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

[Alexandra Schnoes]

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