[BioPython] Entrez.einfo error?

[Nick Matzke]

Looks like PubMed is down at the moment also, so it's all an NCBI 
problem.  Cheers!
Nick


Nick Matzke wrote:
> Hi all,
> 
> This exact code worked fine for me on Friday, I wonder if it could be a 
> temporary problem at Entrez?  A similar problem seems to occur with 
> other Entrez queries.
> 
> Running biopython 1.49 in IPython...
> 
> ============
> from Bio import Entrez
> 
> Entrez.email = "matzke at berkeley.edu"
> 
> handle = Entrez.einfo(db="structure")
> 
> 
> ---------------------------------------------------------------------------
> IOError                                   Traceback (most recent call last)
> 
> /bioinformatics/pyeg/<ipython console> in <module>()
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/Bio/Entrez/__init__.pyc 
> in einfo(cgi, **keywds)
>     195     variables = {}
>     196     variables.update(keywds)
> --> 197     return _open(cgi, variables)
>     198
>     199 def esummary(cgi=None, **keywds):
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/Bio/Entrez/__init__.pyc 
> in _open(cgi, params)
>     320     options = urllib.urlencode(params, doseq=True)
>     321     cgi += "?" + options
> --> 322     handle = urllib.urlopen(cgi)
>     323
>     324     # Wrap the handle inside an UndoHandle.
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/urllib.pyc 
> in urlopen(url, data, proxies)
>      80         opener = _urlopener
>      81     if data is None:
> ---> 82         return opener.open(url)
>      83     else:
>      84         return opener.open(url, data)
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/urllib.pyc 
> in open(self, fullurl, data)
>     188         try:
>     189             if data is None:
> --> 190                 return getattr(self, name)(url)
>     191             else:
>     192                 return getattr(self, name)(url, data)
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/urllib.pyc 
> in open_http(self, url, data)
>     323         if realhost: h.putheader('Host', realhost)
>     324         for args in self.addheaders: h.putheader(*args)
> --> 325         h.endheaders()
>     326         if data is not None:
>     327             h.send(data)
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/httplib.pyc 
> in endheaders(self)
>     858             raise CannotSendHeader()
>     859
> --> 860         self._send_output()
>     861
>     862     def request(self, method, url, body=None, headers={}):
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/httplib.pyc 
> in _send_output(self)
>     730         msg = "\r\n".join(self._buffer)
>     731         del self._buffer[:]
> --> 732         self.send(msg)
>     733
>     734     def putrequest(self, method, url, skip_host=0, 
> skip_accept_encoding=0):
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/httplib.pyc 
> in send(self, str)
>     697         if self.sock is None:
>     698             if self.auto_open:
> --> 699                 self.connect()
>     700             else:
>     701                 raise NotConnected()
> 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/httplib.pyc 
> in connect(self)
>     665         msg = "getaddrinfo returns an empty list"
>     666         for res in socket.getaddrinfo(self.host, self.port, 0,
> --> 667                                       socket.SOCK_STREAM):
>     668             af, socktype, proto, canonname, sa = res
>     669             try:
> 
> IOError: [Errno socket error] (7, 'No address associated with nodename')
>  > 
> /Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/httplib.py(667)connect() 
> 
>     666         for res in socket.getaddrinfo(self.host, self.port, 0,
> --> 667                                       socket.SOCK_STREAM):
>     668             af, socktype, proto, canonname, sa = res
> 
> 
> 
> 
> 
> ipdb> record = Entrez.read(handle)
> *** NameError: name 'Entrez' is not defined
> 
> ============
> 
> 
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong. When people 
thought the earth was spherical, they were wrong. But if you think that 
thinking the earth is spherical is just as wrong as thinking the earth 
is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 
14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
====================================================