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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pbcommand">Debian Med / python-pbcommand</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pbcommand/-/commit/b72d2670bd01df5367c61b5ec14fb64b5bff5555">b72d2670</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-12-07T16:24:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.1+git20201023.cc0ed3d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pbcommand/-/commit/3e33ced73e5c5b53f57ac2c87faa0fa1278462a0">3e33ced7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-12-07T16:42:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.1+git20201023.cc0ed3d</pre>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#b99fa999cc9661f1ff593fd72b1422d09c0b62e1">
pbcommand/models/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#8a415a54b830fd7f9a9e3e378681e4ffd3ce3104">
pbcommand/models/common.py
</a>
</li>
<li class="file-stats">
<a href="#2c344dcf56b437e7cbb495d1d0230b7c4a75d497">
pbcommand/models/legacy.py
</a>
</li>
<li class="file-stats">
<a href="#61b23662391a3b54836000f357a4c9b51d930362">
pbcommand/models/report.py
</a>
</li>
<li class="file-stats">
<a href="#6a398774ccb657a31d4a07214baabcbda6cd39cd">
pbcommand/pb_io/common.py
</a>
</li>
<li class="file-stats">
<a href="#bb082aada8e535a1155a8a39f97473524faf272a">
pbcommand/services/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#1a0981a4b2458240c866e6f023adda456c0f778c">
pbcommand/services/_service_access_layer.py
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<li class="file-stats">
<a href="#871f89bee0833d15c661ca42e3f1644683e9e096">
pbcommand/services/job_poller.py
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</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#d1972d953870d92f76fda233025dabf694f05195">
tests/test_models_legacy.py
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</li>
<li class="file-stats">
<a href="#5939fca8460e7402d7b88587f2433eb2d8d6ed1a">
tests/test_models_report.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="b99fa999cc9661f1ff593fd72b1422d09c0b62e1">
<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#b99fa999cc9661f1ff593fd72b1422d09c0b62e1"><strong>pbcommand/models/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">@@ -6,6 +6,6 @@ from .common import (FileType, FileTypes, TaskOptionTypes,</td>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
6
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<td class="diff-line-num new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">BasePacBioOption</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" 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">
7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntOption</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioBooleanOption</span><span class="p">,</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">PacBioStringOption</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioFloatOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntChoiceOption</span><span class="p">,</span></span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntChoiceOption</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">PacBioFileOption</span></span><span class="p"><span class="idiff right">,</span></span></span>
</pre>
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10
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<td class="diff-line-num new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">PacBioFloatChoiceOption</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioStringChoiceOption</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">PacBioAlarm</span><span class="p">,</span> <span class="n" style="color: #333;">PipelinePreset</span><span class="p">)</span></span></pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">PacBioAlarm</span><span class="p">,</span> <span class="n" style="color: #333;">PipelinePreset</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">EntryPoint</span></span><span class="p">)</span></span></pre>
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<li id="8a415a54b830fd7f9a9e3e378681e4ffd3ce3104">
<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#8a415a54b830fd7f9a9e3e378681e4ffd3ce3104"><strong>pbcommand/models/common.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">@@ -930,7 +930,7 @@ def write_dict_to_json(d, file_name, permission="w"):</td>
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<td class="diff-line-num old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="931" 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">
931
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"></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;">RX_TASK_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'^([A-z0-9_]*)\.tasks\.([A-z0-9_]*)$'</span><span class="p">)</span></span>
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933
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="python"><span class="n" style="color: #333;">RX_TASK_OPTION_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'^([A-z0-9_<span class="idiff left right">]*)\.task_options\.([A-z0-9_</span>\.]*)'</span><span class="p">)</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="python"><span class="n" style="color: #333;">RX_TASK_OPTION_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'^([A-z0-9_\.]*)'</span><span class="p">)</span></span>
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934
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"></span>
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935
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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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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_id</span><span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="p">,</span> <span class="n" style="color: #333;">idtype</span><span class="p">,</span> <span class="n" style="color: #333;">tid</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">@@ -1076,6 +1076,13 @@ def _strict_validate_string_or_raise(value):</td>
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1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="n" style="color: #333;">_type_error_msg</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">))</span></span>
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1077
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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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1078
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1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="python"></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_strict_validate_file_or_raise</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Not supporting unicode in python2.</span></span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" 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="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="n" style="color: #333;">_type_error_msg</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">))</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="python"></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="python"></span>
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PacBioIntOption</span><span class="p">(</span><span class="n" style="color: #333;">BasePacBioOption</span><span class="p">):</span></span>
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="python"> <span class="n" style="color: #333;">OPTION_TYPE_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">INT</span></span>
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1088
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<pre style="margin: 0;"> <span id="LC1088" 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">@@ -1108,6 +1115,14 @@ class PacBioStringOption(BasePacBioOption):</td>
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_strict_validate_string_or_raise</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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1109
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="python"></span>
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1110
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="python"></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PacBioFileOption</span><span class="p">(</span><span class="n" style="color: #333;">BasePacBioOption</span><span class="p">):</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="python"> <span class="n" style="color: #333;">OPTION_TYPE_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">FILE</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="python"></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate_core_type</span><span class="p">(</span><span class="n" style="color: #333;">cls</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="LC1123" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_strict_validate_file_or_raise</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="LC1124" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_strict_validate_default_and_choices</span><span class="p">(</span><span class="n" style="color: #333;">core_type_validator_func</span><span class="p">):</span></span>
