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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plip">Debian Med / plip</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93">a768dc00</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-11T19:26:03+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.6+dfsg</pre>
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<h4>4 changed files:</h4>
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<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<a href="#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">
plip/basic/config.py
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<a href="#e352319b84deb5f40d3f1a26b4a5cde456ac918d">
plip/exchange/webservices.py
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<a href="#d209d711b9b399c1e719fb9f3ab88df52dad6612">
plip/test/test_command_line.py
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<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changelog</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">---------</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># 2.1.6</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* fetch URL for PDB files updated to avoid issues with RCSB API changes</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># 2.1.5</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">* option added to handle specific model in NMR structures</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">* fixes a bug in alt-location handling</span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4"><strong>plip/basic/config.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.1.<span class="idiff left right">5</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.1.<span class="idiff left right">6</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai'</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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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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<li id="e352319b84deb5f40d3f1a26b4a5cde456ac918d">
<a href="https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93#e352319b84deb5f40d3f1a26b4a5cde456ac918d"><strong>plip/exchange/webservices.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ def check_pdb_status(pdbid):</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbid</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pdbid</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">f'checking status of PDB-ID </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pdbid</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>logger.info(f'checking status of PDB-ID {pdbid}')</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @todo re-implement state check with ew RCSB API, see https://www.rcsb.org/news?year=2020&article=5eb18ccfd62245129947212a&feature=true</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</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">@@ -41,7 +41,7 @@ def fetch_pdb(pdbid):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'downloading file from PDB'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get URL for current entry</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @todo needs update to react properly on response codes of RCSB servers</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">pdburl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">f'http<span class="idiff left right">://www.rcsb.org/pdb/files</span>/</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pdbid</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.pdb'</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">pdburl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">f'http<span class="idiff left right">s://files.rcsb.org/download</span>/</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pdbid</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.pdb'</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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="LC46" class="line" lang="python"> <span class="n" style="color: #333;">pdbfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">pdburl</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If no PDB file is available, a text is now shown with "We're sorry, but ..."</span></span>
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<li id="d209d711b9b399c1e719fb9f3ab88df52dad6612">
<a href="https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93#d209d711b9b399c1e719fb9f3ab88df52dad6612"><strong>plip/test/test_command_line.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">@@ -40,6 +40,11 @@ class CommandLineTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">f'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ../plipcmd.py -i 4v59 -o </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode</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="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pdb_format_available</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="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"""A valid PDB ID is provided, but there is no entry in PDB format from wwPDB"""</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">f'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ../plipcmd.py -i 1acj -o </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</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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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode</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>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valid_pdb</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="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""A PDB ID with no valid PDB record is provided."""</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">f'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ../plipcmd.py -x -f ./pdb/1eve.pdb -o </span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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