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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/3b215029f9fc75bbae630757fe23ea1d6058fc7c">3b215029</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-13T13:00:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cherry pick py3 test fixes from upstream
In preparation for eventually running the tests here
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/bda14bcc60e353066e95ea901d4c1adc07bf80dd">bda14bcc</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-13T13:58:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update copyright
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#7d50ce949dd83a42315e1f32258188ca8a9ffb91">
<span class="new-file">
+
debian/patches/fix_tests
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/toil/compare/84a960a4aab9a80e29e91358ecd7b3d3a56e8b8b...bda14bcc60e353066e95ea901d4c1adc07bf80dd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,6 +11,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-docker,</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-dill,</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-future,</span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-pytest-xdist,</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> cwltool,</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># documentation</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-urllib3,</span>
</pre>
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<br>
</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/toil/compare/84a960a4aab9a80e29e91358ecd7b3d3a56e8b8b...bda14bcc60e353066e95ea901d4c1adc07bf80dd#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,10 +5,65 @@ Files-Excluded: src/toil.egg-info/*</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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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">
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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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Copyright: Benedict Paten <benedict@soe.usc.edu></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> 2015-201<span class="idiff left right">6</span> Regents of the University of California</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> 2015<span class="idiff left right"> </span> UCSC Computational Genomics Lab</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 2015-201<span class="idiff left right">8</span> Regents of the University of California</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> 2015<span class="idiff left right">-2018</span> UCSC Computational Genomics Lab</span>
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<td class="diff-line-num old_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">
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">License: Apache-2.0</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Files: ./src/toil/test/cwl/cwlTest.py</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Copyright: 2015, Curoverse, Inc</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">License: Apache-2.0</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Files: ./src/toil/batchSystems/slurm.py</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Copyright: 2016, Duke Center for Genomic and Computational Biology</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License: Apache-2.0</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Files: ./src/toil/batchSystems/htcondor.py</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Copyright: 2018, HTCondor Team, Computer Sciences Department,</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">License: Apache-v2.0</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Files: ./docs/vendor/sphinxcontrib/fulltoc.py</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Copyright: 2012, New Dream Network, LLC (DreamHost)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">License: Apache-2.0</span>
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27
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Files: ./src/toil/wdl/wdl_parser.py</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Copyright: 2015, Broad Institute, Inc.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are met:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> * Redistributions of source code must retain the above copyright notice, this</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> list of conditions and the following disclaimer.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * Redistributions in binary form must reproduce the above copyright notice,</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> this list of conditions and the following disclaimer in the documentation</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> * Neither the name Broad Institute, Inc. nor the names of its</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> contributors may be used to endorse or promote products derived from</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> this software without specific prior written permission.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Files: ./src/toil/batchSystems/lsfHelper.py</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Copyright: 2013-2017 "Rory Kirchne" <rory.kirchner@gmail.com> and contributors</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">License: Expat</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Files: ./contrib/azure/LICENSE</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Copyright: 2015, Microsoft Azure</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">License: Expat</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Files: ./src/toil/batchSystems/lsf.py</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Copyright: 2013, Thomas Keane <tk2@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">License: Expat</span>
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12
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">Files: debian/*</span>
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13
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">Copyright: 2017 Steffen Moeller <moeller@debian.org></span>
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14
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">License: Apache-2.0</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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">@@ -28,3 +83,22 @@ License: Apache-2.0</td>
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28
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> .</span>
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29
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> On Debian systems, the complete text of the Apache version 2.0 license</span>
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30
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> can be found in "/usr/share/common-licenses/Apache-2.0".</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">License: Expat</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> of this software and associated documentation files (the "Software"), to deal</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> in the Software without restriction, including without limitation the rights</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> copies of the Software, and to permit persons to whom the Software is</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> furnished to do so, subject to the following conditions:</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> .</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> The above copyright notice and this permission notice shall be included in all</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> copies or substantial portions of the Software.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> .</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> SOFTWARE.</span></pre>
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<li id="7d50ce949dd83a42315e1f32258188ca8a9ffb91">
