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<h3>
Olivier Sallou pushed to branch master
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/8c8e541f4f9538222ad7524bd2d61d5e7f7f17e3">8c8e541f</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-10-16T13:14:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.19</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-core/commit/cf50b621a96866c41a73d0cd624c2a6b70807167">cf50b621</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-10-16T13:14:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.0.19'
Update to upstream version '3.0.19'
with Debian dir 26a36730c4a70b5b50553c146ad0b2d519140595</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-core/commit/618bb2fc27e628623bf89c0ed7cdcc174e28ee66">618bb2fc</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-10-16T13:15:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release 3.0.19
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-core/commit/b2f2c94b5db84f54ab08f624766354587dfb192a">b2f2c94b</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-10-16T13:30:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set to unreleased
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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</li>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#a5b5d0c7b9c558d9142a199ec517b633dd40faf5">
tests/biomaj_tests.py
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</li>
<li class="file-stats">
<a href="#333adc8a2fe990b188d6baf64f9a272a1cd87d5e">
<span class="new-file">
+
tests/global_hardlinks.properties
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<li class="file-stats">
<a href="#86519cd9b3a0739fe0d9127d90925f2a92b2cdc2">
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+
tests/hardlinks.properties
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</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#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;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<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="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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<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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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 old old_line" data-linenumber="6" 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="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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="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: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">except</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" 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/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#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="LC2" class="line" lang="plaintext"> Add ftps and directftps protocols</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> #4 Harden hardlinks</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> copy_files_with_regexp: remove duplicates</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">3.0.18:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Allow to use hardlinks in copy_files and copy_files_with_regexp</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">3.0.17:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Fix --log option</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">3.0.16:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Add some warnings if some file is missing</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">3.0.15:</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -8,3 +8,5 @@ Properties can be overriden by environment variables with pattern BIOMAJ_X_Y_Z f</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown">Example:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">use BIOMAJ_LDAP_HOST for ldap.host</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![PyPI version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badge.fury.io/py/biomaj-core.svg</span><span class="p">)</span>](https://badge.fury.io/py/biomaj-core)</span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#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">@@ -8,6 +8,7 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biomaj_core.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Utils</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biomaj_core.bmajindex</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BmajIndex</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;"><</span> <span class="s" style="color: #d14;">'3'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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">@@ -40,8 +41,10 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'db.type'</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="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'db.formats'</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="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'keep.old.version'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="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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<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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<pre style="margin: 0;">-<span id="LC44" 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>
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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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<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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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC50" 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="diff-line-num unfold js-unfold new_line" data-linenumber="194" 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">@@ -191,9 +194,11 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_option</span><span class="p">(</span><span class="s" style="color: #d14;">'log'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">hdlr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LOGLEVEL</span><span class="p">[</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_option</span><span class="p">(</span><span class="s" style="color: #d14;">'log'</span><span class="p">)])</span></span>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LOGLEVEL</span><span class="p">[</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_option</span><span class="p">(</span><span class="s" style="color: #d14;">'log'</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC197" 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;">setLevel</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;">log_level</span><span class="p">)</span></span>
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194
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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195
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">hdlr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LOGLEVEL</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'historic.logfile.level'</span><span class="p">)])</span></span>
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196
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200
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<pre style="margin: 0;"> <span id="LC200" 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;">log_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LOGLEVEL</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;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'historic.logfile.level'</span><span class="p">)]</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" 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;">setLevel</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;">log_level</span><span class="p">)</span></span>
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197
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%(asctime)</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%(levelname)-5.5</span><span class="s" style="color: #d14;">s [</span><span class="si" style="color: #d14;">%(name)</span><span class="s" style="color: #d14;">s][</span><span class="si" style="color: #d14;">%(threadName)</span><span class="s" style="color: #d14;">s] </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span></span>
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198
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">hdlr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">formatter</span><span class="p">)</span></span>
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199
