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<h3>

Olivier Sallou 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/5de3aa6af2d0f6468e5d5c6be0b8262675f2ad7c">5de3aa6a</a></strong>

<div>

<span>by Olivier Sallou</span>

<i>at 2019-03-09T09:47:57Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.21</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/772007909b3565d785b421d270e4bcdc88eece21">77200790</a></strong>

<div>

<span>by Olivier Sallou</span>

<i>at 2019-03-09T09:47:57Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.0.21'

Update to upstream version '3.0.21'

with Debian dir 901aa17e9e50a8505565edf8ab321bb9be8fe37d</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/132af15f997cef3496b55cf4a1e164dfd6020955">132af15f</a></strong>

<div>

<span>by Olivier Sallou</span>

<i>at 2019-03-09T10:10:48Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release 3.0.21

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/commit/ed679a76b1b461ea9a602d52c04a8dad1d429b14">ed679a76</a></strong>

<div>

<span>by Olivier Sallou</span>

<i>at 2019-03-09T10:10:48Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove irods support as lib is not in debian

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">

CHANGES.txt

</a>

</li>

<li class="file-stats">

<a href="#fb7176d365e710cc181c48f4865958ad172b3f9d">

biomaj_download/biomaj_download_web.py

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#bec28f8b18dab9e47b3c5bb82d31f95da57ff7ee">

<span class="new-file">

+

debian/patches/remove_irods.patch

</span>

</a>

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<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="new-file">

+

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#19359a61ae2446b51b549167b014da2fcf265768">

requirements.txt

</a>

</li>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

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<li class="file-stats">

<a href="#a5b5d0c7b9c558d9142a199ec517b633dd40faf5">

tests/biomaj_tests.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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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="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>

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<td class="diff-line-num new_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">

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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="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">python</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.7"</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC5" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.4"</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.7'</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.4'</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.5'</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.6'</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: teal;">services</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">redis</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Apply only on main branches</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">redis</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"><span class="na" style="color: teal;">branches</span><span class="pi">:</span></span>

</pre>

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11

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">  <span class="na" style="color: teal;">except</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC12" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">/^feature.*$/</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC13" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to install dependencies</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#before_install:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC15" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - "sudo apt-get update -qq"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC16" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - "sudo apt-get install -qq libldap2-dev libsasl2-dev"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">/^feature.*$/"</span></span>

</pre>

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<td class="diff-line-num old_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">

17

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">-r</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">requirements.txt"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">coverage"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">python-coveralls"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC21" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">python</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">setup.py</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">-q</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC22" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - "echo data_file=$TRAVIS_BUILD_DIR/.coverage >> .coveragerc"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC23" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to run tests</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install -r requirements.txt</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install coverage nose</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install python-coveralls</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py -q install</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="18" 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">

18

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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="LC18" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">   <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py test</span></span>

</pre>

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26

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<td class="diff-line-num new_line old" data-linenumber="19" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">   <span class="pi">-</span> <span class="s" style="color: #d14;">flake8 --ignore E501 biomaj_download/*.py biomaj_download/download</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line old" data-linenumber="19" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#after_success:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC28" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#  - coveralls</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line old" data-linenumber="19" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"></span></pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">nosetests -a '!network'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">flake8 --ignore E501 biomaj_download/*.py biomaj_download/download</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="21" 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">

21

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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="LC21" class="line" lang="yaml"><span class="na" style="color: teal;">deploy</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="22" 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">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml">  <span class="na" style="color: teal;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="23" 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">

23

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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="LC23" class="line" lang="yaml">  <span class="na" style="color: teal;">skip_existing</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml">  <span class="na" style="color: teal;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">osallou</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml">  <span class="na" style="color: teal;">password</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="26" 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">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml">    <span class="na" style="color: teal;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;">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</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="27" 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">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml">  <span class="na" style="color: teal;">distributions</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist bdist_wheel</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml">  <span class="na" style="color: teal;">on</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" 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="29" 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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml">    <span class="na" style="color: teal;">tags</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0.21:</span>

