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<h3>
Olivier Sallou pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/biomaj3-core">Debian Med / biomaj3-core</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e">86e7d0c0</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-10-25T09:12:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.14</pre>
</li>
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<h4>5 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
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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="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</li>
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e#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: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.7"</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.4"</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Apply only on main branches</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="na" style="color: teal;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: teal;">except</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">/^feature.*$/</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to install dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#before_install:</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - "sudo apt-get update -qq"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - "sudo apt-get install -qq libldap2-dev libsasl2-dev"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">/^feature.*$/"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">flake8"</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">-r</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">requirements.txt"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">coverage"</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">python-coveralls"</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">python</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">setup.py</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">-q</span><span class="nv" style="color: teal;"> </span><span class="s" style="color: #d14;">install"</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - "echo data_file=$TRAVIS_BUILD_DIR/.coverage >> .coveragerc"</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># command to run tests</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#before_script:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - sleep 10</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#script: nosetests --with-coverage --cover-package=biomaj -a '!network'</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#script: nosetests --with-coverage --cover-package=biomaj</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install flake8</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install -r requirements.txt</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install coverage</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install python-coveralls</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py -q install</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py test</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">flake8 --ignore E501,E123 biomaj_core/*.py</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - coveralls</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"></span></pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py test</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">flake8 --ignore E501,E123 biomaj_core/*.py</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"><span class="na" style="color: teal;">deploy</span><span class="pi">:</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: teal;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: teal;">skip_existing</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: teal;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">osallou</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: teal;">password</span><span class="pi">:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: teal;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;">OA4CxuI5Mcnk+hB9XoJK0W3i5EFv0cuZINr0TLDIiwxpt2446hHnJdxjVDnnZGanQnztgeFwOlIWZWbsytKsTWjd0rv6WtWXWxbJ8qgp+wE0IGaDV4Iceks9wogEiCjAs2URS8Kc2OdokhjWVcOZN8z9bABNPwSBaf5QBc++v96DGCTFF2JaOZlE6DL+AAKPldyXPYfRDcaTMw8CFnQ+TeJYJMX5Jm/U2RKLU37iZaDd2PV6IA1kHf5ZDaRkvsqR1Ycu67GjaUWYxLO3/GJsK9vMJLZeOi1/bBp2rwW8TYlbdFkGII0g+hGLCTwySrVPpWsv+zLaA9GgTIt8w2N6aOALob+Kgk64TRM/C0m01ABqnOyc6wfC+EbaaFMZYMjcJxexOlpM9HY3BPUPBUzdxP2M/g9hIBcLfYQeScM4a42wRFmCAN3CUUvhXvDXFrUQFrfrM/1jjMv/EnBIy1TEmDNa6aGfMh4/bEWW7Vyg+n72Zs1RrgFofE4MhVSWRq640e4DtFBtbJOp0f44AfSdMtUmOz3MulUTgE79XOvPZS0KIvQfVBv9G0XV3+iO4NXwGaxvbazuUicEdEit2EU26EypTMQI9NijIMeEzFzYAtwafL06oyTtL9D7ygu2VQHhbh7mz9ncZcx/hgl3MAvbQ/AEs08b060Jc15vDw8dko0=</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: teal;">distributions</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist bdist_wheel</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: teal;">on</span><span class="pi">:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: teal;">tags</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0.14:</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Fix checks on local_endpoint_XXX in config.yml</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> In rabbitmq not defined on config.yml add an empty dict</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">3.0.13:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Add archive integrity checks</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">3.0.12:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Add irods support</span>
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1
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">3.0.11:</span>
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2
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Add get_module_version static method, checks module version and latest version on pypi</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Allow .args fo process to be empty</span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e#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">@@ -403,7 +403,7 @@ class BiomajConfig(object):</td>
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403
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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404
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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;">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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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;">'sftp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'http'</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;">'https'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directftp'</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>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="s" style="color: #d14;">'https'</span><span class="p">,</span> <span class="s" style="color: #d14;">'directftp'</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'irods'</span></span><span class="p">]</span></span>
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407
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407
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<pre style="margin: 0;"> <span id="LC407" 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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408
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<pre style="margin: 0;"> <span id="LC408" 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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409
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<pre style="margin: 0;"> <span id="LC409" 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 old_line" data-linenumber="422" 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>
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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">@@ -422,6 +422,19 @@ class BiomajConfig(object):</td>
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422
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422
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<pre style="margin: 0;"> <span id="LC422" 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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423
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423
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<pre style="margin: 0;"> <span id="LC423" 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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424
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424
