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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-datacache">Debian Med / python-datacache</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e">9f1f5c72</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-18T18:46:02+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.5</pre>
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<h4>27 changed files:</h4>
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.gitignore
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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.travis.yml
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LICENSE
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<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
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Makefile
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<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
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PKG-INFO
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#c1f93a35960719be64589bf34fed936dcd8f6aa4">
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datacache.egg-info/PKG-INFO
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datacache.egg-info/SOURCES.txt
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datacache.egg-info/dependency_links.txt
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<a href="#c330ce10f77297c6dd6f299305adc9bb5ab9fc95">
requirements.txt
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datacache.egg-info/requires.txt
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datacache.egg-info/top_level.txt
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<a href="#34fecaefcf0dd8ab14163a8ef21d189041f8db72">
datacache/__init__.py
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<li class="file-stats">
<a href="#cecc86da25398cd6e507203d2ee255369bcfa596">
datacache/cache.py
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<li class="file-stats">
<a href="#f95155d7d411ecf9ea99c8c6406b476695a3494c">
datacache/common.py
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<li class="file-stats">
<a href="#e0a520c5974a873a14158fd7e985726dbf7c65eb">
datacache/database.py
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<a href="#0e69383aa089378fe0718955ce01c3e4093517f4">
datacache/database_helpers.py
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<a href="#7eea9ad08e1271d658a960a87df2c6ea578cd901">
datacache/database_table.py
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<a href="#5eede143f6d8eba797eec90bf587d381552de1ac">
datacache/database_types.py
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<a href="#c494d917b58e9a110cc0e99d7fc15592cb27daac">
datacache/download.py
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datacache/fasta.py
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setup.cfg
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setup.py
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test/__init__.py
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<a href="#59ce3c49e5c5806b46ba8e446b2b0fb3bc583d5e">
test/test_cache_object.py
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<a href="#570f45465ad5df111e6ed14b56f7e04e2e0958b8">
test/test_download.py
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test/test_fasta_db.py
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<li class="file-stats">
<a href="#5004304f2e154c337a31a6fbcb908033422860e0">
test/test_fasta_dict.py
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong>
deleted
</a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Byte-compiled / optimized / DLL files</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">__pycache__/</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">*.py[cod]</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"># C extensions</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">*.so</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># Distribution / packaging</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">.Python</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">env/</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">bin/</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">build/</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">develop-eggs/</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">dist/</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">eggs/</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">lib/</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">lib64/</span>
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<td class="old_line diff-line-num old" data-linenumber="18" 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="LC18" class="line" lang="plaintext">parts/</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">sdist/</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">var/</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">*.egg-info/</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">.installed.cfg</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">*.egg</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># Installer logs</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">pip-log.txt</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">pip-delete-this-directory.txt</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"># Unit test / coverage reports</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">htmlcov/</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">.tox/</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">.coverage</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">.cache</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">nosetests.xml</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">coverage.xml</span>
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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"># Translations</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">*.mo</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"># Mr Developer</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">.mr.developer.cfg</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">.project</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">.pydevproject</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"># Rope</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">.ropeproject</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"># Django stuff:</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">*.log</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">*.pot</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"># Sphinx documentation</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">docs/_build/</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># What's need to do run tests via Travis https://travis-ci.org/</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - "2.6"</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.7"</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to install dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">."</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-r</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">requirements.txt"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to run tests</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">cd test && nose2</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Apache License</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Version 2.0, January 2004</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> http://www.apache.org/licenses/</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> 1. Definitions.</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> "License" shall mean the terms and conditions for use, reproduction,</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> and distribution as defined by Sections 1 through 9 of this document.</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> "Licensor" shall mean the copyright owner or entity authorized by</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> the copyright owner that is granting the License.</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> "Legal Entity" shall mean the union of the acting entity and all</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> other entities that control, are controlled by, or are under common</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> control with that entity. For the purposes of this definition,</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> "control" means (i) the power, direct or indirect, to cause the</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> direction or management of such entity, whether by contract or</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> otherwise, or (ii) ownership of fifty percent (50%) or more of the</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> outstanding shares, or (iii) beneficial ownership of such entity.</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> "You" (or "Your") shall mean an individual or Legal Entity</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> exercising permissions granted by this License.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> "Source" form shall mean the preferred form for making modifications,</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> including but not limited to software source code, documentation</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> source, and configuration files.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> "Object" form shall mean any form resulting from mechanical</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> transformation or translation of a Source form, including but</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> not limited to compiled object code, generated documentation,</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> and conversions to other media types.</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> "Work" shall mean the work of authorship, whether in Source or</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> Object form, made available under the License, as indicated by a</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> copyright notice that is included in or attached to the work</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> (an example is provided in the Appendix below).</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> "Derivative Works" shall mean any work, whether in Source or Object</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> form, that is based on (or derived from) the Work and for which the</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> editorial revisions, annotations, elaborations, or other modifications</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> represent, as a whole, an original work of authorship. For the purposes</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> of this License, Derivative Works shall not include works that remain</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> separable from, or merely link (or bind by name) to the interfaces of,</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> the Work and Derivative Works thereof.</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> "Contribution" shall mean any work of authorship, including</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> the original version of the Work and any modifications or additions</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> to that Work or Derivative Works thereof, that is intentionally</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> submitted to Licensor for inclusion in the Work by the copyright owner</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> or by an individual or Legal Entity authorized to submit on behalf of</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> the copyright owner. For the purposes of this definition, "submitted"</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> means any form of electronic, verbal, or written communication sent</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> to the Licensor or its representatives, including but not limited to</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> communication on electronic mailing lists, source code control systems,</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> and issue tracking systems that are managed by, or on behalf of, the</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> Licensor for the purpose of discussing and improving the Work, but</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> excluding communication that is conspicuously marked or otherwise</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> designated in writing by the copyright owner as "Not a Contribution."</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> "Contributor" shall mean Licensor and any individual or Legal Entity</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> on behalf of whom a Contribution has been received by Licensor and</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> subsequently incorporated within the Work.