</pre>

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<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">

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<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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">  Fix traefik labels</span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">3.0.20:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  Update pika dependency release</span>

</pre>

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<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">

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  Add tags for traefik support</span>

</pre>

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1

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">3.0.19:</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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">  Check archives after download</span>

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<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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  Fix python regexps syntax (deprecation)</span>

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<br>

</li>

<li id="fb7176d365e710cc181c48f4865958ad172b3f9d">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#fb7176d365e710cc181c48f4865958ad172b3f9d"><strong>biomaj_download/biomaj_download_web.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,7 +30,7 @@ download_time_metric = Counter("biomaj_download_file_time", "Bank download file</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">config_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'config.yml'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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="32" 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="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'BIOMAJ_CONFIG'</span> <span class="ow" style="font-weight: 600;">in</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>

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<td class="diff-line-num old old_line" data-linenumber="33" 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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<td class="diff-line-num new_line old" data-linenumber="33" 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="LC33" class="line" lang="python">    <span class="idiff left right">    </span><span class="n" style="color: #333;">config_file</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="p">[</span><span class="s" style="color: #d14;">'BIOMAJ_CONFIG'</span><span class="p">]</span></span>

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<td class="diff-line-num new old_line" data-linenumber="34" 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="LC33" class="line" lang="python">    <span class="n" style="color: #333;">config_file</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="p">[</span><span class="s" style="color: #d14;">'BIOMAJ_CONFIG'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="34" 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="LC34" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="35" 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="LC35" class="line" lang="python"><span class="n" style="color: #333;">config</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="36" 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="36" 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="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">config_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ymlfile</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" 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="41" 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">@@ -41,7 +41,19 @@ with open(config_file, 'r') as ymlfile:</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">consul_declare</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="42" 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="42" 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="LC42" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'host'</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" 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="43" 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="LC43" class="line" lang="python">        <span class="n" style="color: #333;">consul_agent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">consul</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Consul</span><span class="p">(</span><span class="n" style="color: #333;">host</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'host'</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python">        <span class="n" style="color: #333;">consul_agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">service</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="s" style="color: #d14;">'biomaj-download'</span><span class="p">,</span> <span class="n" style="color: #333;">service_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span> <span class="n" style="color: #333;">address</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'hostname'</span><span class="p">],</span> <span class="n" style="color: #333;">port</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'port'</span><span class="p">],</span> <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'biomaj'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" 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="LC44" class="line" lang="python">        <span class="n" style="color: #333;">consul_agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">service</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" 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="LC45" class="line" lang="python">            <span class="s" style="color: #d14;">'biomaj-download'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" 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="LC46" class="line" lang="python">            <span class="n" style="color: #333;">service_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" 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="LC47" class="line" lang="python">            <span class="n" style="color: #333;">address</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'hostname'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" 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="LC48" class="line" lang="python">            <span class="n" style="color: #333;">port</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'port'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="python">            <span class="n" style="color: #333;">tags</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">                <span class="s" style="color: #d14;">'biomaj'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="python">                <span class="s" style="color: #d14;">'api'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">                <span class="s" style="color: #d14;">'traefik-int.backend=biomaj-download'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">                <span class="s" style="color: #d14;">'traefik-int.frontend.rule=PathPrefix:/api/download'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="python">                <span class="s" style="color: #d14;">'traefik-int.enable=true'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">            <span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" 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="LC56" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">        <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">consul</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Check</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">http</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'http://'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'hostname'</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'port'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/api/download'</span><span class="p">,</span> <span class="n" style="color: #333;">interval</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python">        <span class="n" style="color: #333;">consul_agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">agent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_check'</span><span class="p">,</span> <span class="n" style="color: #333;">check</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">check</span><span class="p">,</span> <span class="n" style="color: #333;">service_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'consul'</span><span class="p">][</span><span class="s" style="color: #d14;">'id'</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>