<a href="https://salsa.debian.org/med-team/toil/compare/84a960a4aab9a80e29e91358ecd7b3d3a56e8b8b...bda14bcc60e353066e95ea901d4c1adc07bf80dd#7d50ce949dd83a42315e1f32258188ca8a9ffb91"><strong>debian/patches/fix_tests</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: cherry pick py3 testing fixes from upstream</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/lib/docker.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/lib/docker.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20,7 +20,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> from docker.errors import APIError</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> from docker.errors import NotFound</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> from docker.errors import DockerException</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from docker.utils.types import LogConfig</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from docker.api.container import ContainerApiMixin</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> from toil.lib.retry import retry</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/test/jobStores/jobStoreTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/test/jobStores/jobStoreTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,11 +31,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import threading</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> import shutil</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> import time</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> import uuid</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from stubserver import FTPStubServer</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> from abc import abstractmethod, ABCMeta</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> from itertools import chain, islice, count</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> from threading import Thread</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -59,7 +59,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> from toil.job import Job, JobNode</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> from toil.jobStores.abstractJobStore import (NoSuchJobException,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> NoSuchFileException)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from toil.jobStores.googleJobStore import googleRetry</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> from toil.jobStores.fileJobStore import FileJobStore</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> from toil.test import (ToilTest,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> needs_aws,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -102,7 +101,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> @classmethod</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> @memoize</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> def __new__(cls, *args):</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return super(AbstractJobStoreTest.Test, cls).__new__(*args)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return super(AbstractJobStoreTest.Test, cls).__new__(cls)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> def _createConfig(self):</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> return Config()</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -403,18 +402,22 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> """Tests the sharing of files."""</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> jobstore1 = self.jobstore_initialized</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> jobstore2 = self.jobstore_resumed_noconfig</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bar = 'bar'</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.version_info >= (3, 0):</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bar = b'bar'</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> with jobstore1.writeSharedFileStream('foo') as f:</span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('bar')</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(bar)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> # ... read that file on worker, ...</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> with jobstore2.readSharedFileStream('foo') as f:</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals('bar', f.read())</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(bar, f.read())</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # ... and read it again on jobstore1.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> with jobstore1.readSharedFileStream('foo') as f:</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals('bar', f.read())</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(bar, f.read())</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> with jobstore1.writeSharedFileStream('nonEncrypted', isProtected=False) as f:</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('bar')</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(bar)</span></span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> self.assertUrl(jobstore1.getSharedPublicUrl('nonEncrypted'))</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> self.assertRaises(NoSuchFileException, jobstore1.getSharedPublicUrl, 'missing')</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -435,12 +438,19 @@</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> # Check file exists</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> self.assertTrue(jobstore2.fileExists(fileOne))</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> self.assertTrue(jobstore1.fileExists(fileOne))</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ one = 'one'</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ two = 'two'</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ three = 'three'</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.version_info >= (3, 0):</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ one = b'one'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ two = b'two'</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ three = b'three'</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> # ... write to the file on jobstore2, ...</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> with jobstore2.updateFileStream(fileOne) as f:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('one')</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(one)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # ... read the file as a stream on the jobstore1, ....</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> with jobstore1.readFileStream(fileOne) as f:</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), 'one')</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(), one)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> # ... and copy it to a temporary physical file on the jobstore1.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> fh, path = tempfile.mkstemp()</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -452,27 +462,27 @@</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> shutil.copyfile(tmpPath, path)</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> finally:</span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> os.unlink(tmpPath)</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(path, 'r+') as f:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), 'one')</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(path, 'rb+') as f:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(), one)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> # Write a different string to the local file ...</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> f.seek(0)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> f.truncate(0)</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('two')</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(two)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> # ... and create a second file from the local file.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> fileTwo = jobstore1.writeFile(path, jobOnJobStore1.jobStoreID)</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> with jobstore2.readFileStream(fileTwo) as f:</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), 'two')</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(), two)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> # Now update the first file from the local file ...</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> jobstore1.updateFile(fileOne, path)</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> with jobstore2.readFileStream(fileOne) as f:</span>