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1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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1128
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<pre style="margin: 0;"> <span id="LC1128" 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">@@ -1324,3 +1339,19 @@ class PipelinePreset:</td>
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="python"> <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="p">.</span><span class="n" style="color: #333;">description</span><span class="p">),</span></span>
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"options"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">options</span><span class="p">)),</span></span>
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1326
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"taskOptions"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_options</span><span class="p">))])</span></span>
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">EntryPoint</span><span class="p">(</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">"EntryPoint"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"entry_id"</span><span class="p">,</span> <span class="s" style="color: #d14;">"file_type_id"</span><span class="p">,</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"optional"</span><span class="p">])):</span></span>
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_dict</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">):</span></span>
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1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EntryPoint</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"entryId"</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"fileTypeId"</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">],</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">))</span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="python"></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">short_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">file_type_id</span><span class="p">.</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" XML"</span></span>
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">file_ext</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="LC1357" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FileTypes</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">()[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">file_type_id</span><span class="p">].</span><span class="n" style="color: #333;">ext</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#2c344dcf56b437e7cbb495d1d0230b7c4a75d497"><strong>pbcommand/models/legacy.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">@@ -2,24 +2,15 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Models carried over from pbsmrtpipe, still required for SMRT Link interface.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</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;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">itertools</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">collections</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">namedtuple</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Pipeline</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="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;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">display_name</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="n" style="color: #333;">bindings</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">entry_bindings</span><span class="p">,</span> <span class="n" style="color: #333;">parent_pipeline_ids</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;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">(),</span> <span class="n" style="color: #333;">task_options</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="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> Both entry_points and bindings are provided as "simple" format (e.g, [("alpha:0", "beta:1"])</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;"> This really should have been abstracted away into containers to make the interface clear. This was a fundamental</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> design mistake.</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> :param bindings: List of "simple" binding format [("alpha:0:0", "beta:0:0")]</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> :param entry_bindings: List of "simple" bindings [("$entry:e1", "my_task:0")]</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span><span class="p">,</span> <span class="n" style="color: #333;">parent_pipeline_ids</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;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">task_options</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="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +19,7 @@ class Pipeline:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># set of [(a, b), ...]</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bindings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bindings</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># set of [(a, b), ...]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_<span class="idiff left">bindings</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="n" style="color: #333;"><span class="idiff">x</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">entry_bindings</span></span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_<span class="idiff left">points</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">entry_points</span></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># list of strings</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tags</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parent_pipeline_ids</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,56 +34,41 @@ class Pipeline:</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">idx</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">all_bindings</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="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bindings</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;">entry_bindings</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">required_inputs</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="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">o</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_points</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">optional</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">optional_inputs</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="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">o</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_points</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">optional</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__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="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Only communicate the entry id</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">ek</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">e<span class="idiff left">id</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">eid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_</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="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">entry_binding</span>s</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">ek</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p"><span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"entryId"</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">e</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="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">entry_point</span>s</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">e</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ek</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">_d</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;">k</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;">__class__</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <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 class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">d</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;">display_name</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">bindings</span><span class="p">),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<{k} id={i} nbindings={b} entry bindings={e} >"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">_d</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary</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="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">verbose</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">outs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outs</span><span class="p">.