</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> 2. Grant of Copyright License. Subject to the terms and conditions of</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> this License, each Contributor hereby grants to You a perpetual,</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> worldwide, non-exclusive, no-charge, royalty-free, irrevocable</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> copyright license to reproduce, prepare Derivative Works of,</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> publicly display, publicly perform, sublicense, and distribute the</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> Work and such Derivative Works in Source or Object form.</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> 3. Grant of Patent License. Subject to the terms and conditions of</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> this License, each Contributor hereby grants to You a perpetual,</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> worldwide, non-exclusive, no-charge, royalty-free, irrevocable</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> (except as stated in this section) patent license to make, have made,</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> use, offer to sell, sell, import, and otherwise transfer the Work,</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> where such license applies only to those patent claims licensable</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> by such Contributor that are necessarily infringed by their</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> Contribution(s) alone or by combination of their Contribution(s)</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> with the Work to which such Contribution(s) was submitted. If You</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> institute patent litigation against any entity (including a</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> cross-claim or counterclaim in a lawsuit) alleging that the Work</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> or a Contribution incorporated within the Work constitutes direct</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> or contributory patent infringement, then any patent licenses</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> granted to You under this License for that Work shall terminate</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> as of the date such litigation is filed.</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"> 4. Redistribution. You may reproduce and distribute copies of the</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> Work or Derivative Works thereof in any medium, with or without</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> modifications, and in Source or Object form, provided that You</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> meet the following conditions:</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> (a) You must give any other recipients of the Work or</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> Derivative Works a copy of this License; and</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"> (b) You must cause any modified files to carry prominent notices</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"> stating that You changed the files; and</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> (c) You must retain, in the Source form of any Derivative Works</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> that You distribute, all copyright, patent, trademark, and</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> attribution notices from the Source form of the Work,</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> excluding those notices that do not pertain to any part of</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> the Derivative Works; and</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> (d) If the Work includes a "NOTICE" text file as part of its</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> distribution, then any Derivative Works that You distribute must</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> include a readable copy of the attribution notices contained</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> within such NOTICE file, excluding those notices that do not</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> pertain to any part of the Derivative Works, in at least one</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> of the following places: within a NOTICE text file distributed</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> as part of the Derivative Works; within the Source form or</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> documentation, if provided along with the Derivative Works; or,</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> within a display generated by the Derivative Works, if and</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"> wherever such third-party notices normally appear. The contents</span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> of the NOTICE file are for informational purposes only and</span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"> do not modify the License. You may add Your own attribution</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> notices within Derivative Works that You distribute, alongside</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> or as an addendum to the NOTICE text from the Work, provided</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> that such additional attribution notices cannot be construed</span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> as modifying the License.</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> You may add Your own copyright statement to Your modifications and</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext"> may provide additional or different license terms and conditions</span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext"> for use, reproduction, or distribution of Your modifications, or</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"> for any such Derivative Works as a whole, provided Your use,</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"> reproduction, and distribution of the Work otherwise complies with</span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> the conditions stated in this License.</span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> 5. Submission of Contributions. Unless You explicitly state otherwise,</span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"> any Contribution intentionally submitted for inclusion in the Work</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> by You to the Licensor shall be under the terms and conditions of</span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> this License, without any additional terms or conditions.</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> Notwithstanding the above, nothing herein shall supersede or modify</span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> the terms of any separate license agreement you may have executed</span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> with Licensor regarding such Contributions.</span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> 6. Trademarks. This License does not grant permission to use the trade</span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> names, trademarks, service marks, or product names of the Licensor,</span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> except as required for reasonable and customary use in describing the</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> origin of the Work and reproducing the content of the NOTICE file.</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"> 7. Disclaimer of Warranty. Unless required by applicable law or</span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"> agreed to in writing, Licensor provides the Work (and each</span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"> Contributor provides its Contributions) on an "AS IS" BASIS,</span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or</span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"> implied, including, without limitation, any warranties or conditions</span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A</span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"> PARTICULAR PURPOSE. You are solely responsible for determining the</span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"> appropriateness of using or redistributing the Work and assume any</span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> risks associated with Your exercise of permissions under this License.</span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> 8. Limitation of Liability. In no event and under no legal theory,</span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"> whether in tort (including negligence), contract, or otherwise,</span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> unless required by applicable law (such as deliberate and grossly</span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"> negligent acts) or agreed to in writing, shall any Contributor be</span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"> liable to You for damages, including any direct, indirect, special,</span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> incidental, or consequential damages of any character arising as a</span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> result of this License or out of the use or inability to use the</span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> Work (including but not limited to damages for loss of goodwill,</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> work stoppage, computer failure or malfunction, or any and all</span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"> other commercial damages or losses), even if such Contributor</span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> has been advised of the possibility of such damages.</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> 9. Accepting Warranty or Additional Liability. While redistributing</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"> the Work or Derivative Works thereof, You may choose to offer,</span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> and charge a fee for, acceptance of support, warranty, indemnity,</span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> or other liability obligations and/or rights consistent with this</span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext"> License. However, in accepting such obligations, You may act only</span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> on Your own behalf and on Your sole responsibility, not on behalf</span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext"> of any other Contributor, and only if You agree to indemnify,</span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext"> defend, and hold each Contributor harmless for any liability</span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext"> incurred by, or claims asserted against, such Contributor by reason</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"> of your accepting any such warranty or additional liability.</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext"> END OF TERMS AND CONDITIONS</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> APPENDIX: How to apply the Apache License to your work.</span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> To apply the Apache License to your work, attach the following</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> boilerplate notice, with the fields enclosed by brackets "{}"</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> replaced with your own identifying information. (Don't include</span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> the brackets!) The text should be enclosed in the appropriate</span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> comment syntax for the file format. We also recommend that a</span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> file or class name and description of purpose be included on the</span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"> same "printed page" as the copyright notice for easier</span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"> identification within third-party archives.</span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"> Copyright {yyyy} {name of copyright owner}</span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> Licensed under the Apache License, Version 2.0 (the "License");</span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"> you may not use this file except in compliance with the License.