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">hdlr</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">@@ -281,19 +286,9 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;"> Get a boolean property from bank or general configration. Optionally in section.</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">section</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">escape</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_in_env</span><span class="p">(</span><span class="n" style="color: #333;">prop</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_in_env</span><span class="p">(</span><span class="n" style="color: #333;">prop</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">prop</span><span class="p">,</span> <span class="n" style="color: #333;">section</span><span class="p">,</span> <span class="n" style="color: #333;">escape</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'true'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_bool</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">prop</span><span class="p">,</span> <span class="n" style="color: #333;">section</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GENERAL'</span><span class="p">,</span> <span class="n" style="color: #333;">escape</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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">@@ -402,8 +397,8 @@ class BiomajConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC397" 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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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">protocol</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'protocol'</span><span class="p">)</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">allowed_protocols</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'none'</span><span class="p">,</span> <span class="s" style="color: #d14;">'multi'</span><span class="p">,</span> <span class="s" style="color: #d14;">'local'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">sftp'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'http</span>'</span><span class="p">,</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">https'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'directftp</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttps'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rsync'</span><span class="p">,</span> <span class="s" style="color: #d14;">'irods'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">allowed_protocols</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'none'</span><span class="p">,</span> <span class="s" style="color: #d14;">'multi'</span><span class="p">,</span> <span class="s" style="color: #d14;">'local'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">ftps'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'http'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'https</span>'</span><span class="p">,</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">directftp'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'directftps</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttps'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rsync'</span><span class="p">,</span> <span class="s" style="color: #d14;">'irods'</span><span class="p">]</span></span>
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407
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protocol</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">allowed_protocols</span><span class="p">:</span></span>
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408
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Protocol not supported: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">protocol</span><span class="p">)</span></span>
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409
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404
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<pre style="margin: 0;"> <span id="LC404" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="412" 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">@@ -417,7 +412,7 @@ class BiomajConfig(object):</td>
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417
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'remote.dir'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">):</span></span>
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418
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'remote.dir must end with a /'</span><span class="p">)</span></span>
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419
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protocol</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'direc<span class="idiff left right">ftp</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttps'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span>\</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protocol</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'direc<span class="idiff left">tftp'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'directftps</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directhttps'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span>\</span>
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421
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'remote.files'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span>\</span>
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422
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'remote.list'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'remote.files not set'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#069849a9be10cc3a9a83d68a6da4a50907b711ea"><strong>biomaj_core/utils.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">errno</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</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">@@ -152,17 +153,18 @@ class Utils(object):</td>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> Each file is a dict like with (at least) parameters: year, month, day</span></span>
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154
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" 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;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC157" 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="LC158" 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="LC159" 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="LC161" 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="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">release</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" 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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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" 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="o" style="font-weight: 600;">.</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="LC161" 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="o" style="font-weight: 600;">.</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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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_date</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rel_date</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">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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<pre style="margin: 0;">-<span id="LC164" 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="LC165" 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="LC162" 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="o" style="font-weight: 600;">.</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="LC163" 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="o" style="font-weight: 600;">.</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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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_date</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rel_date</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC166" 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="LC167" 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="LC168" 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="LC169" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC170" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +197,8 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="p">}[</span><span class="n" style="color: #333;">date</span><span class="p">]</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></span>
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199
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<pre style="margin: 0;"> <span id="LC199" 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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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_files</span><span class="p">(</span><span class="n" style="color: #333;">files_to_copy</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">move</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_files</span><span class="p">(</span><span class="n" style="color: #333;">files_to_copy</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">move</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> Copy or move files to to_dir, keeping directory structure.</span></span>
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -214,6 +217,8 @@ class Utils(object):</td>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> :type move: bool</span></span>
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215
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;"> :param lock: thread lock object for multi-threads</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> :type lock: Lock</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> :param use_hardlinks: use hard links (if possible)</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> :type link: bool</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC223" 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="o" style="font-weight: 600;">.</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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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">nb_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">files_to_copy</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="249" 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">@@ -244,14 +249,48 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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245