</pre>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), 'two')</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(), two)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> finally:</span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> os.unlink(path)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> # Create a third file to test the last remaining method.</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> with jobstore2.writeFileStream(jobOnJobStore1.jobStoreID) as (f, fileThree):</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('three')</span></span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(three)</span></span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> with jobstore1.readFileStream(fileThree) as f:</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), 'three')</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(), three)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> # Delete a file explicitly but leave files for the implicit deletion through the parent</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> jobstore2.deleteFile(fileOne)</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -510,22 +520,28 @@</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> # Collects stats and logging messages.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> stats = set()</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ one = 'one'</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ two = 'two'</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ three = 'three'</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.version_info >= (3, 0):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ one = b'one'</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ two = b'two'</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ three = b'three' </span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> # No stats or logging added yet. Expect nothing.</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> self.assertEquals(0, jobstore1.readStatsAndLogging(callback))</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> self.assertEquals(set(), stats)</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> # Test writing and reading.</span>
</pre>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jobstore2.writeStatsAndLogging('1')</span></span>
</pre>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jobstore2.writeStatsAndLogging(one)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> self.assertEquals(1, jobstore1.readStatsAndLogging(callback))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals({'1'}, stats)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals({one}, stats)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> self.assertEquals(0, jobstore1.readStatsAndLogging(callback)) # readStatsAndLogging purges saved stats etc</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jobstore2.writeStatsAndLogging('1')</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- jobstore2.writeStatsAndLogging('2')</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jobstore2.writeStatsAndLogging(one)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ jobstore2.writeStatsAndLogging(two)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> stats = set()</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> self.assertEquals(2, jobstore1.readStatsAndLogging(callback))</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals({'1', '2'}, stats)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals({one, two}, stats)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> largeLogEntry = os.urandom(self._largeLogEntrySize())</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> stats = set()</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -634,7 +650,7 @@</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> @classmethod</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> def makeImportExportTests(cls):</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> </span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- testClasses = [FileJobStoreTest, AWSJobStoreTest, AzureJobStoreTest, GoogleJobStoreTest]</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ testClasses = [FileJobStoreTest, AWSJobStoreTest, AzureJobStoreTest]</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> activeTestClassesByName = {testCls.__name__: testCls</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> for testCls in testClasses</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -714,7 +730,13 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> assignedPort = http.server_address[1]</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> url = 'http://localhost:%d' % assignedPort</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> with self.jobstore_initialized.readFileStream(self.jobstore_initialized.importFile(url)) as readable:</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(readable.read(), StubHttpRequestHandler.fileContents)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f1 = readable.read()</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f2 = StubHttpRequestHandler.fileContents</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if isinstance(f1, bytes) and not isinstance(f2, bytes):</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f1 = f1.decode()</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if isinstance(f2, bytes) and not isinstance(f1, bytes):</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f1 = f1.encode()</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(f1, f2)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> finally:</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> http.shutdown()</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> httpThread.join()</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -723,6 +745,7 @@</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> def testImportFtpFile(self):</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> '''Test importing a file over FTP'''</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from stubserver import FTPStubServer</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> file = {'name':'foo', 'content':'foo bar baz qux'}</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> ftp = FTPStubServer(0)</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> ftp.run()</span>
</pre>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -785,7 +808,7 @@</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> checksumThread = Thread(target=checksumThreadFn)</span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> checksumThread.start()</span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> try:</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(random_device) as readable:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(random_device, 'rb') as readable:</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> with self.jobstore_initialized.writeFileStream(job.jobStoreID) as (writable, fileId):</span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> for i in range(int(partSize * partsPerFile / bufSize)):</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> buf = readable.read(bufSize)</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -813,8 +836,8 @@</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> checksum = hashlib.md5()</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> fh, path = tempfile.mkstemp()</span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with os.fdopen(fh, 'r+') as writable:</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(random_device) as readable:</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with os.fdopen(fh, 'wb+') as writable:</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(random_device, 'rb') as readable:</span></span>
</pre>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> for i in range(int(partSize * partsPerFile / bufSize)):</span>
</pre>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> buf = readable.read(bufSize)</span>
</pre>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> writable.write(buf)</span>