</span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> You may obtain a copy of the License at</span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"> http://www.apache.org/licenses/LICENSE-2.0</span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext"> Unless required by applicable law or agreed to in writing, software</span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"> distributed under the License is distributed on an "AS IS" BASIS,</span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext"> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext"> See the License for the specific language governing permissions and</span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> limitations under the License.</span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Compatibility for us old-timers.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Note: This makefile include remake-style target comments.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># These comments before the targets start with #:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># remake --tasks to shows the targets and the comments</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">PHONY</span><span class="o" style="font-weight: 600;">=</span>check clean dist distclean <span class="nb" style="color: #0086b3;">test</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">GIT2CL</span> <span class="o" style="font-weight: 600;">?=</span> git2cl</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">PYTHON</span> <span class="o" style="font-weight: 600;">?=</span> python</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">PYTHON3</span> <span class="o" style="font-weight: 600;">?=</span> python3</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: the default target - same as running "check"</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">check</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="nl">check</span><span class="o" style="font-weight: 600;">:</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd test</span> <span class="o" style="font-weight: 600;">&&</span> nose2</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Clean up temporary files</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> ./setup.py <span class="nv" style="color: #008080;">$@</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Create source (tarball) and binary (egg) distribution</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"><span class="nl">dist</span><span class="o" style="font-weight: 600;">:</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> ./setup.py sdist bdist</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Create source tarball</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"><span class="nl">sdist</span><span class="o" style="font-weight: 600;">:</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> ./setup.py sdist</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Create binary egg distribution</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"><span class="nl">bdist_egg</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> ./setup.py bdist_egg</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># It is too much work to figure out how to add a new command to distutils</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># to do the following. I'm sure distutils will someday get there.</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"><span class="nv" style="color: #008080;">DISTCLEAN_FILES</span> <span class="o" style="font-weight: 600;">=</span> build dist <span class="k" style="font-weight: 600;">*</span>.egg-info <span class="k" style="font-weight: 600;">*</span>.pyc <span class="k" style="font-weight: 600;">*</span>.so py<span class="k" style="font-weight: 600;">*</span>.py</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Remove ALL dervied files</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"><span class="nl">distclean</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="p">-</span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-fr</span> <span class="nv" style="color: #008080;">$(DISTCLEAN_FILES)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Install package locally</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> ./setup.py <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Same as 'check' target</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">check</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="make"><span class="nl">rmChangeLog</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm </span>ChangeLog <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#: Create a ChangeLog from git via git log and git2cl</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="make"><span class="nl">ChangeLog</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">rmChangeLog</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="make"> git log <span class="nt" style="color: #000080;">--pretty</span> <span class="nt" style="color: #000080;">--numstat</span> <span class="nt" style="color: #000080;">--summary</span> | <span class="nv" style="color: #008080;">$(GIT2CL)</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PHONY)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Name: datacache</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.1.5</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Summary: Helpers for transparently downloading datasets</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/openvax/datacache</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Author: Alex Rubinsteyn</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Author-email: alex.rubinsteyn@mssm.edu</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: http://www.apache.org/licenses/LICENSE-2.0.html</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Description: DataCache</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> =========</span>
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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"> Helpers for transparently downloading datasets</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> API</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"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> - **fetch_file**\ (download_url, filename = *None*, decompress =</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> *False*, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> - **fetch_and_transform**\ (transformed_filename, transformer, loader,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> source_filename, source_url, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> - **fetch_fasta_dict**\ (download_url, filename = *None*, subdir =</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> *None*)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> - **fetch_fasta_db**\ (table_name, download_url, fasta_filename =</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> *None*, key_column = *‘id’*, value_column = *‘seq’*, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> - **fetch_csv_db**\ (table_name, download_url, csv_filename = *None*,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> subdir = *None*, \**pandas_kwargs)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">datacache</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://travis-ci.org/openvax/datacache"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://travis-ci.org/openvax/datacache.svg?branch=master"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Build Status"</span> <span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://coveralls.io/github/openvax/datacache?branch=master"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://pypi.python.org/pypi/datacache/"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/pypi/v/datacache.svg?maxAge=1000"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"PyPI"</span> <span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">DataCache</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=========</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">Helpers for transparently downloading datasets</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,4 +23,3 @@ Helpers for transparently downloading datasets</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"> key_column = <span class="ge" style="font-style: italic;">*'id'*</span>, value_column = <span class="ge" style="font-style: italic;">*'seq'*</span>, subdir = <span class="ge" style="font-style: italic;">*None*</span>)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">*</span> <span class="gs" style="font-weight: 600;">**fetch_csv_db**</span>(table_name, download_url, csv_filename = <span class="ge" style="font-style: italic;">*None*</span>, subdir = <span class="ge" style="font-style: italic;">*None*</span>,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"> <span class="se" style="color: #d14;">\*\*</span>pandas_kwargs)</span></pre>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#c1f93a35960719be64589bf34fed936dcd8f6aa4"><strong>datacache.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Name: datacache</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.1.5</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Summary: Helpers for transparently downloading datasets</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/openvax/datacache</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Author: Alex Rubinsteyn</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Author-email: alex.rubinsteyn@mssm.edu</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: http://www.apache.org/licenses/LICENSE-2.0.html</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Description: DataCache</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> =========</span>
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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"> Helpers for transparently downloading datasets</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> API</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"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> - **fetch_file**\ (download_url, filename = *None*, decompress =</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> *False*, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> - **fetch_and_transform**\ (transformed_filename, transformer, loader,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> source_filename, source_url, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> - **fetch_fasta_dict**\ (download_url, filename = *None*, subdir =</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> *None*)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> - **fetch_fasta_db**\ (table_name, download_url, fasta_filename =</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> *None*, key_column = *‘id’*, value_column = *‘seq’*, subdir = *None*)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> - **fetch_csv_db**\ (table_name, download_url, csv_filename = *None*,</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> subdir = *None*, \**pandas_kwargs)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> </span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Classifier: Development Status :: 3 - Alpha</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Classifier: Environment :: Console</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Classifier: Operating System :: OS Independent</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Classifier: Intended Audience :: Science/Research</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Classifier: License :: OSI Approved :: Apache Software License</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span></pre>
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<li id="91312de6ffced5e9e3dd40c6c562e66a486e69ac">