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mktime</span><span class="p">(</span><span class="n" style="color: #333;">start_time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">timetuple</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_hardlinks</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC253" 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="LC254" 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;">link</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC255" 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;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Using hardlinks to copy </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ENOSYS</span><span class="p">,</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ENOTSUP</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Your system doesn't support hard links. Using regular copy."</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file (the stats are copied at the end</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of the function)</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EPERM</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"The FS at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s doesn't support hard links. Using regular copy."</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file (the stats are copied at the end</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of the function)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EXDEV</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Cross device hard link is impossible (source: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, dest: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s). Using regular copy."</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">)</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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248
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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249
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mktime</span><span class="p">(</span><span class="n" style="color: #333;">end_time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">timetuple</span><span class="p">())</span></span>
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250
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'download_time'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_time</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_time</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">use_hardlinks</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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252
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"></span>
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253
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291
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<pre style="margin: 0;"> <span id="LC291" 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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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_files_with_regexp</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">regexps</span><span class="p">,</span> <span class="n" style="color: #333;">move</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_files_with_regexp</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">regexps</span><span class="p">,</span> <span class="n" style="color: #333;">move</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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255
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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256
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;"> Copy or move files from from_dir to to_dir matching regexps.</span></span>
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257
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> Copy keeps the original file stats.</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">@@ -266,20 +305,28 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"><span class="s" style="color: #d14;"> :type move: bool</span></span>
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267
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"><span class="s" style="color: #d14;"> :param lock: thread lock object for multi-threads</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"><span class="s" style="color: #d14;"> :type lock: Lock</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"><span class="s" style="color: #d14;"> :param use_hardlinks: use hard links (if possible)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="s" style="color: #d14;"> :type link: bool</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;"> :return: list of copied files with their size</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC312" 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="o" style="font-weight: 600;">.</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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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">files_to_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root</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="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;">walk</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">topdown</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">files_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">files</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;">walk</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">topdown</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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274
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">reg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">regexps</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">file_relative_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</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="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_relative_path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">file_relative_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_relative_path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sometimes files appear twice.... check not already managed</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_relative_path</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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279
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"**/*"</span><span class="p">:</span></span>
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280
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">files_to_copy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span> <span class="n" style="color: #333;">file_relative_path</span><span class="p">})</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">files_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">file_relative_path</span><span class="p">)</span></span>
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281
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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282
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">reg</span><span class="p">,</span> <span class="n" style="color: #333;">file_relative_path</span><span class="p">):</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">files_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">file_relative_path</span><span class="p">)</span></span>
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283
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">files_to_copy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">'name'</span><span class="p">:</span> <span class="n" style="color: #333;">file_relative_path</span><span class="p">})</span></span>
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284
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" 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="352" 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">@@ -305,8 +352,43 @@ class Utils(object):</td>
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">move</span><span class="p">:</span></span>
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306
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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307
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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308
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<td class="diff-line-num new_line old" data-linenumber="355" 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="LC308" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_hardlinks</span><span class="p">:</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" 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;">link</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" 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;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Using hardlinks to copy </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ENOSYS</span><span class="p">,</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ENOTSUP</span><span class="p">):</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Your system doesn't support hard links. Using regular copy."</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" 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;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file (the stats are copied at the end</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of the function)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</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="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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;">elif</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EPERM</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="370" 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">