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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biomaj3-download (3.0.21-1) unstable; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream release </span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * d/rules: use DEB_BUILD_MAINT_OPTIONS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * d/patches: remove irods protocol support as python lib is not</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">    available in Debian.</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org>  Sat, 09 Mar 2019 09:48:16 +0000</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">biomaj3-download (3.0.19-1) unstable; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<li id="bec28f8b18dab9e47b3c5bb82d31f95da57ff7ee">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#bec28f8b18dab9e47b3c5bb82d31f95da57ff7ee"><strong>debian/patches/remove_irods.patch</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: python irods not available, remove it from supported protocols</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: biomaj supports irods as download protocol but irods is not</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> available in Debian. In the meanwhile remove support for this protocol</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Updated: 2019-03-09</span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Forwarded: no</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/requirements.txt</span></span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/requirements.txt</span></span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,4 +14,3 @@</span></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> biomaj_zipkin</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> flake8</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> humanfriendly</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python-irodsclient</span></span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -54,8 +54,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">                          'prometheus_client>=0.0.18',</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">                          'protobuf',</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">                          'requests',</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         'humanfriendly',</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         'python-irodsclient'</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                         'humanfriendly'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">                         ],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">     'tests_require': ['nose', 'mock'],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">     'test_suite': 'nose.collector',</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/biomaj_download/download/protocolirods.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/biomaj_download/download/protocolirods.py</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5,8 +5,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> from biomaj_core.utils import Utils</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> from biomaj_download.download.interface import DownloadInterface</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from irods.session import iRODSSession</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from irods.models import Collection, DataObject, User</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> class IRODSDownload(DownloadInterface):</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,27 +29,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">         self.zone = str(param['zone'])</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">     def list(self, directory=''):</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        session = iRODSSession(host=self.server, port=self.port, user=self.user, password=self.password, zone=self.zone)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff">         rfiles = []</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">         rdirs = []</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        rfile = {}</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        date = None</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for result in session.query(Collection.name, DataObject.name, DataObject.size, DataObject.owner_name, DataObject.modify_time).filter(User.name == self.user).get_results():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            # if the user is biomaj : he will have access to all the irods data (biomaj ressource) : drwxr-xr-x</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            # Avoid duplication</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if rfile != {} and rfile['name'] == str(result[DataObject.name]) and date == str(result[DataObject.modify_time]).split(" ")[0].split('-'):</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                continue</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile = {}</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            date = str(result[DataObject.modify_time]).split(" ")[0].split('-')</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['permissions'] = "-rwxr-xr-x"</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['size'] = int(result[DataObject.size])</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['month'] = int(date[1])</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['day'] = int(date[2])</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['year'] = int(date[0])</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['name'] = str(result[DataObject.name])</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['download_path'] = str(result[Collection.name])</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfiles.append(rfile)</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        session.cleanup()</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        raise Exception("IRODS:NotSupported")</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">         return (rfiles, rdirs)</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">     def download(self, local_dir, keep_dirs=True):</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -65,67 +45,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">         :return: list of downloaded files</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">         '''</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">         logging.debug('IRODS:Download')</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        try:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            os.chdir(local_dir)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        except TypeError:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            logging.error("IRODS:list:Could not find offline_dir")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        nb_files = len(self.files_to_download)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        cur_files = 1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # give a working directory to copy the file from irods</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        remote_dir = self.remote_dir</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for rfile in self.files_to_download:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if self.kill_received:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                raise Exception('Kill request received, exiting')</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            file_dir = local_dir</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if 'save_as' not in rfile or rfile['save_as'] is None:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                rfile['save_as'] = rfile['name']</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if keep_dirs:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                file_dir = local_dir + os.path.dirname(rfile['save_as'])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            file_path = file_dir + '/' + os.path.basename(rfile['save_as'])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" 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="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            # For unit tests only, workflow will take in charge directory creation before to avoid thread multi access</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if not os.path.exists(file_dir):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                os.makedirs(file_dir)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            logging.debug('IRODS:Download:Progress:' + str(cur_files) + '/' + str(nb_files) + ' downloading file ' + rfile['name'])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            logging.debug('IRODS:Download:Progress:' + str(cur_files) + '/' + str(nb_files) + ' save as ' + rfile['save_as'])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            cur_files += 1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            start_time = datetime.now()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            start_time = time.mktime(start_time.timetuple())</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            self.remote_dir = rfile['root']</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" 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="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            error = self.irods_download(file_dir, str(self.remote_dir), str(rfile['name']))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if error:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                rfile['download_time'] = 0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                rfile['error'] = True</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                raise Exception("IRODS:Download:Error:" + rfile['root'] + '/' + rfile['name'])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" 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="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            else:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                archive_status = Utils.archive_check(file_path)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if not archive_status:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    self.logger.error('Archive is invalid or corrupted, deleting file')</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    rfile['error'] = True</span></span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    if os.path.exists(file_path):</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        os.remove(file_path)</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    raise Exception("IRODS:Download:Error:" + rfile['root'] + '/' + rfile['name'])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            end_time = datetime.now()</span></span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            end_time = time.mktime(end_time.timetuple())</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            rfile['download_time'] = end_time - start_time</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            self.set_permissions(file_path, rfile)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.remote_dir = remote_dir</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return(self.files_to_download)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        raise Exception("IRODS:NotSupported")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff">     def irods_download(self, file_dir, file_path, file_to_download):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        error = False</span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        logging.debug('IRODS:IRODS DOWNLOAD')</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        session = iRODSSession(host=self.server, port=self.port, user=self.user, password=self.password, zone=self.zone)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        try:</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            file_to_get = str(file_path) + str(file_to_download)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            # Write the file to download in the wanted file_dir : with the python-irods iget</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            obj = session.data_objects.get(file_to_get, file_dir)</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        except ExceptionIRODS as e:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            logging.error("RsyncError:" + str(e))</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            logging.error("RsyncError: irods object" + str(obj))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        session.cleanup()</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return(error)</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return("irods not supported")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> class ExceptionIRODS(Exception):</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">remove_irods.patch</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="19359a61ae2446b51b549167b014da2fcf265768">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>