<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#91312de6ffced5e9e3dd40c6c562e66a486e69ac"><strong>datacache.egg-info/SOURCES.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README.md</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">setup.py</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">datacache/__init__.py</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">datacache/cache.py</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">datacache/common.py</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">datacache/database.py</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">datacache/database_helpers.py</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">datacache/database_table.py</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">datacache/database_types.py</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">datacache/download.py</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">datacache.egg-info/PKG-INFO</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">datacache.egg-info/SOURCES.txt</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">datacache.egg-info/dependency_links.txt</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">datacache.egg-info/requires.txt</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">datacache.egg-info/top_level.txt</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">test/test_cache_object.py</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">test/test_database_objects.py</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">test/test_database_types.py</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">test/test_db_from_dataframes.py</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">test/test_download.py</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">test/test_fasta_dict.py</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">test/test_names.py</span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#77fda5448c58c6d9512b23dfe2fd21adac3daa86"><strong>datacache.egg-info/dependency_links.txt</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pandas>=0.15.2</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">appdirs>=1.4.0</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/progressbar" rel="nofollow noreferrer noopener" target="_blank">progressbar</a>>=2.2</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biopython" rel="nofollow noreferrer noopener" target="_blank">biopython</a>>=1.65</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">progressbar33>=2.4</span>
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5
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">requests>=2.5.1</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/typechecks" rel="nofollow noreferrer noopener" target="_blank">typechecks</a>>=0.0.<span class="idiff left right">0</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/nose" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff left">nose</span></a><span class="idiff right">>=1.3.3</span></span></pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">typechecks>=0.0.<span class="idiff left right">2</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">mock</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">datacache</span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#34fecaefcf0dd8ab14163a8ef21d189041f8db72"><strong>datacache/__init__.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,12 +12,13 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.download</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_and_transform</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_csv_dataframe</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.fasta</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_fasta_dict</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.database_helpers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">db_from_dataframe</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">db_from_dataframes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">fetch_fasta_db</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">db_from_dataframes_with_absolute_path</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">fetch_csv_db</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">connect_if_correct_version</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="p">)</span></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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">@@ -28,4 +29,23 @@ from .common import (</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">clear_cache</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">build_local_filename</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.cache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Cache</span></span></pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.cache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Cache</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.1.5'</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">'fetch_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'fetch_and_transform'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'fetch_csv_dataframe'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'db_from_dataframe'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'db_from_dataframes'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'db_from_dataframes_with_absolute_path'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'fetch_csv_db'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'connect_if_correct_version'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">'ensure_dir'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">'get_data_dir'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'build_path'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">'clear_cache'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'build_local_filename'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'Cache'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="p">]</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#cecc86da25398cd6e507203d2ee255369bcfa596"><strong>datacache/cache.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,8 @@</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">exists</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">remove</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,13 +66,19 @@ class Cache(object):</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> exists.</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">download</span><span class="p">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">url</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decompress</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decompress</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> Return the local path to the downloaded copy of a given URL.</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> Don't download the file again if it's already present,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +96,9 @@ class Cache(object):</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decompress</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">force</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">force</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">use_wget_if_available</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_local_paths</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">path</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,5 +134,5 @@ class Cache(object):</td>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">db_filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_filename</span><span class="p">,</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">key_column_name</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">key_column_name</span><span class="p">,</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">primary_key</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">key_column_name</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#f95155d7d411ecf9ea99c8c6406b476695a3494c"><strong>datacache/common.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,7 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hashlib</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">makedirs</span><span class="p">,</span> <span class="n" style="color: #333;">environ</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,11 +27,13 @@ def ensure_dir(path):</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_data_dir</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">envkey</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">envkey</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">envkey</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">environ</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="n" style="color: #333;">envkey</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subdir</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"datacache"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">appdirs</span><span class="p">.</span><span class="n" style="color: #333;">user_cache_dir</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">envkey</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">environ</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">envkey</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">envdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="n" style="color: #333;">envkey</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subdir</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">envdir</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">envdir</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">appdirs</span><span class="p">.</span><span class="n" style="color: #333;">user_cache_dir</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subdir</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"datacache"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">data_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_data_dir</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#e0a520c5974a873a14158fd7e985726dbf7c65eb"><strong>datacache/database.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">.</span> Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span> Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,11 +12,16 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sqlite3</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typechecks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">require_integer</span><span class="p">,</span> <span class="n" style="color: #333;">require_string</span><span class="p">,</span> <span class="n" style="color: #333;">require_iterable_of</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">METADATA_TABLE_NAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_datacache_metadata"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Database</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +65,7 @@ class Database(object):</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute_sql</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sql</span><span class="p">,</span> <span class="n" style="color: #333;">commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">"""Log and then execute a SQL query"""</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running sqlite query: </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">sql</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running sqlite query: </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">sql</span><span class="p">)</span></span>
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64
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">sql</span><span class="p">)</span></span>
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65
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">commit</span><span class="p">:</span></span>
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66
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">commit</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="159" 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">@@ -154,7 +159,7 @@ class Database(object):</td>
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154
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n_columns</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">):</span></span>
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155
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Rows must all have %d values"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">n_columns</span><span class="p">)</span></span>
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156
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">blank_slots</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"?"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_columns</span><span class="p">))</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Inserting %d rows into table %s"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">),</span> <span class="n" style="color: #333;">table_name</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Inserting %d rows into table %s"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">),</span> <span class="n" style="color: #333;">table_name</span><span class="p">)</span></span>
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158
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">sql</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"INSERT INTO %s VALUES (%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span> <span class="n" style="color: #333;">blank_slots</span><span class="p">)</span></span>
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159
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">executemany</span><span class="p">(</span><span class="n" style="color: #333;">sql</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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160
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" 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="197" 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">@@ -192,9 +197,10 @@ class Database(object):</td>
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192
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> Which columns should be indexed</span></span>
