[Biopython-dev] [Bug 2918] New: Entrez parser fails on Jython - XMLParser lacks SetParamEntityParsing

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2918

           Summary: Entrez parser fails on Jython - XMLParser lacks
                    SetParamEntityParsing
           Product: Biopython
           Version: 1.52
          Platform: All
               URL: http://bugs.jython.org/issue1447
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
                CC: kellrott at ucsd.edu


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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