</span><span class="n" style="color: #333;">append</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># out a list of tuples</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_printer</span><span class="p">(</span><span class="n" style="color: #333;">xs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">xs</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;">sx</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;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)])</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">f</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;">sx</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_format_inputs</span><span class="p">(</span><span class="n" style="color: #333;">inputs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">short_name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ep</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">inputs</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Pipeline Summary"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Pipeline Id: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pipeline_id</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Name : {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">display_name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Description: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"EntryPoints: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_bindings</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;">_printer</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">entry_bindings</span><span class="p">,</span> <span class="n" style="color: #333;">key</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="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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Workflow Summary"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Workflow Id : {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pipeline_id</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Name : {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">display_name</span><span class="p">))</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Description : {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">))</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Required Inputs: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">_format_inputs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">required_inputs</span><span class="p">)))</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optional_inputs</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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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Optional Inputs: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">_format_inputs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optional_inputs</span><span class="p">)))</span></span>
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73
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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;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tags</span><span class="p">:</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Tags : {} "</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tags</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="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Tags <span class="idiff left right"> </span>: {} "</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tags</span><span class="p">)))))</span></span>
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75
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_options</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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76
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">"Task Options:"</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">option_id</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">iter_options</span><span class="p">():</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">" {o} = {v}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">option_id</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">opt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_options</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">" {o} = {v}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">option_id</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">default</span><span class="p">))</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">(</span><span class="s" style="color: #d14;">" {n} ({t})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">OPTION_TYPE_ID</span><span class="p">))</span></span>
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79
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">outs</span><span class="p">)</span></span></pre>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">iter_options</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">option_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_options</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">option_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">option_ids</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">option_id</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_options</span><span class="p">[</span><span class="n" style="color: #333;">option_id</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_dict</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">bindings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># obsolete</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">epoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">e</span><span class="p">[</span><span class="s" style="color: #d14;">"entryId"</span><span class="p">],</span> <span class="n" style="color: #333;">e</span><span class="p">[</span><span class="s" style="color: #d14;">"fileTypeId"</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"entryPoints"</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The pipeline instance only needs to the key-value pair</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">task_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">o</span><span class="p">[</span><span class="s" style="color: #d14;">"id"</span><span class="p">]:</span> <span class="n" style="color: #333;">o</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'taskOptions'</span><span class="p">]}</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">],</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">bindings</span><span class="p">,</span> <span class="n" style="color: #333;">epoints</span><span class="p">,</span> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'tags'</span><span class="p">],</span> <span class="n" style="color: #333;">task_options</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">task_options</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_from_json</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">json_in</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">.</span><span class="n" style="color: #333;">from_dict</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="p">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">json_in</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#61b23662391a3b54836000f357a4c9b51d930362"><strong>pbcommand/models/report.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">@@ -361,7 +361,7 @@ class Plot(BaseReportElement):</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">PLOT_TYPE</span></span>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_attrs_simple</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="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="s" style="color: #d14;">'image'</span><span class="p">,</span> <span class="s" style="color: #d14;">'caption'</span><span class="p">,</span> <span class="s" style="color: #d14;">'title'</span><span class="p">,</span> <span class="s" style="color: #d14;">'plotType'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="s" style="color: #d14;">'image'</span><span class="p">,</span> <span class="s" style="color: #d14;">'caption'</span><span class="p">,</span> <span class="s" style="color: #d14;">'title'</span><span class="p">,</span> <span class="s" style="color: #d14;">'plotType'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'thumbnail'</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_attrs_complex_list</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="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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">@@ -869,10 +869,15 @@ class Report(BaseReportElement):</td>