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193
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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194
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Creating index on %s (%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">index_columns</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">"Creating index on %s (%s)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">index_columns</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">index_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s_index_%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">"_"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">index_columns</span><span class="p">))</span></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#0e69383aa089378fe0718955ce01c3e4093517f4"><strong>datacache/database_helpers.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,24 +12,28 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">remove</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">splitext</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">split</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">exists</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">splitext</span><span class="p">,</span> <span class="n" style="color: #333;">exists</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typechecks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">require_string</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">require_integer</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">require_iterable_of</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_path</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">normalize_filename</span></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.download</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">fetch_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">fetch_csv_dataframe</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_path</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.download</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_csv_dataframe</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.database</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Database</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.database_table</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DatabaseTable</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.database_types</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">db_type</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">connect_if_correct_version</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return a sqlite3 database connection if the version in the database's</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> metadata matches the version argument.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="49" 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">@@ -45,37 +49,29 @@ def connect_if_correct_version(db_path, version):</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_cached_db</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">db_<span class="idiff left right">filename</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">db_<span class="idiff left right">path</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> Either create or retrieve sqlite database.</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> db_<span class="idiff left right">filename</span> : str</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">Name of</span> sqlite3 database file</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> db_<span class="idiff left right">path</span> : str</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">Path to</span> sqlite3 database file</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> tables : dict</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary mapping table names to datacache.DatabaseTable objects</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> subdir : str, optional</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> version : int, optional</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> Version acceptable as cached data.</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> Returns sqlite3 connection</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">require_string</span><span class="p">(</span><span class="n" style="color: #333;">db_<span class="idiff left">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"db_filename</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">require_string</span><span class="p">(</span><span class="n" style="color: #333;">db_<span class="idiff left">path</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"db_path</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">require_iterable_of</span><span class="p">(</span><span class="n" style="color: #333;">tables</span><span class="p">,</span> <span class="n" style="color: #333;">DatabaseTable</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">subdir</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected subdir to be None or str, got %s : %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">require_integer</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">"version"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">db_filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if the database file doesn't already exist and we encounter an error</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># later, delete the file before raising an exception</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">delete_on_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,20 +87,21 @@ def _create_cached_db(</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">has_tables</span><span class="p">(</span><span class="n" style="color: #333;">table_names</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">has_version</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">version</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Found existing table in database %s"</span><span class="p">,</span> <span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Found existing table in database %s"</span><span class="p">,</span> <span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">table_names</span><span class="p">())</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Dropping tables from database %s: %s"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">"Dropping tables from database %s: %s"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">table_names</span><span class="p">()))</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">drop_tables</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">drop_<span class="idiff left right">all_</span>tables</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"Creating database %s containing: %s"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">table_names</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">create</span><span class="p">(</span><span class="n" style="color: #333;">tables</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"Failed to create tables %s in database %s"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">table_names</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,38 +111,75 @@ def _create_cached_db(</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">connection</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_fasta_db</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">fasta_filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">key_column</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">value_column</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'seq'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_tables</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_dataframes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_primary_keys</span><span class="o" style="font-weight: 600;">=</span><span class="p">{},</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_indices</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}):</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> Download a FASTA file from `download_url` and store it locally as a sqlite3 database.</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_dataframes : dict</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary mapping each table name to a DataFrame</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_primary_keys : dict</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary mapping each table to its primary key</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_indices : dict</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary mapping each table to a set of indices</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> Returns list of DatabaseTable objects</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">tables</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">table_name</span><span class="p">,</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table_names_to_dataframes</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">table_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_names_to_indices</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span> <span class="p">[])</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">primary_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_names_to_primary_keys</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">table_name</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DatabaseTable</span><span class="p">.</span><span class="n" style="color: #333;">from_dataframe</span><span class="p">(</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_indices</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">primary_key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">primary_key</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tables</span></span>
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128
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">base_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_filename</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">db_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s.%s.%s.db"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">base_filename</span><span class="p">,</span> <span class="n" style="color: #333;">key_column</span><span class="p">,</span> <span class="n" style="color: #333;">value_column</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">db_from_dataframes_with_absolute_path</span><span class="p">(</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_dataframes</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_primary_keys</span><span class="o" style="font-weight: 600;">=</span><span class="p">{},</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_indices</span><span class="o" style="font-weight: 600;">=</span><span class="p">{},</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">overwrite</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> Create a sqlite3 database from a collection of DataFrame objects</span></span>
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131
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fasta_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> db_path : str</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> Path to database file to create</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">fasta_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DatabaseTable</span><span class="p">.</span><span class="n" style="color: #333;">from_fasta_dict</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">fasta_dict</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">key_column</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">key_column</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">value_column</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value_column</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_dataframes : dict</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary from table names to DataFrame objects</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_primary_keys : dict, optional</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> Name of primary key column for each table</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> table_names_to_indices : dict, optional</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> Dictionary from table names to list of column name tuples</span></span>
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144
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> overwrite : bool, optional</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> If the database already exists, overwrite it?</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> version : int, optional</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">overwrite</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">):</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">tables</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_tables</span><span class="p">(</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_dataframes</span><span class="p">,</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_primary_keys</span><span class="p">,</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_indices</span><span class="p">)</span></span>
