisfy you."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="n" style="color: #333;">directives_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cl_directives</span><span class="p">(</span><span class="s" style="color: #d14;">'--input_ctd exampleTool_preset_params.ctd --write_param_ctd new_preset_params.ctd'</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;">pretty_print</span><span class="p">(</span><span class="n" style="color: #333;">directives_1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="n" style="color: #333;">directives_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cl_directives</span><span class="p">(</span><span class="s" style="color: #d14;">'-inctd exampleTool_preset_params_2.ctd -toolctd '</span><span class="p">,</span> <span class="n" style="color: #333;">input_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'inctd'</span><span class="p">,</span> <span class="n" style="color: #333;">write_tool_ctd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'toolctd'</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>
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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">@@ -227,23 +226,23 @@ pretty_print(directives_2)</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If I found directives['write_tool_ctd'], I'd immediately output the tool's CTD model with</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># model.write_ctd(directives['write_tool_ctd']), etc.</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="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Finally, writing CTDs with logging information, passing a dictionary with a 'log' keyword, using any or all of the </span>"</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"</span>fields shown below."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"><span class="n" style="color: #333;">time_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">pytz</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utc</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isoformat</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Finally, writing CTDs with logging information, passing a dictionary</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"with a 'log' keyword, using any or all of the </span>fields shown below."</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;">time_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">datetime</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">timezone</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utc</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isoformat</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># do stuff</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Output of my program, however I generated or logged it'</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"><span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Standard error output of my program, however I caught or redirected them'</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"><span class="n" style="color: #333;">warnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Warnings of my program'</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="n" style="color: #333;">exitstatus</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1'</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"><span class="n" style="color: #333;">time_finish</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">pytz</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utc</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isoformat</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;">time_finish</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">datetime</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">timezone</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utc</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isoformat</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"><span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;">'time_start'</span><span class="p">:</span> <span class="n" style="color: #333;">time_start</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># make sure to give it a legal XML date string if you can.</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;">'time_finish'</span><span class="p">:</span> <span class="n" style="color: #333;">time_finish</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># You can generate them with datetime.datetime.now(pytz.utc).isoformat()</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;">'status'</span><span class="p">:</span> <span class="n" style="color: #333;">exitstatus</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;">'output'</span><span class="p">:</span> <span class="n" style="color: #333;">output</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;">'warning'</span><span class="p">:</span> <span class="n" style="color: #333;">warnings</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;">'error'</span><span class="p">:</span> <span class="n" style="color: #333;">errors</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'time_start'</span><span class="p">:</span> <span class="n" style="color: #333;">time_start</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># make sure to give it a legal XML date string if you can.</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'time_finish'</span><span class="p">:</span> <span class="n" style="color: #333;">time_finish</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># You can generate them with datetime.datetime.now(pytz.utc).isoformat()</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'status'</span><span class="p">:</span> <span class="n" style="color: #333;">exitstatus</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'output'</span><span class="p">:</span> <span class="n" style="color: #333;">output</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'warning'</span><span class="p">:</span> <span class="n" style="color: #333;">warnings</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="idiff left right"> </span><span class="s" style="color: #d14;">'error'</span><span class="p">:</span> <span class="n" style="color: #333;">errors</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_ctd</span><span class="p">(</span><span class="s" style="color: #d14;">'exampleTool_w_logging.ctd'</span><span class="p">,</span> <span class="n" style="color: #333;">validated_3</span><span class="p">,</span> <span class="n" style="color: #333;">log</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">@@ -252,4 +251,3 @@ model.write_ctd('exampleTool_w_logging.ctd', validated_3, log)</td>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Methods you might find helpful to deal with argument dictionaries (see docstrings):</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># CTDopts.set_nested_key(dictionary, tuple_w_levels, value) and</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># CTDopts.get_nested_key(dictionary, tuple_w_levels for nested dictionaries</span></span></pre>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[pycodestyle]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ignore = E501</span></pre>
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<a href="https://salsa.debian.org/med-team/ctdopts/-/commit/30fee58ca58ca32825ce7d779474a85b1fd8f7c5#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -2,7 +2,7 @@ from distutils.core import setup</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" 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;">'CTDopts'</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'1.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'1.<span class="idiff left right">3</span>'</span><span class="p">,</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'CTDopts'</span><span class="p">],</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/genericworkflownodes/CTDopts'</span><span class="p">,</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">license</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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