370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"The FS at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s doesn't support hard links. Using regular copy."</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" 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;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">)</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file (we copy the stats here because</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it's not done at the end of the function)</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</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;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EXDEV</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Cross device hard link is impossible (source: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, dest: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s). Using regular copy."</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" 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;">warn</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy this file (we copy the stats here because</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it's not done at the end of the function)</span></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't try links anymore</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copystat</span><span class="p">(</span><span class="n" style="color: #333;">from_file</span><span class="p">,</span> <span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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310
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'size'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">getsize</span><span class="p">(</span><span class="n" style="color: #333;">to_file</span><span class="p">)</span></span>
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">f_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromtimestamp</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;">getmtime</span><span class="p">(</span><span class="n" style="color: #333;">to_file</span><span class="p">))</span></span>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f_stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">year</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">@@ -384,3 +466,28 @@ class Utils(object):</td>
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384
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">archivefile</span><span class="p">)</span></span>
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC470" 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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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_bool</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="474" 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">
474
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<pre style="margin: 0;">+<span id="LC474" 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;">value</span><span class="p">:</span></span>
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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">
475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="476" 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">
476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="477" 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">
477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'true'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="478" 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">
478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="479" 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">
479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="480" 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">
480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="481" 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">
481
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<pre style="margin: 0;">+<span id="LC481" 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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<td class="diff-line-num new new_line" data-linenumber="482" 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">
482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="483" 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">
483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="484" 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">
484
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<pre style="margin: 0;">+<span id="LC484" 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 new new_line" data-linenumber="485" 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">
485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_int</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="486" 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">
486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="488" 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">
488
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC488" 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;">value</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="489" 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">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="490" 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">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="491" 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">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="492" 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">
492
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<pre style="margin: 0;">+<span id="LC492" 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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<td class="diff-line-num new new_line" data-linenumber="493" 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">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biomaj3-core (3.0.19-1) UNRELEASED; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<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"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Wed, 16 Oct 2019 13:14:38 +0000</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">biomaj3-core (3.0.16-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release </span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ config = {</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'download_url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'author_email'</span><span class="p">:</span> <span class="s" style="color: #d14;">'olivier.sallou@irisa.fr'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">6</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">9</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'classifiers'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="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="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'Environment :: Console'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#a5b5d0c7b9c558d9142a199ec517b633dd40faf5"><strong>tests/biomaj_tests.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.attrib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">attr</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">stat</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +27,7 @@ class UtilsForTest:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> Setup the temp dirs and files.</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties_hl</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bank_properties</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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28
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">(</span><span class="s" style="color: #d14;">'biomaj'</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">@@ -50,6 +54,9 @@ class UtilsForTest:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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51
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<pre style="margin: 0;"> <span id="LC55" 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;">__copy_global_properties</span><span class="p">()</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties_hl</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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;">__copy_global_properties_hl</span><span class="p">()</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bank_properties</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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54
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<pre style="margin: 0;"> <span id="LC61" 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;">__copy_test_bank_properties</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +93,8 @@ class UtilsForTest:</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'error.properties'</span><span class="p">,</span> <span class="s" style="color: #d14;">'local.properties'</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'localprocess.properties'</span><span class="p">,</span> <span class="s" style="color: #d14;">'testhttp.properties'</span><span class="p">,</span></span>
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88
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">'computed.properties'</span><span class="p">,</span> <span class="s" style="color: #d14;">'computed2.properties'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'sub1.properties'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sub2.properties'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'sub1.properties'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sub2.properties'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">'hardlinks.properties'</span><span class="p">]</span></span>