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145
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_create_cached_db</span><span class="p">(</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">db_filename</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">table</span><span class="p">],</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tables</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">db_from_dataframes</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,7 +190,9 @@ def db_from_dataframes(</td>
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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157
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">overwrite</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">"""Create a sqlite3 database with</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> Create a sqlite3 database from a collection of DataFrame objects</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> db_filename : str</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,25 +214,16 @@ def db_from_dataframes(</td>
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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179
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> version : int, optional</span></span>
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180
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">subdir</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)):</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected subdir to be None or str, got %s : %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">subdir</span><span class="p">)))</span></span>
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181
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">db_filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">overwrite</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">db_path</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">tables</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">table_name</span><span class="p">,</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dataframes</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">table_indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indices</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span> <span class="p">[])</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">primary_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">primary_keys</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">table_name</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DatabaseTable</span><span class="p">.</span><span class="n" style="color: #333;">from_dataframe</span><span class="p">(</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_name</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_indices</span><span class="p">,</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">primary_key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">primary_key</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_create_cached_db</span><span class="p">(</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">db_from_dataframes_with_absolute_path</span><span class="p">(</span></span>
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197
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">tables</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tables</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subdir</span><span class="p">,</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_dataframes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dataframes</span><span class="p">,</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_primary_keys</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">primary_keys</span><span class="p">,</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">table_names_to_indices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">indices</span><span class="p">,</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">overwrite</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">overwrite</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">db_from_dataframe</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#7eea9ad08e1271d658a960a87df2c6ea578cd901"><strong>datacache/database_table.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,8 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.database_types</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">db_type</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DatabaseTable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#5eede143f6d8eba797eec90bf587d381552de1ac"><strong>datacache/database_types.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,30 +14,32 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">"""Convert from Python type names to sqlite3 column types"""</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">_dtype_to_db_type_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'int'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'int8'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'int16'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'int32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'int64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'uint8'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'uint16'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'uint32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'uint64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'bool'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'float'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'float32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'float64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">'object'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'object_'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'string_'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'str'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'int'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'int8'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'int16'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'int32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'int64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'uint8'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'uint16'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'uint32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'uint64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'bool'</span><span class="p">:</span> <span class="s" style="color: #d14;">'INT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'float'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'float32'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'float64'</span><span class="p">:</span> <span class="s" style="color: #d14;">'FLOAT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'object'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'object_'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'string_'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="idiff left right"> </span> <span class="s" style="color: #d14;">'str'</span><span class="p">:</span> <span class="s" style="color: #d14;">'TEXT'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_lookup_type_name</span><span class="p">(</span><span class="n" style="color: #333;">type_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,10 +12,12 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">os</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff right">remove</span></span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">os.path</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">exists</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">splitext</span></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;"><span class="idiff left right">os</span></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">subprocess</span></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">shutil</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">move</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NamedTemporaryFile</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">zipfile</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,57 +25,99 @@ import zipfile</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">requests</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">urllib</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_path</span><span class="p">,</span> <span class="n" style="color: #333;">build_local_filename</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">urllib.request</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">urllib.error</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">urllib.parse</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python 3</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">urllib_response</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">req</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">Request</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">req</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python 2</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">urllib2</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_download</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"http"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">response</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">requests</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">raise_for_status</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">content</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">req</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">Request</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">response</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">req</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">urllib_response</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">req</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib2</span><span class="p">.</span><span class="n" style="color: #333;">Request</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">urllib2</span><span class="p">.</span><span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">req</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_download</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_download_to_temp_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">base_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"download"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">ext</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"tmp"</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">download_url</span><span class="p">:</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"URL not provided"</span><span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ext</span><span class="p">,</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">base_name</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tmp</span><span class="p">:</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download_using_python</span><span class="p">():</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w+b"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">_download</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">))</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">use_wget_if_available</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">download_using_python</span><span class="p">()</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># first try using wget to download since this works on Travis</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># even when FTP otherwise fails</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">wget_command_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"wget"</span><span class="p">,</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"-O"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"--no-verbose"</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="p">]</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"ftp"</span><span class="p">):</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">wget_command_list</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"--passive-ftp"</span><span class="p">])</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">timeout</span><span class="p">:</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">wget_command_list</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"-T"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">timeout</span><span class="p">])</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">wget_command_list</span><span class="p">)))</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">wget_command_list</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">errno</span><span class="p">.