[Biopython] Problem with Bio.Entrez...

[Nathan J. Edwards]

Seems to be a problem with Entrez XML parsing:

from Bio import Entrez
Entrez.email = 'xxxyy at georgetown.edu'

handle = Entrez.einfo(db='pubmed')
result = Entrez.read(handle)

results in:

Traceback (most recent call last):
   File "C:/Documents and Settings/Nathan/My 
Documents/BCHB524/testing.py", line 5, in <module>
     result = Entrez.read(handle)
   File 
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\__init__.py", 
line 261, in read
     record = handler.read(handle)
   File 
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 
150, in read
     self.parser.ParseFile(handle)
   File 
"C:\BCHB524-2010\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 
295, in endElementHandler
     current[name] = value
TypeError: 'str' object does not support item assignment

error is in Parser.endElementHandler:

             current = self.stack[-1]
             try:
                 current.append(value)
             except AttributeError:
295:            current[name] = value

because current is the empty string "".

The problem is probably that the empty string shouldn't be on the stack, 
given the logic here and elsewhere, but a simple test for the empty 
string does get things working again.

             current = self.stack[-1]
	    if current == "":
		return
             try:
                 current.append(value)
             except AttributeError:
295:            current[name] = value


Cheers!

- n

-- 
Dr. Nathan Edwards                      nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
            Georgetown University Medical Center
Room 1215, Harris Building          Room 347, Basic Science
3300 Whitehaven St, NW              3900 Reservoir Road, NW
Washington DC 20007                     Washington DC 20007
Phone: 202-687-7042                     Phone: 202-687-1618
Fax: 202-687-0057                         Fax: 202-687-7186