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">table_id</span><span class="p">,</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span>
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_to_sum</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC873" 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;">values</span><span class="p">)</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="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_sum_attributes</span><span class="p">(</span><span class="n" style="color: #333;">attributes_list</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_merge_attributes_d</span><span class="p">(</span><span class="n" style="color: #333;">attributes_list</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"> <span class="n" style="color: #333;">labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_merge_attributes_names</span><span class="p">(</span><span class="n" style="color: #333;">attributes_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">values</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;">labels</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_to_</span>sum</span><span class="p">(</span><span class="n" style="color: #333;">values</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;">labels</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])</span></span>
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="python"> <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;">values</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()]</span></span>
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="python"></span>
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_merge_tables</span><span class="p">(</span><span class="n" style="color: #333;">tables</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#6a398774ccb657a31d4a07214baabcbda6cd39cd"><strong>pbcommand/pb_io/common.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">@@ -5,10 +5,11 @@ import warnings</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></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;">pbcommand.models</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">PipelineChunk</span><span class="p">,</span> <span class="n" style="color: #333;">PipelineDataStoreViewRules</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;">TaskOptionTypes</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioFloatChoiceOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">PacBioStringChoiceOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">PacBioStringChoiceOption</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">PacBioFileOption</span></span><span class="p"><span class="idiff right">,</span></span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntChoiceOption</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioStringOption</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">PacBioFloatOption</span><span class="p">,</span> <span class="n" style="color: #333;">PacBioBooleanOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntOption</span><span class="p">,</span> <span class="n" style="color: #333;">PipelinePreset</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">PacBioIntOption</span><span class="p">,</span> <span class="n" style="color: #333;">PipelinePreset</span><span class="p">,</span> <span class="n" style="color: #333;">EntryPoint</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.models.legacy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Pipeline</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.schemas</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">validate_datastore_view_rules</span><span class="p">,</span> <span class="n" style="color: #333;">validate_presets</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">to_ascii</span><span class="p">,</span> <span class="n" style="color: #333;">to_utf8</span></span>
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<pre style="margin: 0;"> <span id="LC15" 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">@@ -121,7 +122,8 @@ def __simple_option_by_type(</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">klass_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">INT</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioIntOption</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;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">FLOAT</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioFloatOption</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">STR</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioStringOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">BOOL</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioBooleanOption</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">BOOL</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioBooleanOption</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">TaskOptionTypes</span><span class="p">.</span><span class="n" style="color: #333;">FILE</span><span class="p">:</span> <span class="n" style="color: #333;">PacBioFileOption</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>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">klass_map</span><span class="p">[</span><span class="n" style="color: #333;">option_type</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,3 +209,18 @@ def load_pipeline_presets_from(d):</td>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">.</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="bp" style="color: #999;">None</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">.</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="bp" style="color: #999;">None</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">presets</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">_json_path_or_d</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_pipeline_interface_from</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">bindings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># obsolete</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">epts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">EntryPoint</span><span class="p">.</span><span class="n" style="color: #333;">from_dict</span><span class="p">(</span><span class="n" style="color: #333;">d</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;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"entryPoints"</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">pacbio_option_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"taskOptions"</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">d</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="LC221" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">bindings</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">epts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">'tags'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">task_options</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opts</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#bb082aada8e535a1155a8a39f97473524faf272a"><strong>pbcommand/services/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.models</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">JobExeError</span><span class="p">,</span> <span class="n" style="color: #333;">JobResult</span><span class="p">,</span> <span class="n" style="color: #333;">LogLevels</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="n" style="color: #333;">ServiceResourceTypes</span><span class="p">,</span> <span class="n" style="color: #333;">JobTypes</span><span class="p">,</span> <span class="n" style="color: #333;">JobStates</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"> <span class="n" style="color: #333;">ServiceJob</span><span class="p">,</span> <span class="n" style="color: #333;">ServiceEntryPoint</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"> <span class="n" style="color: #333;">ServiceJob</span><span class="p">,</span> <span class="n" style="color: #333;">ServiceEntryPoint</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"> <span class="n" style="color: #333;">add_smrtlink_server_args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># this module imports the models, so the model loading</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># must be called first to avoid cyclic-dependencies</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;">._service_access_layer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ServiceAccessLayer</span><span class="p">,</span> <span class="n" style="color: #333;">SmrtLinkAuthClient</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._service_access_layer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">ServiceAccessLayer</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">SmrtLinkAuthClient</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">get_smrtlink_client</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">get_smrtlink_client_from_args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># There's some crufty legacy naming. Using a cleaner model here</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">SmrtLinkClient</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ServiceAccessLayer</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#1a0981a4b2458240c866e6f023adda456c0f778c"><strong>pbcommand/services/_service_access_layer.