</span><span class="n" style="color: #333;">ENOENT</span><span class="p">:</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># wget not found</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">download_using_python</span><span class="p">()</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp_path</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_download_and_decompress_if_necessary</span><span class="p">(</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">full_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> Downloads remote file at `download_url` to local file at `full_path`</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Downloading %s to %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">base_name</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"http"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">response</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">requests</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">raise_for_status</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">content</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">response</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urllib_response</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">response</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ext</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">base_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Downloading %s to %s"</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">base_name</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_download_to_temp_file</span><span class="p">(</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">base_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">base_name</span><span class="p">,</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">ext</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ext</span><span class="p">,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">use_wget_if_available</span><span class="p">)</span></span>
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67
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"zip"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"zip"</span><span class="p">):</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Decompressing zip into %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Decompressing zip into %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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70
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">zipfile</span><span class="p">.</span><span class="n" style="color: #333;">ZipFile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">z</span><span class="p">:</span></span>
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71
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</span><span class="p">.</span><span class="n" style="color: #333;">namelist</span><span class="p">()</span></span>
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72
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Empty zip archive"</span></span>
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73
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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74
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">chosen_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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75
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">in case</span> zip archive contains multiple files, choose the biggest</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left">If</span> zip archive contains multiple files, choose the biggest<span class="idiff right">.</span></span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">biggest_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">chosen_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">z</span><span class="p">.</span><span class="n" style="color: #333;">infolist</span><span class="p">():</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,33 +126,34 @@ def _download(filename, full_path, download_url):</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">biggest_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">file_size</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">extract_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</span><span class="p">.</span><span class="n" style="color: #333;">extract</span><span class="p">(</span><span class="n" style="color: #333;">chosen_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">extract_path</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"gz"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Decompressing gzip into %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Decompressing gzip into %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="n" style="color: #333;">GzipFile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">src</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">contents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dst</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w<span class="idiff left right">b</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dst</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">dst</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">contents</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">((</span><span class="s" style="color: #d14;">"html"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htm"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Extracting HTML table into CSV %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_html</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infer_types</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">download_url</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">((</span><span class="s" style="color: #d14;">"html"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htm"</span><span class="p">))</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">full_path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endswith</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">".csv"</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Extracting HTML table into CSV %s..."</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_html</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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96
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span></span>
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97
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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98
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">file_exists</span><span class="p">(</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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105
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> Return True if a local file corresponding to these arguments</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> exists.</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_local_filename</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">decompress</span><span class="p">)</span></span>
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110
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">full_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_file</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,7 +161,9 @@ def fetch_file(</td>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> Download a remote file and store it locally in a cache directory. Don't</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> download it again if it's already present (unless `force` is True.)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" 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="190" 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">@@ -143,15 +190,27 @@ def fetch_file(</td>
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143
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> By default, a remote file is not downloaded if it's already present.</span></span>
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144
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> However, with this argument set to True, it will be overwritten.</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> timeout : float, optional</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> Timeout for download in seconds, default is None which uses</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> global timeout.</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> use_wget_if_available: bool, optional</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> If the `wget` command is available, use that for download instead</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> of Python libraries (default True)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> Returns the full path of the local file.</span></span>
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147
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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148
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_local_filename</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">decompress</span><span class="p">)</span></span>
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149
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">full_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">force</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Fetching %s from URL %s"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">_download</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">full_path</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">force</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Fetching %s from URL %s"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">_download_and_decompress_if_necessary</span><span class="p">(</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">full_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">full_path</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">use_wget_if_available</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Cached file %s from URL %s"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Cached file %s from URL %s"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">download_url</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">full_path</span></span>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"></span>
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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">@@ -168,14 +227,14 @@ def fetch_and_transform(</td>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="s" style="color: #d14;"> object.</span></span>
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169
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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170
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">transformed_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">build_path</span><span class="p">(</span><span class="n" style="color: #333;">transformed_filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">transformed_path</span><span class="p">):</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">transformed_path</span><span class="p">):</span></span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">source_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span><span class="n" style="color: #333;">source_url</span><span class="p">,</span> <span class="n" style="color: #333;">source_filename</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Generating data file %s from %s"</span><span class="p">,</span> <span class="n" style="color: #333;">transformed_path</span><span class="p">,</span> <span class="n" style="color: #333;">source_path</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Generating data file %s from %s"</span><span class="p">,</span> <span class="n" style="color: #333;">transformed_path</span><span class="p">,</span> <span class="n" style="color: #333;">source_path</span><span class="p">)</span></span>
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transformer</span><span class="p">(</span><span class="n" style="color: #333;">source_path</span><span class="p">,</span> <span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">ing</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Cached data file: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">logg<span class="idiff left right">er</span></span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Cached data file: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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177