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90
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">prop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">properties</span><span class="p">:</span></span>
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91
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">from_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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">curdir</span><span class="p">,</span> <span class="n" style="color: #333;">prop</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">to_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;">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;">conf_dir</span><span class="p">,</span> <span class="n" style="color: #333;">prop</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="134" 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">@@ -126,6 +134,29 @@ class UtilsForTest:</td>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">fout</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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128
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__copy_global_properties_hl</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties_hl</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties_hl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">conf_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'global_hardlinks.properties'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">curdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">global_template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">curdir</span><span class="p">,</span> <span class="s" style="color: #d14;">'global_hardlinks.properties'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</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;">global_properties_hl</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC144" 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;">global_template</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;">fin</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fin</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'conf.dir'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"conf.dir="</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">conf_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'log.dir'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"log.dir="</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'data.dir'</span><span class="p">):</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"data.dir="</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'process.dir'</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"process.dir="</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">process_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'lock.dir'</span><span class="p">):</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"lock.dir="</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lock_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">fout</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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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>
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129
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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130
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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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestBiomajUtils</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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131
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="163" 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="194" 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">@@ -163,6 +194,24 @@ class TestBiomajUtils(unittest.TestCase):</td>
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163
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">endpoint</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;">get_service_endpoint</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="s" style="color: #d14;">'process'</span><span class="p">)</span></span>
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164
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195
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<pre style="margin: 0;"> <span id="LC195" 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;">endpoint</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'http://localhost'</span><span class="p">)</span></span>
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165
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_use_hardlinks_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> Test that hardlinks are disabled by default and can be overridden.</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties</span><span class="p">,</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">allow_user_config</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Must be disabled in local.properties</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BiomajConfig</span><span class="p">(</span><span class="s" style="color: #d14;">'local'</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertFalse</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_bool</span><span class="p">(</span><span class="s" style="color: #d14;">"use_hardlinks"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Must be enabled for hardlinks.properties (override)</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BiomajConfig</span><span class="p">(</span><span class="s" style="color: #d14;">'hardlinks'</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_bool</span><span class="p">(</span><span class="s" style="color: #d14;">"use_hardlinks"</span><span class="p">))</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Reload file with use_hardlinks=1</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">BiomajConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_config</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">global_properties_hl</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">allow_user_config</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BiomajConfig</span><span class="p">(</span><span class="s" style="color: #d14;">'local'</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_bool</span><span class="p">(</span><span class="s" style="color: #d14;">"use_hardlinks"</span><span class="p">))</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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166
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mimes</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="LC216" class="line" lang="python"> <span class="n" style="color: #333;">fasta_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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span></span>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">'bank/test2.fasta'</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">@@ -186,6 +235,39 @@ class TestBiomajUtils(unittest.TestCase):</td>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy_files_with_regexp</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'.*</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">.py'</span><span class="p">])</span></span>
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187
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236
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<pre style="margin: 0;"> <span id="LC236" 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;">to_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'/biomaj_tests.py'</span><span class="p">))</span></span>
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188
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_copy_with_regexp_hardlink</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="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> Test copy with hardlinks: we create files in data_dir and try to</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> link them. This should work unless /tmp don't accept hardlinks.</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create 5 files and a directory in data_dir. We don't destroy them</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># since they are in /tmp.</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".dat"</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">regexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".*</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">orig_file_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkstemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">suffix</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">to_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="LC252" class="line" lang="python"> <span class="n" style="color: #333;">new_file_full</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">to_dir</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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orig_file_full</span><span class="p">]</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">from_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy_files_with_regexp</span><span class="p">(</span><span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">regexp</span><span class="p">],</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">use_hardlinks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if files was copied</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="n" style="color: #333;">new</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">orig_file_full</span><span class="p">,</span> <span class="n" style="color: #333;">new_file_full</span><span class="p">):</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" 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;">new</span><span class="p">))</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if it's really a hardlink. This may fail so we catch</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># any exceptions.