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">@@ -205,23 +205,6 @@ def _transform_job_tasks(j):</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">JobTask</span><span class="p">.</span><span class="n" style="color: #333;">from_d</span><span class="p">(</span><span class="n" style="color: #333;">d</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;">j</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_import_dataset_by_type</span><span class="p">(</span><span class="n" style="color: #333;">dataset_type_or_id</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC209" 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;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">dataset_type_or_id</span><span class="p">,</span> <span class="n" style="color: #333;">DataSetFileType</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">ds_type_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataset_type_or_id</span><span class="p">.</span><span class="n" style="color: #333;">file_type_id</span></span>
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<pre style="margin: 0;">-<span id="LC212" 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="LC213" class="line" lang="python"> <span class="n" style="color: #333;">ds_type_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataset_type_or_id</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wrapper</span><span class="p">(</span><span class="n" style="color: #333;">total_url</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">avoid_duplicate_import</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="LC216" class="line" lang="python"> <span class="n" style="color: #333;">_d</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;">datasetType</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ds_type_id</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">avoidDuplicateImport</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">avoid_duplicate_import</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_process_rpost_with_transform</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">ServiceJob</span><span class="p">.</span><span class="n" style="color: #333;">from_d</span><span class="p">)(</span><span class="n" style="color: #333;">total_url</span><span class="p">,</span> <span class="n" style="color: #333;">_d</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">wrapper</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_job_by_id_or_raise</span><span class="p">(</span><span class="n" style="color: #333;">sal</span><span class="p">,</span> <span class="n" style="color: #333;">job_id</span><span class="p">,</span> <span class="n" style="color: #333;">error_klass</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">error_messge_extras</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="LC210" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sal</span><span class="p">.</span><span class="n" style="color: #333;">get_job_by_id</span><span class="p">(</span><span class="n" style="color: #333;">job_id</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="711" 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">@@ -711,25 +694,34 @@ class ServiceAccessLayer: # pragma: no cover</td>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_job_resource_type</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">JobTypes</span><span class="p">.</span><span class="n" style="color: #333;">MERGE_DS</span><span class="p">,</span> <span class="n" style="color: #333;">job_id</span><span class="p">,</span> <span class="n" style="color: #333;">ServiceResourceTypes</span><span class="p">.</span><span class="n" style="color: #333;">DATASTORE</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_import_dataset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dataset_type</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python"> <span class="n" style="color: #333;">avoid_duplicate_import</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="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_dataset</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="LC698" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"> <span class="n" style="color: #333;">avoid_duplicate_import</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="c1" style="color: #998; font-style: italic;"># This returns a job resource</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="python"> <span class="n" style="color: #333;">url</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;">_to_url</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"> <span class="s" style="color: #d14;">"{p}/{x}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">JobTypes</span><span class="p">.</span><span class="n" style="color: #333;">IMPORT_DS</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ServiceAccessLayer</span><span class="p">.</span><span class="n" style="color: #333;">ROOT_JOBS</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_import_dataset_by_type</span><span class="p">(</span><span class="n" style="color: #333;">dataset_type</span><span class="p">)(</span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">headers</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;">_get_headers</span><span class="p">(),</span> <span class="n" style="color: #333;">avoid_duplicate_import</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">avoid_duplicate_import</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> <span class="s" style="color: #d14;">"path"</span><span class="p">:</span> <span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python"> <span class="s" style="color: #d14;">"avoidDuplicateImport"</span><span class="p">:</span> <span class="n" style="color: #333;">avoid_duplicate_import</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_process_rpost_with_transform</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">ServiceJob</span><span class="p">.</span><span class="n" style="color: #333;">from_d</span><span class="p">)(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">headers</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;">_get_headers</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset<span class="idiff left">_by_type</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">dataset_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">path_to_xml</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">avoid_duplicate_import</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">job_or_error</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="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_import_dataset</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">dataset_type</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset</span><span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">path_to_xml</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">avoid_duplicate_import</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">job_or_error</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="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">import_dataset</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"> <span class="n" style="color: #333;">path_to_xml</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="n" style="color: #333;">avoid_duplicate_import</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">avoid_duplicate_import</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="python"> <span class="n" style="color: #333;">custom_err_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Import {<span class="idiff left">d} {p}"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</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">path_to_xml</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">dataset_type</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"> <span class="n" style="color: #333;">custom_err_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Import {<span class="idiff left">p}"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</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 right">path_to_xml</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="n" style="color: #333;">job_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_job_id_or_error</span><span class="p">(</span><span class="n" style="color: #333;">job_or_error</span><span class="p">,</span> <span class="n" style="color: #333;">custom_err_msg</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">custom_err_msg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_block_for_job_to_complete</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job_id</span><span class="p">,</span> <span class="n" style="color: #333;">sleep_time</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;">_sleep_time</span><span class="p">)</span></span>
