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Issue #2918 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15395?detail_id=1733">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Tracking issue migrated to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1041">https://github.com/biopython/biopython/issues/1041</a></p>
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<h1><a href="https://redmine.open-bio.org/issues/2918#change-15395">Bug #2918: Entrez parser fails on Jython - XMLParser lacks SetParamEntityParsing</a></h1>
<ul><li>Author: Peter Cock</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Other</li>
<li>Target version: 1.52</li>
<li>URL: http://bugs.jython.org/issue1447</li></ul>
<p>I'm filing this as a bug report so we can track it, but the underlying issue is a known Jython bug, <a class="external" href="http://bugs.jython.org/issue1447">http://bugs.jython.org/issue1447</a> (thanks Kyle for reporting this already).</p>
<p>It can be shown just by running our unit test:
======================================================================<br />ERROR: Test parsing XML returned by EFetch, Journals database<br />----------------------------------------------------------------------<br />Traceback (most recent call last):<br /> File "/Users/pjcock/repositories/biopython/Tests/test_Entrez.py", line 3443, in test_journals<br /> record = Entrez.read(input)<br /> File "/Users/pjcock/repositories/biopython/Bio/Entrez/__init__.py", line 259, in read<br /> record = handler.run(handle)<br /> File "/Users/pjcock/repositories/biopython/Bio/Entrez/Parser.py", line 85, in run<br /> self.parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)<br />AttributeError: 'XMLParser' object has no attribute 'SetParamEntityParsing'</p>
<pre><code>~/jython2.5.0/jython run_tests.py test_Entrez.py<br />test_Entrez ... FAIL</code></pre>
<p>...</p>
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