[Biopython-dev] [Bug 3006] New: esearch medline fails with xml format

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3006

           Summary: esearch medline fails with xml format
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: georg.lipps at fhnw.ch


I used to retrieve Pubmed records with python 2.5.1 however lately the efetch
with xml produces an error. The problem has arosen at the year change maybe
related to the DTD definition file:

Here is a short code which produces the error:


from Bio import Entrez
from Bio import Medline


def retrieve_medline(doi):
    # Uses the doi to obtain the medline id and then retrieves the medline
entry
    # Returns the medline entry as text and python object or an empty string
    print "...queing medline with DOI", doi
    handle = Entrez.esearch(db="pubmed", term=doi, retmode="XML")
    record=Entrez.read(handle)
    if record["Count"]<>"1":
        return None, None
    handle=Entrez.efetch(db="pubmed", id=record["IdList"], retmode="text",
rettype="medline")
    xml=Entrez.efetch(db="pubmed", id=record["IdList"], retmode="XML",
rettype="medline")
    return handle.read(), Entrez.read(xml)



doi='10.1038/nature07389'
article, xml=retrieve_medline(doi)
print article





OUTPUT:

Traceback (most recent call last):
  File "U:/Literatur/pdf to RM converter/test.py", line 24, in <module>
    article, xml=retrieve_medline(doi)
  File "U:/Literatur/pdf to RM converter/test.py", line 15, in retrieve_medline
    return handle.read(), Entrez.read(xml)
  File "C:\Program Files\python25\lib\site-packages\Bio\Entrez\__init__.py",
line 283, in read
    record = handler.run(handle)
  File "C:\Program Files\python25\lib\site-packages\Bio\Entrez\Parser.py", line
95, in run
    self.parser.ParseFile(handle)
  File "C:\Program Files\python25\lib\site-packages\Bio\Entrez\Parser.py", line
131, in startElement
    return
UnboundLocalError: local variable 'object' referenced before assignment


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