</pre>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -842,11 +865,11 @@</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> job = self.jobstore_initialized.create(self.arbitraryJob)</span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> nullFile = self.jobstore_initialized.writeFile('/dev/null', job.jobStoreID)</span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> with self.jobstore_initialized.readFileStream(nullFile) as f:</span>
</pre>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), "")</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert not f.read()</span></span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> with self.jobstore_initialized.writeFileStream(job.jobStoreID) as (f, nullStream):</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> pass</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> with self.jobstore_initialized.readFileStream(nullStream) as f:</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(), "")</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert not f.read()</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> self.jobstore_initialized.delete(job.jobStoreID)</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> </span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> @slow</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -856,7 +879,7 @@</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> dirPath = self._createTempDir()</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> filePath = os.path.join(dirPath, 'large')</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> hashIn = hashlib.md5()</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(filePath, 'w') as f:</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(filePath, 'wb') as f:</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> for i in range(0, 10):</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> buf = os.urandom(self._partSize())</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> f.write(buf)</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -874,7 +897,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> # Reread the file to confirm success.</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> hashOut = hashlib.md5()</span>
</pre>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(filePath, 'r') as f:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(filePath, 'rb') as f:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> while True:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> buf = f.read(self._partSize())</span>
</pre>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> if not buf:</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -962,11 +985,15 @@</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> # will get blocked on the write. Technically anything</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> # greater than the pipe buffer size plus the libc</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> # buffer size (64K + 4K(?)) should trigger this bug,</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # but this gives us a lot of extra room just to be</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # sure.</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write('a' * 300000)</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # but this gives us a lot of extra room just to be sure.</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # python 3 requires self.fileContents to be a bytestring</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ a = 'a'</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.version_info >= (3, 0):</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ a = b'a'</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f.write(a * 300000)</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> with self.jobstore_initialized.readFileStream(fileID) as f:</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(f.read(1), "a")</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEquals(f.read(1), a)</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> # If it times out here, there's a deadlock</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> @abstractmethod</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1091,14 +1118,14 @@</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> return url</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> else:</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> content = os.urandom(size)</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(localFilePath, 'w') as writable:</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(localFilePath, 'wb') as writable:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> writable.write(content)</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> return url, hashlib.md5(content).hexdigest()</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> </span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> def _hashTestFile(self, url):</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> localFilePath = FileJobStore._extractPathFromUrl(urlparse.urlparse(url))</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open(localFilePath, 'r') as f:</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with open(localFilePath, 'rb') as f:</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> return hashlib.md5(f.read()).hexdigest()</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> </span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> def _createExternalStore(self):</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1119,54 +1146,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> os.unlink(path)</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> </span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@needs_google</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class GoogleJobStoreTest(AbstractJobStoreTest.Test):</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- projectID = os.getenv('TOIL_GOOGLE_PROJECTID')</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- headers = {"x-goog-project-id": projectID}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _createJobStore(self):</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from toil.jobStores.googleJobStore import GoogleJobStore</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return GoogleJobStore(GoogleJobStoreTest.projectID + ":" + self.namePrefix)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _corruptJobStore(self):</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # The Google job store has only one resource, the bucket, so we can't corrupt it without</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # fully deleting it.</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pass</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _prepareTestFile(self, bucket, size=None):</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from toil.jobStores.googleJobStore import GoogleJobStore</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fileName = 'testfile_%s' % uuid.uuid4()</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url = 'gs://%s/%s' % (bucket.name, fileName)</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if size is None:</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return url</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- with open('/dev/urandom', 'r') as readable:</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- contents = readable.read(size)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GoogleJobStore._writeToUrl(StringIO(contents), urlparse.urlparse(url))</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return url, hashlib.md5(contents).hexdigest()</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _hashTestFile(self, url):</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from toil.jobStores.googleJobStore import GoogleJobStore</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- contents = GoogleJobStore._getBlobFromURL(urlparse.urlparse(url)).download_as_string()</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return hashlib.md5(contents).hexdigest()</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @googleRetry</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _createExternalStore(self):</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from