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loader</span><span class="p">(</span><span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">transformed_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#9ef0cc6d5bfc3cc64e310eaacf2ec8cbb4ae6d13"><strong>datacache/fasta.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2015. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You may obtain a copy of the License at</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># http://www.apache.org/licenses/LICENSE-2.0</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Unless required by applicable law or agreed to in writing, software</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># distributed under the License is distributed on an "AS IS" BASIS,</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.download</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_file</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_fasta_dict</span><span class="p">(</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> Download a remote FASTA file from `download_url` and save it locally as `filename`.</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> Load the file using BioPython and return an index mapping from entry keys to their sequence.</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">download_url</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[egg_info]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tag_build = </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">tag_date = 0</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014<span class="idiff left right">-2018</span>. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,35 +25,32 @@ readme_path = os.path.join(current_directory, readme_filename)</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">readme_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">readme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">readme<span class="idiff left right">_markdown</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to load %s"</span><span class="p">,</span> <span class="n" style="color: #333;">readme_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">readme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">readme<span class="idiff left right">_markdown</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pypandoc</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">readme</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pypandoc</span><span class="p">.</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">readme</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rst"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"md"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">readme<span class="idiff left">_restructured</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pypandoc</span><span class="p">.</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">readme<span class="idiff right">_markdown</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rst"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"md"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">readme_restructured</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readme_markdown</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to convert %s to reStructuredText"</span><span class="p">,</span> <span class="n" style="color: #333;">readme_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="n" style="color: #333;">requirements_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">current_directory</span><span class="p">,</span> <span class="s" style="color: #d14;">"requirements.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">requirements_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">requirements</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'datacache/__init__.py'</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="sa">r</span><span class="s" style="color: #d14;">'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">MULTILINE</span><span class="p">).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"datacache"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">"0.4.7"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left right">version</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Helpers for transparently downloading datasets"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Alex Rubinsteyn"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"alex<span class="idiff left"> {dot} </span>rubinsteyn<span class="idiff right"> {at} mssm {dot} </span>edu"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff left right">hammerlab</span>/datacache"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"alex<span class="idiff left">.</span>rubinsteyn<span class="idiff right">@mssm.</span>edu"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/<span class="idiff left right">openvax</span>/datacache"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"http://www.apache.org/licenses/LICENSE-2.0.html"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 3 - Alpha"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,7 +61,14 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">requirements</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readme</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">"pandas>=0.15.2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">"appdirs>=1.4.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">"progressbar33>=2.4"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">"requests>=2.5.1"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">"typechecks>=0.0.2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"mock"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readme_restructured</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"datacache"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#7ac8b74ac3c1c5140ed772c822cc328b0793f984"><strong>test/__init__.py</strong>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#59ce3c49e5c5806b46ba8e446b2b0fb3bc583d5e"><strong>test/test_cache_object.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">@@ -29,7 +29,7 @@ def test_cache_fetch_google():</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">eq_</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">local_path</span><span class="p">(</span><span class="n" style="color: #333;">TEST_URL</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">TEST_FILENAME</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'datacache.cache.download._download'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'datacache.cache.download._download<span class="idiff left right">_and_decompress_if_necessary</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_cache_fetch_force</span><span class="p">(</span><span class="n" style="color: #333;">mock_download</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Cache</span><span class="p">(</span><span class="s" style="color: #d14;">"datacache_test"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">"http://www.google.com"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"google"</span><span class="p">,</span> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#570f45465ad5df111e6ed14b56f7e04e2e0958b8"><strong>test/test_download.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,16 +18,20 @@ FASTA_FILENAME = 'Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa'</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa.gz'</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_decompress</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">URL</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"datacache"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">path1</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">FASTA_FILENAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"TCAATTTCGTGCCAG"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s1</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_decompress</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">use_wget_if_available</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">timeout</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">6</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">URL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"datacache"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">use_wget_if_available</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">use_wget_if_available</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">timeout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">timeout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">path1</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">FASTA_FILENAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"TCAATTTCGTGCCAG"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s1</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_subdirs</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span><span class="n" style="color: #333;">URL</span><span class="p">,</span> <span class="n" style="color: #333;">decompress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">subdir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"datacache"</span><span class="p">)</span></span>
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<li id="211311cd08c5d4d95686f7b867563b6e84ea9ce1">
<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#211311cd08c5d4d95686f7b867563b6e84ea9ce1"><strong>test/test_fasta_db.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014. Mount Sinai School of Medicine</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># you may not use this file except in compliance with the License.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You may obtain a copy of the License at</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># http://www.apache.org/licenses/LICENSE-2.0</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Unless required by applicable law or agreed to in writing, software</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datacache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_fasta_db</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">FASTA_FILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa'</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa.gz'</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download_fasta_db</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_fasta_db</span><span class="p">(</span><span class="s" style="color: #d14;">"DNA"</span><span class="p">,</span> <span class="n" style="color: #333;">URL</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-datacache/-/commit/9f1f5c72f159ca05891e8b34d71c7961b51f1b6e#5004304f2e154c337a31a6fbcb908033422860e0"><strong>test/test_fasta_dict.py</strong></a>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># limitations under the License.</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datacache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_fasta_dict</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datacache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fetch_file</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'ftp://ftp.ensembl.org/pub/release-75'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75'</span><span class="p">,</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'.dna_rm.chromosome.MT.fa.gz'</span><span class="p">,</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_fasta_dict</span><span class="p">(</span><span class="n" style="color: #333;">path_or_url</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_file</span><span class="p">(</span><span class="n" style="color: #333;">path_or_url</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">value_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gzip"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"ascii"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">value_buffer</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">value_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">value_buffer</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">value_buffer</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">value_buffer</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">FASTA_FILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa'</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa.gz'</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download_fasta_dict</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_fasta_dict</span><span class="p">(</span><span class="n" style="color: #333;">URL</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="s" style="color: #d14;">'keys'</span><span class="p">),</span> <span class="n" style="color: #333;">d</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="s" style="color: #d14;">'values'</span><span class="p">),</span> <span class="n" style="color: #333;">d</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span></pre>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fetch_fasta_dict</span><span class="p">(</span><span class="n" style="color: #333;">URL</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FASTA_FILENAME</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">d2</span><span class="p">)</span></span></pre>
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