</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">orig_file_stat</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;">stat</span><span class="p">(</span><span class="n" style="color: #333;">orig</span><span class="p">)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">new_file_stat</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;">stat</span><span class="p">(</span><span class="n" style="color: #333;">new</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" 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;">orig_file_stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_ino</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">new_file_stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_ino</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" 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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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"In </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: copy worked but hardlinks were not used."</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">()</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"></span>
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189
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_copy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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190
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">from_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">local_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'biomaj_tests.py'</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">@@ -194,6 +276,33 @@ class TestBiomajUtils(unittest.TestCase):</td>
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194
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy_files</span><span class="p">(</span><span class="n" style="color: #333;">files_to_copy</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">)</span></span>
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195
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277
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<pre style="margin: 0;"> <span id="LC277" 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;">to_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'/biomaj_tests.py'</span><span class="p">))</span></span>
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196
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_copy_hardlink</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> Test copy with hardlinks: we create a file in data_dir and try to</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> link it. This should work unless /tmp don't accept hardlinks.</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create a file and a directory in data_dir. We don't destroy them</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># since they are in /tmp.</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">orig_file_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkstemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">orig_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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">orig_file_full</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">to_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="LC289" class="line" lang="python"> <span class="n" style="color: #333;">new_file_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">orig_file</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">from_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">data_dir</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">files_to_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[{</span><span class="s" style="color: #d14;">'root'</span><span class="p">:</span> <span class="n" style="color: #333;">from_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'name'</span><span class="p">:</span> <span class="n" style="color: #333;">orig_file</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy_files</span><span class="p">(</span><span class="n" style="color: #333;">files_to_copy</span><span class="p">,</span> <span class="n" style="color: #333;">to_dir</span><span class="p">,</span> <span class="n" style="color: #333;">use_hardlinks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if file was copied</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" 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;">new_file_full</span><span class="p">))</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if it's really a hardlink. This may fail so we catch</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># any exceptions.</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">orig_file_stat</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;">stat</span><span class="p">(</span><span class="n" style="color: #333;">orig_file_full</span><span class="p">)</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">new_file_stat</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;">stat</span><span class="p">(</span><span class="n" style="color: #333;">new_file_full</span><span class="p">)</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" 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;">orig_file_stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_ino</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">new_file_stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_ino</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" 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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<td class="diff-line-num new new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"In </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: copy worked but hardlinks were not used."</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">()</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"></span>
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197
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306
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<pre style="margin: 0;"> <span id="LC306" 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;">'check'</span><span class="p">)</span></span>
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198
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_check_method</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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199
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check .name, .exe and .args are well check during bank configuration</span></span>
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<li id="333adc8a2fe990b188d6baf64f9a272a1cd87d5e">
<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#333adc8a2fe990b188d6baf64f9a272a1cd87d5e"><strong>tests/global_hardlinks.properties</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[GENERAL]</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="properties"><span class="py">test</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="properties"><span class="py">conf.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/config</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="properties"><span class="py">log.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/log</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="properties"><span class="py">process.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/process</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#The root directory where all databases are stored.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#If your data is not stored under one directory hirearchy</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#you can override this value in the database properties file.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="properties"><span class="py">data.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="properties"><span class="py">lock.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/lock</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="properties"><span class="py">cache.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/biomaj/cache</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="properties"><span class="py">use_hardlinks</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="properties"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="properties"><span class="py">db.url</span><span class="p">=</span><span class="s" style="color: #d14;">mongodb://localhost:27017</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="properties"><span class="py">db.name</span><span class="p">=</span><span class="s" style="color: #d14;">biomaj_test</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="properties"></span>
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<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="properties"><span class="py">use_ldap</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="properties"><span class="py">ldap.host</span><span class="p">=</span><span class="s" style="color: #d14;">localhost</span></span>
