[Biopython] Problem with Bio.Entrez...

[Michiel de Hoon]

The problem is with the XML returned by NCBI.
Currently, the XML returned by einfo contains <Docsum> elements that are not described in the corresponding DTD (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd). The parser therefore doesn't know how to handle them.
Could you write an email to NCBI that einfo generates XML that is inconsistent with the corresponding DTD?

Best,
--Michiel.

--- On Thu, 8/26/10, Nathan J. Edwards <nje5 at georgetown.edu> wrote:

> From: Nathan J. Edwards <nje5 at georgetown.edu>
> Subject: [Biopython] Problem with Bio.Entrez...
> To: biopython at lists.open-bio.org
> Date: Thursday, August 26, 2010, 9:43 PM
> 
> 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
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