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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/biomaj3-download">Debian Med / biomaj3-download</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/511284eb9c68d85c1be4103b68366eacfdb178ed">511284eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:36:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.19</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/08d65c9ed09a1d4ce4cfdcf115cf06c7a6f42406">08d65c9e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:36:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.0.19'
Update to upstream version '3.0.19'
with Debian dir 73e1c6a5734f30628de28c56765890bf118dec8e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/9781f8355b61b04b585967cdd269a543feb71ea6">9781f835</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:36:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/d42cbe03f7abab54219188ef717af06dd95d294f">d42cbe03</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:36:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/cc4a4996314b6f7a3877ab56d9cbf772bb8cfa14">cc4a4996</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:40:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/64c969877c97f87996ebc8370c0a71c8dae63954">64c96987</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:40:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testsuite: autopkgtest-pkg-python
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/6949d34ca2c0cf7fc85dd5daaaaa6def8d9993f6">6949d34c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:40:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/6fdae3ad1dc01be9176435cc122200f73b9af630">6fdae3ad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:40:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/cafc530e3f261d5b92a7f34fd873edc2b7708eaf">cafc530e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:42:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
</a>
</li>
<li class="file-stats">
<a href="#df5653d5031791e72480c39a18d003ef12827c31">
biomaj_download/download/direct.py
</a>
</li>
<li class="file-stats">
<a href="#ab0038c23ab3b71a66a770429f838f810ea42d79">
biomaj_download/download/ftp.py
</a>
</li>
<li class="file-stats">
<a href="#e6f6f98e9578e6213bf72da1edab3898603e6020">
biomaj_download/download/http.py
</a>
</li>
<li class="file-stats">
<a href="#63b39413137f9b80cf3fdef07da7062560aac6d3">
biomaj_download/download/protocolirods.py
</a>
</li>
<li class="file-stats">
<a href="#e0009ad7b231be5dd99cb4e5293b1e587e3d8608">
biomaj_download/download/rsync.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#a5b5d0c7b9c558d9142a199ec517b633dd40faf5">
tests/biomaj_tests.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0.19:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Check archives after download</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Fix python regexps syntax (deprecation)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1" 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">
1
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">3.0.18:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" 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">
2
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Rename protobuf and use specific package to avoid conflicts</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3" 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">
3
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">3.0.17:</span>
</pre>
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</table>
<br>
</li>
<li id="df5653d5031791e72480c39a18d003ef12827c31">
<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#df5653d5031791e72480c39a18d003ef12827c31"><strong>biomaj_download/download/direct.py</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" 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="238" 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">@@ -238,7 +238,7 @@ class DirectHttpDownload(DirectFTPDownload):</td>
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<td class="diff-line-num old_line" data-linenumber="238" 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">
238
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<td class="diff-line-num new_line" data-linenumber="238" 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">
238
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">encoding</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="239" 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">
239
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<td class="diff-line-num new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'content-type'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="240" 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">
240
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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">content_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="s" style="color: #d14;">'content-type'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="241" 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">
241
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<td class="diff-line-num new_line old" data-linenumber="241" 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="LC241" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'charset=(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'charset=(\S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">encoding</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</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="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">encoding</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="257" 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">@@ -257,7 +257,7 @@ class DirectHttpDownload(DirectFTPDownload):</td>
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257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'size'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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258
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Last-Modified'</span><span class="p">:</span></span>
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259
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sun, 06 Nov 1994</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+),</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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<td class="diff-line-num new old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'(\w+),\s+(\d+)\s+(\w+)\s+(\d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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261
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'hash'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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="265" 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">@@ -265,7 +265,7 @@ class DirectHttpDownload(DirectFTPDownload):</td>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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267
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sunday, 06-Nov-94</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+),</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)-(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+)-(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'(\w+),\s+(\d+)-(\w+)-(\d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'hash'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -273,7 +273,7 @@ class DirectHttpDownload(DirectFTPDownload):</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2000</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">))</span></span>
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274
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sun Nov 6 08:49:37 1994</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d{2}:</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d{2}:</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d{2}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'(\w+)\s+(\w+)\s+(\d+)\s+\d{2}:\d{2}:\d{2}\s+(\d+)'</span><span class="p">,</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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278
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'hash'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#ab0038c23ab3b71a66a770429f838f810ea42d79"><strong>biomaj_download/download/ftp.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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="129" 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">@@ -129,9 +129,18 @@ class FTPDownload(DownloadInterface):</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Could not get errcode:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">nbtry</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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133
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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;">curl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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134
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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;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">skip_check_uncompress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'UNCOMPRESS_SKIP_CHECK'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">error</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">skip_check_uncompress</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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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">archive_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">archive_check</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">archive_status</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Archive is invalid or corrupted, deleting file and retrying download'</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;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</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;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">file_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 class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span></span>
