[Biopython-dev] [Bug 2678] New: Entrez.esearch does not always retrieve or find DTD files

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2678

           Summary: Entrez.esearch does not always retrieve or find DTD
                    files
           Product: Biopython
           Version: 1.49b
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: lpritc at scri.sari.ac.uk


When using Entrez.esearch, I have observed an intermittent failure to recover
DTD files.  These are not being cached on successful search attempts.  It may
be worth including them in the distribution.

Traceback:

/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/Parser.py:279:
UserWarning: DTD file xhtml1-strict.dtd not found in Biopython installation;
trying to retrieve it from NCBI
  warnings.warn("DTD file %s not found in Biopython installation; trying to
retrieve it from NCBI" % filename)
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/Parser.py:279:
UserWarning: DTD file xhtml-lat1.ent not found in Biopython installation;
trying to retrieve it from NCBI
  warnings.warn("DTD file %s not found in Biopython installation; trying to
retrieve it from NCBI" % filename)
Traceback (most recent call last):
  File "./get_entrez_ests.py", line 158, in <module>
    main()
  File "./get_entrez_ests.py", line 45, in main
    options.verbose)
  File "./get_entrez_ests.py", line 76, in get_entrez_session
    results = Entrez.read(handle)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/__init__.py",
line 286, in read
    record = handler.run(handle)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/Parser.py",
line 95, in run
    self.parser.ParseFile(handle)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/Parser.py",
line 283, in external_entity_ref_handler
    parser.ParseFile(handle)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/Entrez/Parser.py",
line 280, in external_entity_ref_handler
    handle = urllib.urlopen(systemId)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/urllib.py",
line 87, in urlopen
    return opener.open(url)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/urllib.py",
line 203, in open
    return getattr(self, name)(url)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/urllib.py",
line 461, in open_file
    return self.open_local_file(url)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/urllib.py",
line 475, in open_local_file
    raise IOError(e.errno, e.strerror, e.filename)
IOError: [Errno 2] No such file or directory: 'xhtml-lat1.ent'


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