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<h3>
Olivier Sallou pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/biomaj3-user">Debian Med / biomaj3-user</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/biomaj3-user/commit/0b2b57265896e7c473b201571c3ff1049b880887">0b2b5726</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2019-11-12T10:30:34Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.10</pre>
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<h4>3 changed files:</h4>
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<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#42a284b660b530675b47e51e935c2aea8fb3652d">
bin/biomaj-users.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/biomaj3-user/commit/0b2b57265896e7c473b201571c3ff1049b880887#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0.10:</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Force yaml loader to skip warning on output</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">3.0.9:</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Add json output to biomaj_user script</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">3.0.8:</span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Fix traefik prefix</span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">3.0.7:</span>
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<li id="42a284b660b530675b47e51e935c2aea8fb3652d">
<a href="https://salsa.debian.org/med-team/biomaj3-user/commit/0b2b57265896e7c473b201571c3ff1049b880887#42a284b660b530675b47e51e935c2aea8fb3652d"><strong>bin/biomaj-users.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ import yaml</td>
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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;">string</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;">sys</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;">bcrypt</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;">json</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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tabulate</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tabulate</span></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biomaj_user.user</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BmajUser</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +22,7 @@ def main():</td>
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21
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Action to perform for user "</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;">SUPPORTED_ACTIONS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"'renew': Create new api key"</span><span class="p">,</span></span>
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC25" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-J'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--json'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"json"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output to json"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--config'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</path/to/config.yml>'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to config.yml. By default read from env variable BIOMAJ_CONFIG"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-E'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--email'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"email"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +46,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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45
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'config.yml'</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ymlfile</span><span class="p">:</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" 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;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">ymlfile</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;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">ymlfile</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Loader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">yaml</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">FullLoader</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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;">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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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">BmajUser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_config</span><span class="p">(</span><span class="n" style="color: #333;">config</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">@@ -58,6 +60,10 @@ def main():</td>
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58
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">passwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SystemRandom</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">choice</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ascii_uppercase</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">digits</span><span class="p">)</span></span>
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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;">for</span> <span class="n" style="color: #333;">_</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;">10</span><span class="p">))</span></span>
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60
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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;">user</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create</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;">passwd</span><span class="p">,</span> <span class="n" style="color: #333;">email</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">email</span><span class="p">)</span></span>
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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="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">json</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">user</span><span class="p">[</span><span class="s" style="color: #d14;">'_id'</span><span class="p">]</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">user</span><span class="p">))</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</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="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"User successfully created"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">tabulate</span><span class="p">([[</span><span class="s" style="color: #d14;">"User"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Password"</span><span class="p">,</span> <span class="s" style="color: #d14;">"API Key"</span><span class="p">],</span></span>
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63
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">user</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">str</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;">passwd</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">user</span><span class="p">[</span><span class="s" style="color: #d14;">'apikey'</span><span class="p">])]],</span></span>
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<a href="https://salsa.debian.org/med-team/biomaj3-user/commit/0b2b57265896e7c473b201571c3ff1049b880887#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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21
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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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22
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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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23
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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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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.<span class="idiff left right">8</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.0.<span class="idiff left right">10</span>'</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="python"> <span class="s" style="color: #d14;">'classifiers'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># How mature is this project? Common values are</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 3 - Alpha</span></span>
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