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135
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">error</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">local_dir</span><span class="p">,</span> <span class="n" style="color: #333;">keep_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="253" 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="262" 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">@@ -253,7 +262,7 @@ class FTPDownload(DownloadInterface):</td>
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253
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">encoding</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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254
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'content-type'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">:</span></span>
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255
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">content_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="s" style="color: #d14;">'content-type'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'charset=(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'charset=(\S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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257
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span><span class="p">:</span></span>
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258
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">encoding</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</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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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">encoding</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -288,7 +297,7 @@ class FTPDownload(DownloadInterface):</td>
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288
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'hash'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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289
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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290
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">e</span></span><span class="p">:</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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292
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># specific ftp case issues at getting date info</span></span>
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293
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">curdate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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294
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">curdate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">year</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#e6f6f98e9578e6213bf72da1edab3898603e6020"><strong>biomaj_download/download/http.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +17,7 @@ except ImportError:</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">HTTPParse</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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19
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19
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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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dir_line</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span><span class="p">,</span> <span class="n" style="color: #333;">dir_name</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">dir_date</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">file_name</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">file_date</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">file_date_format</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;">file_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</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 class="idiff left right">"""</span></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">r'''</span></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> http.parse.dir.line: <img[\s]+src="[\S]+"[\s]+alt="\[DIR\]"[\s]*/?>[\s]*<a[\s]+href="([\S]+)/"[\s]*>.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> http.parse.file.line: <img[\s]+src="[\S]+"[\s]+alt="\[[\s]+\]"[\s]*/?>[\s]<a[\s]+href="([\S]+)".*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})[\s]+([\d\.]+[MKG]{0,1})</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.dir.name: 1</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +25,7 @@ class HTTPParse(object):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.name: 1</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.date: 2</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.size: 3</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">"""</span></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'''</span></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dir_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dir_line</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_line</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dir_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dir_name</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">@@ -85,7 +85,7 @@ class HTTPDownload(FTPDownload):</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">encoding</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="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'content-type'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</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;">content_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="s" style="color: #d14;">'content-type'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'charset=(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'charset=(\S+)'</span><span class="p">,</span> <span class="n" style="color: #333;">content_type</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</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;">encoding</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</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="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">encoding</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" 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">@@ -96,14 +96,14 @@ class HTTPDownload(FTPDownload):</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># lets get the output in a string</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="n" style="color: #333;">encoding</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;"> <span class="idiff left right">'</span>http.parse.dir.line': r'<a[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s]+href="([</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S]+)/".*alt="</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">[DIR</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">]">.*([</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2}-[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2,5}-[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{4}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2}:[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2})',</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.parse.file.line': r'<a[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s]+href="([</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S]+)".*([</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2}-[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">w</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2,5}-[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{4}</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2}:[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d]{2})[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s]+([</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">d</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">.]+[MKG]{0,1})',</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.group.dir.name': 1,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.group.dir.date': 2,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.group.file.name': 1,</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.group.file.date': 2,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">'</span>http.group.file.size': 3,</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">r</span>'''</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> http.parse.dir.line': r'<a[\s]+href="([\S]+)/".*alt="\[DIR\]">.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})',</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> http.parse.file.line': r'<a[\s]+href="([\S]+)".*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})[\s]+([\d\.]+[MKG]{0,1})',</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.dir.name': 1,</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.dir.date': 2,</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.name': 1,</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.date': 2,</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> http.group.file.size': 3,</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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109