<hr>

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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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2

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2

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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>

</pre>

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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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5

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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>==0.1<span class="idiff left right">1.2</span></span>

</pre>

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5

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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>==0.1<span class="idiff left right">3.0</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/redis" rel="nofollow noreferrer noopener" target="_blank">redis</a></span>

</pre>

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7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/PyYAML" rel="nofollow noreferrer noopener" target="_blank">PyYAML</a></span>

</pre>

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ flask</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/python-consul" rel="nofollow noreferrer noopener" target="_blank">python-consul</a></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/prometheus_client" rel="nofollow noreferrer noopener" target="_blank">prometheus_client</a>>=0.0.18</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/requests" rel="nofollow noreferrer noopener" target="_blank">requests</a></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC13" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biomaj_core" rel="nofollow noreferrer noopener" target="_blank">biomaj_core</a>>=3.0.1<span class="idiff left right">2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biomaj_core" rel="nofollow noreferrer noopener" target="_blank">biomaj_core</a>>=3.0.1<span class="idiff left right">6</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biomaj_zipkin" rel="nofollow noreferrer noopener" target="_blank">biomaj_zipkin</a></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/flake8" rel="nofollow noreferrer noopener" target="_blank">flake8</a></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/humanfriendly" rel="nofollow noreferrer noopener" target="_blank">humanfriendly</a></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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="22" 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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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="23" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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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<td class="diff-line-num new_line old" data-linenumber="24" 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="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.<span class="idiff left right">19</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" 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="24" 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="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.<span class="idiff left right">21</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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="27" 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="LC27" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#   3 - Alpha</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="46" 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">@@ -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>

