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

[Alexandra Schnoes]

Thanks, that is somewhat encouraging to hear. I have also emailed NCBI
(that's actually where the multi-repeat subject line came from. My computer
sometimes has weird lags and apparently I hit ctrl-v a couple of times when
copying over the email I sent to NCBI, and didn't notice it. My apologies).
Hopefully one of us will hear something soon!
Alex



On Thu, Feb 16, 2012 at 6:39 PM, Jessica Grant <jgrant at smith.edu> wrote:

> 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.
>
> Jessica
>
>
>
>
>
> 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
>>
>>
>>