[Biopython-dev] [Bug 2447] New: EUtils cannot parse PubMed XML for ACS journals

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 7 08:08:29 UTC 2008


           Summary: EUtils cannot parse PubMed XML for ACS journals
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: baoilleach at gmail.com

Here's the code to reproduce the bug:

from Bio import EUtils
from Bio.EUtils import DBIdsClient

PMID = "17238260"
result = DBIdsClient.from_dbids(EUtils.DBIds("pubmed", PMID))
print result.efetch().read()
summary = result.summary()

The error is:
Traceback (most recent call last):
  File "bug.py", line 8, in ?
    summary = result.summary()
  File "/home/user/Tools/biopython-1.44/Bio/EUtils/DBIdsClient.py", line 105,
in summary
    return parse.parse_summary_xml(self.esummary("xml"))
  File "/home/user/Tools/biopython-1.44/Bio/EUtils/parse.py", line 416, in
    d = convert_summary_Items(docsum.find_elements("Item"))
  File "/home/user/Tools/biopython-1.44/Bio/EUtils/parse.py", line 394, in
    d[name] = summary_type_parser_table[item.Type](item)
  File "/home/user/Tools/biopython-1.44/Bio/EUtils/parse.py", line 321, in
    return convert_summary_Date_string(x.tostring())
  File "/home/user/Tools/biopython-1.44/Bio/EUtils/parse.py", line 351, in
    raise TypeError("Unknown date format: %s" % (s,))
TypeError: Unknown date format:

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