google.cloud import storage</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bucketName = ("import-export-test-" + str(uuid.uuid4()))</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storageClient = storage.Client()</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return storageClient.create_bucket(bucketName)</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @googleRetry</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def _cleanUpExternalStore(self, bucket):</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # this is copied from googleJobStore.destroy</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try:</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bucket.delete(force=True)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # throws ValueError if bucket has more than 256 objects. Then we must delete manually</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ValueError:</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bucket.delete_blobs(bucket.list_blobs)</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bucket.delete()</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> @needs_aws</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> class AWSJobStoreTest(AbstractJobStoreTest.Test):</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> </span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1448,6 +1427,9 @@</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> self.send_header("Content-type", "text/plain")</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> self.send_header("Content-length", len(self.fileContents))</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> self.end_headers()</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # python 3 requires self.fileContents to be a bytestring</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.version_info >= (3, 0):</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.fileContents = self.fileContents.encode('utf-8')</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> self.wfile.write(self.fileContents)</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> </span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> </span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/test/src/fileStoreTest.py</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/test/src/fileStoreTest.py</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1338,10 +1338,13 @@</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> """</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> for name, kind, clazz, value in inspect.classify_class_attrs(cls):</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> if kind == 'static method':</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- method = value.__func__</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- args = inspect.getargspec(method).args</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if args and args[0] == 'job':</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- globals()[name] = method</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ method = value</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ args = inspect.getargspec(method).args</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if args and args[0] == 'job':</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ globals()[name] = method</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except TypeError:</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> </span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> _exportStaticMethodAsGlobalFunctions(hidden.AbstractFileStoreTest)</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/test/src/jobFileStoreTest.py</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/test/src/jobFileStoreTest.py</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,13 +134,24 @@</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> with open(tempFile, 'w') as fH:</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> fH.write(testString)</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> #Write a local copy of the file using the local file</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outputFileStoreIds.append(job.fileStore.writeGlobalFile(tempFile))</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fileStoreID = job.fileStore.writeGlobalFile(tempFile)</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Make sure it returned a valid and correct FileID with the right size</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert isinstance(fileStoreID, FileID)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert fileStoreID.size == len(testString.encode('utf-8'))</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFileStoreIds.append(fileStoreID)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> else:</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> #Use the writeGlobalFileStream method to write the file</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> with job.fileStore.writeGlobalFileStream() as (fH, fileStoreID):</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> fH.write(testString.encode('utf-8'))</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> outputFileStoreIds.append(fileStoreID)</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #Make sure it returned a valid and correct FileID with the right size</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert isinstance(fileStoreID, FileID)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert fileStoreID.size == len(testString.encode('utf-8'))</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> if chainLength > 0:</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> #Make a child that will read these files and check it gets the same results</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> job.addChildJobFn(fileTestJob, outputFileStoreIds, testStrings, chainLength-1)</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/compare/84a960a4aab9a80e29e91358ecd7b3d3a56e8b8b...bda14bcc60e353066e95ea901d4c1adc07bf80dd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -5,3 +5,4 @@ no_galaxy_lib</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">debianize_docs</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">spelling</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">adjust_to_newer_cwltool</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">fix_tests</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/compare/84a960a4aab9a80e29e91358ecd7b3d3a56e8b8b...bda14bcc60e353066e95ea901d4c1adc07bf80dd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -19,8 +19,15 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> find $(CURDIR)/debian -name cwltoil -delete</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"># If you need to rebuild the Sphinx documentation</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># more py3 test fixes need to be cherry-picked from upstream</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># PYBUILD_SYSTEM=custom \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># PYBUILD_TEST_ARGS='TOIL_SKIP_DOCKER=True {interpreter} -m pytest -vv \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># -W ignore \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># -k "not test_bioconda and not test_run_conformance and not testImportFtpFile" -n auto\</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> {dir}/src/toil/test' dh_auto_test --buildsystem pybuild</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> # If you need to rebuild the Sphinx documentation</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"># Add spinxdoc to the dh --with line</span>
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<td class="diff-line-num old_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">#override_dh_auto_build:</span>
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<td class="diff-line-num old_line" data-linenumber="26" 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">
26
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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" class="line" lang="plaintext"># dh_auto_build</span>
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