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<pre style="margin: 0;"> <span id="LC424" 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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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'irods'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">protocol</span><span class="p">:</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'irods.user'</span><span class="p">):</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" 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;">'irods user is not set'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC428" 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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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'irods.password'</span><span class="p">):</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" 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;">'irods password is not set'</span><span class="p">)</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" 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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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'irods.port'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">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;">'irods port is not set'</span><span class="p">)</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" 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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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'irods.protocol'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC436" 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;">'irods protocol is not set'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'local.files'</span><span class="p">):</span></span>
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439
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<pre style="margin: 0;"> <span id="LC439" 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;">'local.files is not set'</span><span class="p">)</span></span>
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427
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e#069849a9be10cc3a9a83d68a6da4a50907b711ea"><strong>biomaj_core/utils.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">@@ -46,8 +46,9 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'web'</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;">config</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'local_endpoint'</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;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC47" 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="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'local_endpoint'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'local_endpoint_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">service</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="s" style="color: #d14;">'local_endpoint_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">service</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()]</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">service_endpoint_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'local_endpoint_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">service</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">service_endpoint_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="n" style="color: #333;">service_endpoint_name</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">][</span><span class="n" style="color: #333;">service_endpoint_name</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC52" 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="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'web'</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;">config</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'local_endpoint'</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;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'web'</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC54" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,6 +56,8 @@ class Utils(object):</td>
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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="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="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">service_config_override</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'rabbitmq'</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;">config</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'rabbitmq'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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58
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'RABBITMQ_HOST'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'RABBITMQ_HOST'</span><span class="p">]:</span></span>
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59
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s" style="color: #d14;">'rabbitmq'</span><span class="p">][</span><span class="s" style="color: #d14;">'host'</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;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'RABBITMQ_HOST'</span><span class="p">]</span></span>
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60
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'RABBITMQ_PORT'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">'RABBITMQ_PORT'</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">@@ -310,6 +313,33 @@ class Utils(object):</td>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">file_to_copy</span><span class="p">[</span><span class="s" style="color: #d14;">'format'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_format</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">files_to_copy</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC316" 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="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">archive_check</span><span class="p">(</span><span class="n" style="color: #333;">archivefile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> Test file archive integrity</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="s" style="color: #d14;"> :param file: full path to file to check and uncompress</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"><span class="s" style="color: #d14;"> :type file: str</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"><span class="s" style="color: #d14;"> :return: True if ok, False if an error occured</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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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;">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="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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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;">if</span> <span class="n" style="color: #333;">archivefile</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;">'.tar.gz'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"tar tfz "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">archivefile</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;">'.tar'</span><span class="p">):</span></span>
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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;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"tar tf "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">archivefile</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;">'.bz2'</span><span class="p">):</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"tar tjf "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">archivefile</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;">'.gz'</span><span class="p">):</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"gunzip -t "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">archivefile</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;">'.zip'</span><span class="p">):</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"unzip -t "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">CalledProcessError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">uncompresserror</span><span class="p">:</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" 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;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Archive integrity error of </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">uncompresserror</span><span class="p">)))</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" 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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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC341" 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="LC342" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC343" 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="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="n" style="color: #333;">archivefile</span><span class="p">,</span> <span class="n" style="color: #333;">remove</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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315
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-core/commit/86e7d0c0e35233a41cfdec81978006c45b72f58e#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">1</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">4</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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