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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;">rfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#63b39413137f9b80cf3fdef07da7062560aac6d3"><strong>biomaj_download/download/protocolirods.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">@@ -3,6 +3,7 @@ import os</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biomaj_core.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Utils</span></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biomaj_download.download.interface</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DownloadInterface</span></span>
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7
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">irods.session</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iRODSSession</span></span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">irods.models</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Collection</span><span class="p">,</span> <span class="n" style="color: #333;">DataObject</span><span class="p">,</span> <span class="n" style="color: #333;">User</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" 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="97" 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">@@ -96,6 +97,15 @@ class IRODSDownload(DownloadInterface):</td>
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96
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'download_time'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'error'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"IRODS:Download:Error:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'root'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">archive_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">archive_check</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">archive_status</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Archive is invalid or corrupted, deleting file'</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;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'error'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">file_path</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"IRODS:Download:Error:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'root'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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99
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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100
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mktime</span><span class="p">(</span><span class="n" style="color: #333;">end_time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">timetuple</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'download_time'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_time</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#e0009ad7b231be5dd99cb4e5293b1e587e3d8608"><strong>biomaj_download/download/rsync.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">@@ -119,7 +119,7 @@ class RSYNCDownload(DownloadInterface):</td>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'save_as'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep_dirs</span><span class="p">:</span></span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">file_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">local_dir</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'save_as'</span><span class="p">])</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S*</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">/$'</span><span class="p">,</span> <span class="n" style="color: #333;">file_dir</span><span class="p">):</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r</span>'\S*\/$'</span><span class="p">,</span> <span class="n" style="color: #333;">file_dir</span><span class="p">):</span></span>
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_dir</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'save_as'</span><span class="p">])</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'save_as'</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biomaj3-download (3.0.19-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper 12</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Testsuite: autopkgtest-pkg-python</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright</span>
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10
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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"> -- Andreas Tille <tille@debian.org> Wed, 30 Jan 2019 10:40:31 +0100</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">biomaj3-download (3.0.18-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> [ Jelmer Vernooij ]</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +17,7 @@ biomaj3-download (3.0.18-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> [ Olivier Sallou ]</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * New upstream release<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * New upstream release</span>
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9
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Thu, 25 Oct 2018 08:52:07 +0000</span>
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11
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">9</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">12</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: biomaj3-download</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: python</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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4
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Olivier Sallou <osallou@debian.org></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 9), dh-python,</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: python</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> protobuf-compiler,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-bcrypt,</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">@@ -23,17 +25,20 @@ Build-Depends: debhelper (>= 9), dh-python,</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python3-yaml,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> python3-biomaj3-core,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> python3-biomaj3-zipkin</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Homepage: https://github.com/genouest/biomaj-download</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/biomaj3-download</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/biomaj3-download.git</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Homepage: https://github.com/genouest/biomaj-download</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Package: python3-biomaj3-download</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">Depends: ${misc:Depends}, ${python3:Depends}</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Recommends: ${python3:Recommends}</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Suggests: ${python3:Suggests}, python3-gunicorn, mongodb, redis-server</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">XB-Python-Egg-Name: biomaj-download</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Suggests: ${python3:Suggests},</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> python3-gunicorn,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> mongodb,</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> redis-server</span>
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37
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Description: BioMAJ download management library</span>
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38
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43
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> BioMAJ downloads remote data banks, checks their status and applies</span>
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39
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> transformation workflows, with consistent state, to provide ready-to-use</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">@@ -45,3 +50,4 @@ Description: BioMAJ download management library</td>
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45
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> .</span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> This package contains the library and microservice to manage downloads</span>
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47
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> in BioMAJ3</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">XB-Python-Egg-Name: biomaj-download</span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -424,7 +424,7 @@ License: AGPL-3</td>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext"> Moreover, your license from a particular copyright holder is</span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="plaintext"> reinstated permanently if the copyright holder notifies you of the</span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="plaintext"> violation by some reasonable means, this is the first time you have</span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="plaintext"> received notice of violation of this License (for any work) from that<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> received notice of violation of this License (for any work) from that</span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="plaintext"> copyright holder, and you cure the violation prior to 30 days after</span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext"> your receipt of the notice.</span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="plaintext"> .</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">@@ -537,7 +537,7 @@ License: AGPL-3</td>
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="plaintext"> Nothing in this License shall be construed as excluding or limiting</span>