</pre>

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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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<td class="diff-line-num old_line" data-linenumber="48" 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="LC48" class="line" lang="python">                         <span class="s" style="color: #d14;">'py-bcrypt'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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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<td class="diff-line-num new_line old" data-linenumber="49" 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="LC49" class="line" lang="python">                         <span class="s" style="color: #d14;">'pika==0.1<span class="idiff left right">1.2</span>'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="50" 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="49" 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="LC49" class="line" lang="python">                         <span class="s" style="color: #d14;">'pika==0.1<span class="idiff left right">3.0</span>'</span><span class="p">,</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" 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="LC51" class="line" lang="python">                         <span class="s" style="color: #d14;">'PyYAML'</span><span class="p">,</span></span>

</pre>

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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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<br>

</li>

<li id="a5b5d0c7b9c558d9142a199ec517b633dd40faf5">

<a href="https://salsa.debian.org/med-team/biomaj3-download/compare/cafc530e3f261d5b92a7f34fd873edc2b7708eaf...ed679a76b1b461ea9a602d52c04a8dad1d429b14#a5b5d0c7b9c558d9142a199ec517b633dd40faf5"><strong>tests/biomaj_tests.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" 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="320" 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">@@ -320,21 +320,21 @@ class TestBiomajDirectFTPDownload(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC320" 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="LC321" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">  <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_ftp_list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python">    <span class="n" style="color: #333;">file_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/<span class="idiff left right">blast/db/FASTA/alu.n.gz.md5</span>'</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC324" 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;">DirectFTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp.<span class="idiff left right">ncbi.nih.gov</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="325" 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="323" 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="LC323" class="line" lang="python">    <span class="n" style="color: #333;">file_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/<span class="idiff left right">debian/doc/mailing-lists.txt</span>'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="325" 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="324" 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="LC324" 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;">DirectFTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp.<span class="idiff left right">fr.debian.org</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" 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;">set_files_to_download</span><span class="p">(</span><span class="n" style="color: #333;">file_list</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="326" 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="LC326" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" 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="327" 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="LC327" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="328" 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">

328

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<td class="diff-line-num new_line" data-linenumber="328" 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">

328

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<pre style="margin: 0;"> <span id="LC328" 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;">file_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="329" 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">

329

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<td class="diff-line-num new_line" data-linenumber="329" 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="LC329" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="330" 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">

330

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<td class="diff-line-num new_line" data-linenumber="330" 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="LC330" class="line" lang="python">  <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="331" 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">

331

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<td class="diff-line-num new_line old" data-linenumber="331" 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="LC331" class="line" lang="python">    <span class="n" style="color: #333;">file_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/<span class="idiff left right">blast/db/FASTA/alu.n.gz.md5</span>'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="332" 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">

332

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<td class="diff-line-num new_line old" data-linenumber="331" 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="LC332" 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;">DirectFTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp.<span class="idiff left right">ncbi.nih.gov</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="333" 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="331" 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">

331

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python">    <span class="n" style="color: #333;">file_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/<span class="idiff left right">debian/doc/mailing-lists.txt</span>'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="333" 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="332" 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="LC332" 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;">DirectFTPDownload</span><span class="p">(</span><span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp.<span class="idiff left right">fr.debian.org</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="333" 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">

333

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<td class="diff-line-num new_line" data-linenumber="333" 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="LC333" 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;">set_files_to_download</span><span class="p">(</span><span class="n" style="color: #333;">file_list</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="334" 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="334" 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="LC334" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="335" 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">

335

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<td class="diff-line-num new_line" data-linenumber="335" 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">

335

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<pre style="margin: 0;"> <span id="LC335" 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 class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="336" 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">