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset_by_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dataset_type</span><span class="p">,</span> <span class="n" style="color: #333;">path_to_xml</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python"> <span class="n" style="color: #333;">avoid_duplicate_import</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="LC723" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">path_to_xml</span><span class="p">,</span> <span class="n" style="color: #333;">avoid_duplicate_import</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python"></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;">_run_import_and_block</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</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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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># func while be self.import_dataset_X</span></span>
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"> <span class="n" style="color: #333;">job_or_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="739" 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">@@ -739,28 +731,32 @@ class ServiceAccessLayer: # pragma: no cover</td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"> <span class="n" style="color: #333;">sleep_time</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;">_sleep_time</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_dataset_subread</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">FileTypes</span><span class="p">.</span><span class="n" style="color: #333;">DS_SUBREADS</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"DEPRECATED METHOD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset_subread</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_import_and_block</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset_subread</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">time_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_dataset_hdfsubread</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">FileTypes</span><span class="p">.</span><span class="n" style="color: #333;">DS_SUBREADS_H5</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"DEPRECATED METHOD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset_hdfsubread</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_import_and_block</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset_hdfsubread</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">time_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_dataset_reference</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">FileTypes</span><span class="p">.</span><span class="n" style="color: #333;">DS_REF</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"DEPRECATED METHOD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset_reference</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_import_and_block</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset_reference</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">time_out</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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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_dataset_barcode</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">FileTypes</span><span class="p">.</span><span class="n" style="color: #333;">DS_BARCODE</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"DEPRECATED METHOD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">import_dataset</span><span class="p">(</span><span class="n" style="color: #333;">path</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>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_import_dataset_barcode</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">time_out</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_import_and_block</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1542" 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">@@ -1542,3 +1538,11 @@ def get_smrtlink_client(host, port, user=None, password=None, sleep_time=5): #</td>
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SmrtLinkAuthClient</span><span class="p">(</span><span class="n" style="color: #333;">host</span><span class="p">,</span> <span class="n" style="color: #333;">user</span><span class="p">,</span> <span class="n" style="color: #333;">password</span><span class="p">,</span> <span class="n" style="color: #333;">sleep_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sleep_time</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1539" 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="LC1540" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ServiceAccessLayer</span><span class="p">(</span><span class="n" style="color: #333;">host</span><span class="p">,</span> <span class="n" style="color: #333;">port</span><span class="p">,</span> <span class="n" style="color: #333;">sleep_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sleep_time</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_smrtlink_client_from_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">get_smrtlink_client</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="python"> <span class="n" style="color: #333;">host</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">host</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="python"> <span class="n" style="color: #333;">port</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">port</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="python"> <span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">user</span><span class="p">,</span></span>
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1548
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<pre style="margin: 0;">+<span id="LC1548" class="line" lang="python"> <span class="n" style="color: #333;">password</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">password</span><span class="p">)</span></span></pre>
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<li id="871f89bee0833d15c661ca42e3f1644683e9e096">
<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#871f89bee0833d15c661ca42e3f1644683e9e096"><strong>pbcommand/services/job_poller.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">@@ -9,7 +9,9 @@ import time</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">requests.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HTTPError</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">urllib3.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ProtocolError</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">requests.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HTTPError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ConnectionError</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.cli.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_default_argparser_with_base_opts</span><span class="p">,</span> <span class="n" style="color: #333;">pacbio_args_runner</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.services._service_access_layer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">get_smrtlink_client</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">@@ -67,6 +69,14 @@ def poll_for_job_completion(job_id,</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC70" 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="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ConnectionError</span><span class="p">,</span> <span class="n" style="color: #333;">ProtocolError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Connection error: {e}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">e</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;">e</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Will retry in {d}s"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">retry_time</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="n" style="color: #333;">retry_time</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if a retryable error occurs, we increment the retry time</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># up to a max of 30 minutes</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">retry_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1800</span><span class="p">,</span> <span class="n" style="color: #333;">retry_time</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sleep_time</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC80" 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="LC81" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if request succeeded, reset the retry_time</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">auth_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#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">@@ -10,12 +10,12 @@ test_deps = [</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">'pylint'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">'pytest'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'pytest-cov'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'pytest-xdist'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'pytest-xdist<span class="idiff left right"> == 1.34.