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538
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="plaintext"> any implied license or other defenses to infringement that may</span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="plaintext"> otherwise be available to you under applicable patent law.</span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="plaintext"> .<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="plaintext"> 12. No Surrender of Others' Freedom.</span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="plaintext"> If conditions are imposed on you (whether by court order, agreement or</span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ mock</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/nose" rel="nofollow noreferrer noopener" target="_blank">nose</a></span>
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3
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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/pycurl" rel="nofollow noreferrer noopener" target="_blank">pycurl</a></span>
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4
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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/py-bcrypt" rel="nofollow noreferrer noopener" target="_blank">py-bcrypt</a></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pika" rel="nofollow noreferrer noopener" target="_blank">pika</a></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pika" rel="nofollow noreferrer noopener" target="_blank">pika</a><span class="idiff left right">==0.11.2</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/redis" rel="nofollow noreferrer noopener" target="_blank">redis</a></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/PyYAML" rel="nofollow noreferrer noopener" target="_blank">PyYAML</a></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/protobuf" rel="nofollow noreferrer noopener" target="_blank">protobuf</a></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ config = {</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</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;">'download_url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</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;">'author_email'</span><span class="p">:</span> <span class="s" style="color: #d14;">'olivier.sallou@irisa.fr'</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;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">8</span>'</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;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">9</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'classifiers'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># How mature is this project? Common values are</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 3 - Alpha</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">@@ -46,7 +46,7 @@ config = {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">'biomaj_zipkin'</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;">'pycurl'</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;">'py-bcrypt'</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;">'pika'</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;">'pika<span class="idiff left right">==0.11.2</span>'</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;">'redis'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'PyYAML'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">'flask'</span><span class="p">,</span></span>
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<li id="a5b5d0c7b9c558d9142a199ec517b633dd40faf5">
<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/a7cedb38c904beb3ff2f042e91084ab1a4379942...cafc530e3f261d5b92a7f34fd873edc2b7708eaf#a5b5d0c7b9c558d9142a199ec517b633dd40faf5"><strong>tests/biomaj_tests.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">@@ -443,9 +443,26 @@ class TestBiomajFTPDownload(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">file_list</span><span class="p">,</span> <span class="n" style="color: #333;">dir_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ftpd.match([r'^alu.*\.gz$'], file_list, dir_list)</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">([</span><span class="s" style="color: #d14;">r'^1.*KB\.zip$'</span><span class="p">],</span> <span class="n" style="color: #333;">file_list</span><span class="p">,</span> <span class="n" style="color: #333;">dir_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="mi" style="color: #099;">1</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="LC450" 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="LC451" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="mi" style="color: #099;">1</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="LC452" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.assertTrue(len(ftpd.files_to_download) == 2)</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download_skip_uncompress_checks</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ftpd = FTPDownload('ftp', 'ftp.ncbi.nih.gov', '/blast/db/FASTA/')</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'UNCOMPRESS_SKIP_CHECK'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'speedtest.tele2.net'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">file_list</span><span class="p">,</span> <span class="n" style="color: #333;">dir_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ftpd.match([r'^alu.*\.gz$'], file_list, dir_list)</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">([</span><span class="s" style="color: #d14;">r'^1.*KB\.zip$'</span><span class="p">],</span> <span class="n" style="color: #333;">file_list</span><span class="p">,</span> <span class="n" style="color: #333;">dir_list</span><span class="p">)</span></span>
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446
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>
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447
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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448
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464
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ftpd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">files_to_download</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'UNCOMPRESS_SKIP_CHECK'</span><span class="p">]</span></span>
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download_in_subdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">ftpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp.ncbi.nih.gov'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/blast/'</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">@@ -577,7 +594,7 @@ class iRodsResult(object):</td>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"COLL_NAME"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">):</span></span>
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Collname</span></span>
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"D_OWNER_NAME"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Dataowner_name</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Dataowner_name</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"></span>
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"></span>
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MockiRODSSession</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">@@ -601,19 +618,19 @@ class MockiRODSSession(object):</td>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Collid</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"COLL_NAME"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Collname</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">configure</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MockiRODSSession</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">query</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">Collname</span><span class="p">,</span> <span class="n" style="color: #333;">Dataname</span><span class="p">,</span> <span class="n" style="color: #333;">Datasize</span><span class="p">,</span> <span class="n" style="color: #333;">Dataowner_name</span><span class="p">,</span> <span class="n" style="color: #333;">Datamodify_time</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">one</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">boo</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;"> <span id="LC636" 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">@@ -640,7 +657,7 @@ class TestBiomajIRODSDownload(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">curdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">examples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">curdir</span><span class="p">,</span><span class="s" style="color: #d14;">'bank'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties</span><span class="p">,</span> <span class="n" style="color: #333;">allow_user_config</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="LC643" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clean</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="674" 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">@@ -657,4 +674,3 @@ class TestBiomajIRODSDownload(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">irodsd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_offline_dir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="p">)</span></span>
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675
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">files_list</span><span class="p">,</span> <span class="n" style="color: #333;">dir_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">irodsd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">files_list</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></pre>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"></span></pre>
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