336

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<td class="diff-line-num new_line" data-linenumber="336" 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="LC336" 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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="337" 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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<td class="diff-line-num new_line old" data-linenumber="337" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC337" 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="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;">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;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span><span class="s" style="color: #d14;">'<span class="idiff left right">alu.n.gz.md5</span>'</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="338" 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="337" 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="LC337" 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="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;">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;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span><span class="s" style="color: #d14;">'<span class="idiff left right">mailing-lists.txt</span>'</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="338" 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="338" 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="LC338" class="line" lang="python"></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="s" style="color: #d14;">'directhttp'</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" 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">@@ -431,17 +431,14 @@ class TestBiomajFTPDownload(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">  <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_ftp_list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC433" 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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<pre style="margin: 0;">-<span id="LC434" 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="LC434" 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="LC435" 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="LC436" 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;">file_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">  <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="s" style="color: #d14;">'test'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python">  <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new_line old" data-linenumber="440" 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="LC441" 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="LC440" 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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<pre style="margin: 0;"> <span id="LC441" 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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<td class="diff-line-num new_line old" data-linenumber="442" 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="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>

</pre>

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<pre style="margin: 0;"> <span id="LC442" 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="LC443" 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="LC444" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" 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="450" 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">@@ -453,11 +450,9 @@ class TestBiomajFTPDownload(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC450" 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="LC451" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC452" 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="LC453" 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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<pre style="margin: 0;"> <span id="LC454" 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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<pre style="margin: 0;"> <span id="LC455" 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="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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<pre style="margin: 0;"> <span id="LC456" 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="LC457" 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="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;">close</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="465" 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="460" 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">@@ -465,19 +460,19 @@ class TestBiomajFTPDownload(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC460" 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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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC462" 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.<span class="idiff left">ncbi.nih.gov'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'/blast</span>/'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="463" 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="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;">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.<span class="idiff left">fr.debian.org'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'/debian</span>/'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="464" 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="LC464" 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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="465" 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="LC465" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC471" 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'^d<span class="idiff left right">b/FASTA/alu.*\.gz</span>$'</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>

</pre>

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<pre style="margin: 0;">+<span id="LC466" 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'^d<span class="idiff left right">oc/mailing-lists.txt</span>$'</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="467" 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="LC467" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: "</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>

</pre>

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<pre style="margin: 0;"> <span id="LC469" 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;">skipTest</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping test due to remote server error"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC470" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC471" 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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="472" 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="LC477" 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;"><span class="idiff left right">2</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC472" 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;"><span class="idiff left right">1</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python">  <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_download_or_copy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="475" 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="LC480" 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.<span class="idiff left">ncbi.nih.gov'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'/blast</span>/'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="475" 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="LC475" 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.<span class="idiff left">fr.debian.org'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'/debian</span>/'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="481" 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="476" 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="LC476" 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;">files_to_download</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<td class="diff-line-num old_line" data-linenumber="482" 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="477" 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="LC477" class="line" lang="python">          <span class="p">{</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span><span class="s" style="color: #d14;">'/test1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">:</span> <span class="s" style="color: #d14;">'2013'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">:</span> <span class="s" style="color: #d14;">'11'</span><span class="p">,</span> <span class="s" style="color: #d14;">'day'</span><span class="p">:</span> <span class="s" style="color: #d14;">'10'</span><span class="p">,</span> <span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="mi" style="color: #099;">10</span><span class="p">},</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python">          <span class="p">{</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span><span class="s" style="color: #d14;">'/test2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">:</span> <span class="s" style="color: #d14;">'2013'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">:</span> <span class="s" style="color: #d14;">'11'</span><span class="p">,</span> <span class="s" style="color: #d14;">'day'</span><span class="p">:</span> <span class="s" style="color: #d14;">'10'</span><span class="p">,</span> <span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="mi" style="color: #099;">10</span><span class="p">},</span></span>

</pre>

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