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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="properties"><span class="py">ldap.port</span><span class="p">=</span><span class="s" style="color: #d14;">389</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="properties"><span class="py">ldap.dn</span><span class="p">=</span><span class="s" style="color: #d14;">nodomain</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="properties"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Use ElasticSearch for index/search capabilities</span></span>
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<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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="properties"><span class="py">use_elastic</span><span class="p">=</span><span class="s" style="color: #d14;">0</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Comma separated list of elasticsearch nodes host1,host2:port2</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="properties"><span class="py">elastic_nodes</span><span class="p">=</span><span class="s" style="color: #d14;">localhost</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="properties"><span class="py">elastic_index</span><span class="p">=</span><span class="s" style="color: #d14;">biomaj_test</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="properties"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="properties"><span class="py">celery.queue</span><span class="p">=</span><span class="s" style="color: #d14;">biomaj</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="properties"><span class="py">celery.broker</span><span class="p">=</span><span class="s" style="color: #d14;">mongodb://localhost:27017/biomaj_celery</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Get directory stats (can be time consuming depending on number of files etc...)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="properties"><span class="py">data.stats</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="properties"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># List of user admin (linux user id, comma separated)</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="properties"><span class="py">admin</span><span class="p">=</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="properties"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Auto publish on updates (do not need publish flag, can be ovveriden in bank property file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="properties"><span class="py">auto_publish</span><span class="p">=</span><span class="s" style="color: #d14;">0</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">########################</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Global properties file</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#To override these settings for a specific database go to its</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#properties file and uncomment or add the specific line you want</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#to override.</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#----------------</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Mail Configuration</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#---------------</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Uncomment thes lines if you want receive mail when the workflow is finished</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="properties"><span class="py">mail.smtp.host</span><span class="p">=</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="properties"><span class="py">mail.admin</span><span class="p">=</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="properties"><span class="py">mail.from</span><span class="p">=</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="properties"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#---------------------</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Proxy authentification</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#---------------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#proxyHost=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#proxyPort=</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#proxyUser=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#proxyPassword=</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="properties"></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Number of thread for processes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="properties"><span class="py">bank.num.threads</span><span class="p">=</span><span class="s" style="color: #d14;">2</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="properties"></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Number of threads to use for downloading</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="properties"><span class="py">files.num.threads</span><span class="p">=</span><span class="s" style="color: #d14;">4</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="properties"></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#to keep more than one release increase this value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="properties"><span class="py">keep.old.version</span><span class="p">=</span><span class="s" style="color: #d14;">0</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="properties"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#----------------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Release configuration</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#----------------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="properties"><span class="py">release.separator</span><span class="p">=</span><span class="s" style="color: #d14;">_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="properties"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#The historic log file is generated in log/</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#define level information for output : DEBUG,INFO,WARN,ERR</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="properties"><span class="py">historic.logfile.level</span><span class="p">=</span><span class="s" style="color: #d14;">DEBUG</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="properties"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#http.parse.dir.line=<a[\s]+href="([\S]+)/".*alt="\[DIR\]">.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="properties"><span class="py">http.parse.dir.line</span><span class="p">=</span><span class="s" style="color: #d14;"><img[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+src="[</span><span class="se" style="color: #d14;">\S</span><span class="s" style="color: #d14;">]+"[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+alt="</span><span class="se" style="color: #d14;">\[</span><span class="s" style="color: #d14;">DIR</span><span class="se" style="color: #d14;">\]</span><span class="s" style="color: #d14;">"[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]*/?>[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]*<a[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+href="([</span><span class="se" style="color: #d14;">\S</span><span class="s" style="color: #d14;">]+)/"[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]*>.*([</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2}-[</span><span class="se" style="color: #d14;">\w\d</span><span class="s" style="color: #d14;">]{2,5}-[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{4}</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2}:[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2})</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="properties"><span class="py">http.parse.file.line</span><span class="p">=</span><span class="s" style="color: #d14;"><img[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+src="[</span><span class="se" style="color: #d14;">\S</span><span class="s" style="color: #d14;">]+"[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+alt="</span><span class="se" style="color: #d14;">\[</span><span class="s" style="color: #d14;">[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+</span><span class="se" style="color: #d14;">\]</span><span class="s" style="color: #d14;">"[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]*/?>[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]<a[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+href="([</span><span class="se" style="color: #d14;">\S</span><span class="s" style="color: #d14;">]+)".*([</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2}-[</span><span class="se" style="color: #d14;">\w\d</span><span class="s" style="color: #d14;">]{2,5}-[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{4}</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2}:[</span><span class="se" style="color: #d14;">\d</span><span class="s" style="color: #d14;">]{2})[</span><span class="se" style="color: #d14;">\s</span><span class="s" style="color: #d14;">]+([</span><span class="se" style="color: #d14;">\d\.</span><span class="s" style="color: #d14;">]+[MKG]{0,1})</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="properties"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="properties"><span class="py">http.group.dir.name</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="properties"><span class="py">http.group.dir.date</span><span class="p">=</span><span class="s" style="color: #d14;">2</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="properties"><span class="py">http.group.file.name</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="properties"><span class="py">http.group.file.date</span><span class="p">=</span><span class="s" style="color: #d14;">2</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="properties"><span class="py">http.group.file.size</span><span class="p">=</span><span class="s" style="color: #d14;">3</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="properties"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="properties"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Bank default access</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="properties"><span class="py">visibility.default</span><span class="p">=</span><span class="s" style="color: #d14;">public</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="properties"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="properties"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[loggers]</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="properties"><span class="py">keys</span> <span class="p">=</span> <span class="s" style="color: #d14;">root, biomaj</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="properties"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[handlers]</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="properties"><span class="py">keys</span> <span class="p">=</span> <span class="s" style="color: #d14;">console</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="properties"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[formatters]</span></span>
