[Biopython-dev] [Biopython (old issues only) - Bug #2918] (Resolved) Entrez parser fails on Jython - XMLParser lacks SetParamEntityParsing

[redmine at redmine.open-bio.org]

Issue #2918 has been updated by Peter Cock.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Tracking issue migrated to GitHub as https://github.com/biopython/biopython/issues/1041

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Bug #2918: Entrez parser fails on Jython - XMLParser lacks SetParamEntityParsing
https://redmine.open-bio.org/issues/2918#change-15395

* Author: Peter Cock
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Other
* Target version: 1.52
* URL: http://bugs.jython.org/issue1447
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I'm filing this as a bug report so we can track it, but the underlying issue is a known Jython bug, http://bugs.jython.org/issue1447 (thanks Kyle for reporting this already).

It can be shown just by running our unit test:

 ~/jython2.5.0/jython run_tests.py test_Entrez.py
test_Entrez ... FAIL
======================================================================
ERROR: Test parsing XML returned by EFetch, Journals database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/pjcock/repositories/biopython/Tests/test_Entrez.py", line 3443, in test_journals
    record = Entrez.read(input)
  File "/Users/pjcock/repositories/biopython/Bio/Entrez/__init__.py", line 259, in read
    record = handler.run(handle)
  File "/Users/pjcock/repositories/biopython/Bio/Entrez/Parser.py", line 85, in run
    self.parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)
AttributeError: 'XMLParser' object has no attribute 'SetParamEntityParsing'

...



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