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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/biomaj3-core">Debian Med / biomaj3-core</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0">921d3c65</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-17T09:28:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.26</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#c2a77122dea90d24656cdf9c52e8ea0eec079673">
biomaj_core/config.py
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<li class="file-stats">
<a href="#069849a9be10cc3a9a83d68a6da4a50907b711ea">
biomaj_core/utils.py
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">arch</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ppc64le</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">amd64</span></span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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;">2.7'</span></span>
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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="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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<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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" 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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<td class="diff-line-num new_line" data-linenumber="9" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" 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="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.7'</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.8'</span></span>
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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="yaml"><span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">except</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">/^feature.*$/"</span></span>
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<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">3.0.19 [unreleased]:</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0.26:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> check use_ldap and use_elastic as bool (true/false or 0/1)</span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">3.0.25:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> utils/get_folder_size: if file not found, catch error and continue</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">3.0.24:</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> get_more_recent_file, return also file info</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">3.0.23:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> PR #9 Add missing ssh defaults for download</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">3.0.21 [3.0.22 ,tag issue]:</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Pin elasticsearch dependency, v7 breaks some API calls</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">3.0.20:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> PR #7 from institut-de-genomique/retry_method, rename default values of retryer.</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Rename wait_condition to wait_policy in default values</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> PR #6 from institut-de-genomique/retry_method, add default values for retryer</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Add default values for retryer (see the corresponding branch biomaj-download).</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">3.0.19:</span>
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2
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Add ftps and directftps protocols</span>
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3
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> #4 Harden hardlinks</span>
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4
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> copy_files_with_regexp: remove duplicates</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Add utils fonctions</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Code cleanup</span>
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5
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">3.0.18:</span>
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6
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Allow to use hardlinks in copy_files and copy_files_with_regexp</span>
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7
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">3.0.17:</span>
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<li id="c2a77122dea90d24656cdf9c52e8ea0eec079673">
<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#c2a77122dea90d24656cdf9c52e8ea0eec079673"><strong>biomaj_core/config.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,11 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'keep.old.sessions'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">'docker.sudo'</span><span class="p">:</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">'auto_publish'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'use_hardlinks'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'use_hardlinks'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">'wait_policy'</span><span class="p">:</span> <span class="s" style="color: #d14;">'wait_fixed(3)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'stop_condition'</span><span class="p">:</span> <span class="s" style="color: #d14;">'stop_after_attempt(3)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'ssh_hosts_file'</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="s" style="color: #d14;">'~/.ssh/known_hosts'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'ssh_new_host'</span><span class="p">:</span> <span class="s" style="color: #d14;">'reject'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Old biomaj level compatibility</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -361,12 +365,12 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">'db.fullname is not set'</span><span class="p">)</span></span>
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362
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'db.formats'</span><span class="p">):</span></span>
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">'db.formats is not set'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'use_ldap'</span><span class="p">):</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">_bool</span></span><span class="p">(</span><span class="s" style="color: #d14;">'use_ldap'</span><span class="p">):</span></span>
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'ldap.host'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'ldap.port'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'ldap.dn'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'use_ldap set to 1 but missing configuration'</span><span class="p">)</span></span>
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368
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'use_elastic'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get<span class="idiff left right">_bool</span></span><span class="p">(</span><span class="s" style="color: #d14;">'use_elastic'</span><span class="p">):</span></span>
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370
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'elastic_nodes'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'elastic_index'</span><span class="p">):</span></span>
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'use_elastic set to 1 but missing configuration'</span><span class="p">)</span></span>
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372
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#069849a9be10cc3a9a83d68a6da4a50907b711ea"><strong>biomaj_core/utils.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" 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">@@ -126,13 +126,17 @@ class Utils(object):</td>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> :param folder: directory path</span></span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> :type folder: str</span></span>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="s" style="color: #d14;">'biomaj'</span><span class="p">)</span></span>
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129
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>
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130
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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131
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">folder_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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132
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">dirs</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>
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133
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ffile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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134
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">ffile</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">folder_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">folder_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'[stat][size] file not found %s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">folder_size</span></span>
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137
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>
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138
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="161" 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">@@ -157,7 +161,7 @@ class Utils(object):</td>
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157
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># release = None</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">rfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'year'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">],</span> <span class="s" style="color: #d14;">'month'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">],</span> <span class="s" style="color: #d14;">'day'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]}</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'year'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">],</span> <span class="s" style="color: #d14;">'month'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">],</span> <span class="s" style="color: #d14;">'day'</span><span class="p">:</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'file'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rfile</span></span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">rel_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">file_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]))</span></span>
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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">@@ -165,6 +169,7 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span></span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'day'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">release</span><span class="p">[</span><span class="s" style="color: #d14;">'file'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rfile</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">release</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/mock" rel="nofollow noreferrer noopener" target="_blank">mock</a></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/future" rel="nofollow noreferrer noopener" target="_blank">future</a></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/elasticsearch" rel="nofollow noreferrer noopener" target="_blank">elasticsearch</a></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/elasticsearch" rel="nofollow noreferrer noopener" target="_blank">elasticsearch</a><span class="idiff left right">==5.5.3</span></span>
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<pre style="margin: 0;"> <span id="LC5" 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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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,11 +17,12 @@ with open(os.path.join(here, 'CHANGES.txt')) as f:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="s" style="color: #d14;">'BioMAJ core library'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'long_description'</span><span class="p">:</span> <span class="n" style="color: #333;">README</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">CHANGES</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'long_description_content_type'</span><span class="p">:</span> <span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'author'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Olivier Sallou'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'download_url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'author_email'</span><span class="p">:</span> <span class="s" style="color: #d14;">'olivier.sallou@irisa.fr'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.<span class="idiff left right">19</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.<span class="idiff left right">26</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'classifiers'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 5 - Production/Stable'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'Environment :: Console'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,8 +37,7 @@ config = {</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that you indicate whether you support Python 2, Python 3 or both.</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 2'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 2.7'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.4'</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'install_requires'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'future'</span><span class="p">,</span></span>
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