[Biopython] Bio/Entrez/efetch: Getting HTTP Error 500 Bio/Entrez/efetch: Getting HTTP Error 500 Bio/Entrez/efetch: Getting HTTP Error 500

Jessica Grant jgrant at smith.edu
Fri Feb 17 02:39:54 UTC 2012

I have a script I have used successfully in the past that uses Entrez.
 Yesterday, a lab-mate was using it but about half way through the files
she was processing she got an error and it wouldn't work after that.  I
went over the script from top to bottom to see what went wrong and couldn't
find a problem.  Your question gives me hope that it is something happening
at ncbi.  Our error was not identical.  Our script seemed to work until it
tried to read the output of the Entrez.efetch and then found no record in
the handle (or something like that...I don't have it in front of me.)

I suggested my lab mate contact the ncbi help desk to see if anything was
wrong on their end, but I dont' know if she did or if she heard back.


On Thu, Feb 16, 2012 at 8:18 PM, Alexandra Schnoes <schnoes at gmail.com>wrote:

> Hi,
> I have some python code (using BioPython 1.58) that uses Bio.Entrez to pull
> out information on 50 papers from pubmed. I have had no problem with this
> code until yesterday when I started getting HTTP Error 500 messages that
> continue until today. For example...
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "sp_tools.py", line 421, in top_papers_dict
>    rettype="medline", retmode="text")
>  File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Entrez/__init__.py",
> line 113, in efetch
>    return _open(cgi, variables)
>  File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Entrez/__init__.py",
> line 360, in _open
>    raise exception
> urllib2.HTTPError: HTTP Error 500: Internal server error
> The parameters I'm using are
> db = pubmed
> rettype = medline
> retmode = text
> Anyone have an idea why this might be happening now?
> Thanks!
> Alexandra
> --
> Alexandra Schnoes, Ph.D.
> Scientist, Babbitt Laboratory
> Program Coordinator, Graduate Student Internships for Career Exploration
> University of California San Francisco
> Tel:  415-502-1248
> Fax: 415-514-9656
> Email: schnoes at gmail.com
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