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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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="properties"><span class="py">keys</span> <span class="p">=</span> <span class="s" style="color: #d14;">generic</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="properties"></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[logger_root]</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="properties"><span class="py">level</span> <span class="p">=</span> <span class="s" style="color: #d14;">INFO</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="properties"><span class="py">handlers</span> <span class="p">=</span> <span class="s" style="color: #d14;">console</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="properties"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[logger_biomaj]</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="properties"><span class="py">level</span> <span class="p">=</span> <span class="s" style="color: #d14;">DEBUG</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="properties"><span class="py">handlers</span> <span class="p">=</span> <span class="s" style="color: #d14;">console</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="properties"><span class="py">qualname</span> <span class="p">=</span> <span class="s" style="color: #d14;">biomaj</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="properties"><span class="py">propagate</span><span class="p">=</span><span class="s" style="color: #d14;">0</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="properties"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[handler_console]</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="properties"><span class="py">class</span> <span class="p">=</span> <span class="s" style="color: #d14;">StreamHandler</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="properties"><span class="py">args</span> <span class="p">=</span> <span class="s" style="color: #d14;">(sys.stderr,)</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="properties"><span class="py">level</span> <span class="p">=</span> <span class="s" style="color: #d14;">DEBUG</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="properties"><span class="py">formatter</span> <span class="p">=</span> <span class="s" style="color: #d14;">generic</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="properties"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[formatter_generic]</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="properties"><span class="py">format</span> <span class="p">=</span> <span class="s" style="color: #d14;">%(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/compare/ef76d0afac733afa8b1ce56d46a65afde7302ab9...b2f2c94b5db84f54ab08f624766354587dfb192a#86519cd9b3a0739fe0d9127d90925f2a92b2cdc2"><strong>tests/hardlinks.properties</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="properties"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[GENERAL]</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">######################</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">### Initialization ###</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="properties"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="properties"><span class="py">db.fullname</span><span class="p">=</span><span class="s" style="color: #d14;">"local system bank test with hardlinks"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="properties"><span class="py">db.name</span><span class="p">=</span><span class="s" style="color: #d14;">local</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="properties"><span class="py">db.type</span><span class="p">=</span><span class="s" style="color: #d14;">nucleic_protein</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="properties"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="properties"><span class="py">offline.dir.name</span><span class="p">=</span><span class="s" style="color: #d14;">offline/test/local_tmp</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="properties"><span class="py">dir.version</span><span class="p">=</span><span class="s" style="color: #d14;">test/local</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="properties"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="properties"><span class="py">frequency.update</span><span class="p">=</span><span class="s" style="color: #d14;">0</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="properties"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="properties"><span class="py">use_hardlinks</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="properties"></span>
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<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="properties"><span class="c" style="color: #998; font-style: italic;">### Synchronization ###</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="properties"></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="properties"><span class="py">files.num.threads</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span>
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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="properties"></span>
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<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="properties"><span class="c" style="color: #998; font-style: italic;"># NCBI (download fasta)</span></span>
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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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="properties"><span class="py">protocol</span><span class="p">=</span><span class="s" style="color: #d14;">local</span></span>
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<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="properties"><span class="py">server</span><span class="p">=</span></span>
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<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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="properties"></span>
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<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="properties"><span class="py">release.file</span><span class="p">=</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="properties"><span class="py">release.regexp</span><span class="p">=</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="properties"><span class="py">release.file.compressed</span><span class="p">=</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="properties"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="properties"><span class="py">remote.dir</span><span class="p">=</span><span class="s" style="color: #d14;">/tmp/</span></span>
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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="properties"><span class="py">remote.files</span><span class="p">=</span><span class="s" style="color: #d14;">^test.*</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="properties"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#Uncomment if you don't want to extract the data files.</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">#no.extract=true</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="properties"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="properties"><span class="py">local.files</span><span class="p">=</span><span class="s" style="color: #d14;">^test.*</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="properties"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">## Post Process ## The files should be located in the projectfiles/process directory</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="properties"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="properties"><span class="py">db.post.process</span><span class="p">=</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="properties"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="properties"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;">### Deployment ###</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="properties"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="properties"><span class="py">keep.old.version</span><span class="p">=</span><span class="s" style="color: #d14;">1</span></span></pre>
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