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pbcommand'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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;">'2.<span class="idiff left right">1.1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" 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;">'2.<span class="idiff left right">2.2</span>'</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;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Pacific Biosciences'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'devnet@pacificbiosciences.com'</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Library and Tools for interfacing with PacBio® data CLI tools'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#d1972d953870d92f76fda233025dabf694f05195"><strong>tests/test_models_legacy.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.models.legacy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Pipeline</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pbcommand.pb_io.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">load_pipeline_interface_from</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestLegacyModels</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,6 +61,6 @@ class TestLegacyModels:</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">json_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">".json"</span><span class="p">).</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC62" 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;">json_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;">json_out</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;">json_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">pipeline_json</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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">Pipeline</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">load_from_json</span></span><span class="p">(</span><span class="n" style="color: #333;">json_file</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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">load_pipeline_interface_from</span></span><span class="p">(</span><span class="n" style="color: #333;">json_file</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;">assert</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">pipeline_id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"cromwell.workflows.dev_diagnostic_subreads"</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">summary</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pbcommand/-/compare/8fca3229adf5cfc005c9373348f7b42529b96cd4...3e33ced73e5c5b53f57ac2c87faa0fa1278462a0#5939fca8460e7402d7b88587f2433eb2d8d6ed1a"><strong>tests/test_models_report.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">@@ -296,26 +296,30 @@ class TestReportModel:</td>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">EXPECTED_VALUES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="s" style="color: #d14;">"n_reads"</span><span class="p">:</span> <span class="mi" style="color: #099;">300</span><span class="p">,</span></span>
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="s" style="color: #d14;">"n_zmws"</span><span class="p">:</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="s" style="color: #d14;">"sample"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Person1,Person2"</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">NAMES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"n_reads"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Number of reads"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"n_zmws"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Number of ZMWs"</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="s" style="color: #d14;">"n_zmws"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Number of ZMWs"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="s" style="color: #d14;">"sample"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Sample"</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">chunks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">Report</span><span class="p">(</span><span class="s" style="color: #d14;">"pbcommand_test"</span><span class="p">,</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_reads"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span></span>
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308
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<pre style="margin: 0;"> <span id="LC310" 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;">"Number of reads"</span><span class="p">),</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_zmws"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Number of ZMWs"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_zmws"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Number of ZMWs"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sample"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Person1"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sample"</span><span class="p">)],</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">dataset_uuids</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"12345"</span><span class="p">]),</span></span>
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">Report</span><span class="p">(</span><span class="s" style="color: #d14;">"pbcommand_test"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">attributes</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_reads"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">250</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC317" 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;">"Number of reads"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_zmws"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Number of ZMWs"</span><span class="p">)]),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"n_zmws"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Number of ZMWs"</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">Attribute</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sample"</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Person2"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sample"</span><span class="p">)]),</span></span>
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316
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="p">]</span></span>
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317
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Report</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">chunks</span><span class="p">)</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">attributes</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"n_reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"n_zmws"</span><span class="p">]</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">attributes</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"n_reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"n_zmws"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"sample"</span></span><span class="p">]</span></span>
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319
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_uuids</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"12345"</span><span class="p">]</span></span>
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320
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">attr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">attributes</span><span class="p">:</span></span>
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321
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">attr</span><span class="p">.</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXPECTED_VALUES</span><span class="p">[</span><span class="n" style="color: #333;">attr</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span></span>
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