[Biopython] Bio.Entrez.epost error with Python 3.2

[Michiel de Hoon]

Looking at this some more, I found this on the mailing list explaining why we are using post=True:

http://lists.open-bio.org/pipermail/biopython/2009-May/005152.html

This page provides some explanation on urllib.parse.urlencode in Python3:

http://docs.python.org/3/library/urllib.request.html#urllib-examples

Best,
-Michiel.

--- On Sat, 1/26/13, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> From: Michiel de Hoon <mjldehoon at yahoo.com>
> Subject: Re: [Biopython] Bio.Entrez.epost error with Python 3.2
> To: "Biopython Mailing List" <biopython at lists.open-bio.org>, "Nicolas Joannin" <nicolas.joannin at gmail.com>
> Date: Saturday, January 26, 2013, 11:06 PM
> For some reason Entrez.epost switched
> to post=False to post=True in the call to _open in
> Bio.Entrez. I don't know why; the other Entrez functions all
> use post=False, and if I use post=False in Entrez.epost it
> seems to work fine. The switch from post=False to post=True
> was made in this commit; Peter, do you remember why we
> switched to post=True?
> 
> https://github.com/biopython/biopython/commit/c928057b6c811c8959daf806ee6159eb09e0928f#Bio/Entrez/__init__.py
> 
> Best,
> -Michiel.
> 
> --- On Sat, 1/26/13, Nicolas Joannin <nicolas.joannin at gmail.com>
> wrote:
> 
> > From: Nicolas Joannin <nicolas.joannin at gmail.com>
> > Subject: [Biopython] Bio.Entrez.epost error with Python
> 3.2
> > To: "Biopython Mailing List" <biopython at lists.open-bio.org>
> > Date: Saturday, January 26, 2013, 7:42 AM
> > Hello everyone,
> > 
> > I am having trouble with using Bio.Entrez.epost: see
> details
> > below.
> > I have tried converting the variables to bytes, but
> > everything I've tried
> > gives the same error message.
> > 
> > I'm guessing that this might be a bug in biopython when
> used
> > with Python 3.
> > If not, could you please tell me where I got this
> wrong, and
> > how I can fix
> > it?
> > 
> > Best regards,
> > Nicolas
> > 
> > 
> > Here are the details:
> > I have tried the following:
> > 
> >    -
> > post_h=Entrez.epost("nuccore",id="160418,160351")
> >    -
> > post_h=Entrez.epost(b"nuccore",id=b"160418,160351")
> >    -
> >
>    post_h=Entrez.epost("nuccore".encode("utf-8"),id="160418,160351".encode("utf-8")
> > 
> > 
> > >>>
> > post_h=Entrez.epost("nuccore",id="160418,160351")
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File
> >
> "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/Bio/Entrez/__init__.py",
> > line 97, in epost
> >     return _open(cgi, variables, post=True)
> >   File
> >
> "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/Bio/Entrez/__init__.py",
> > line 436, in _open
> >     handle = urllib.request.urlopen(cgi,
> > data=options)
> >   File
> >
> "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/urllib/request.py",
> > line 138, in urlopen
> >     return opener.open(url, data, timeout)
> >   File
> >
> "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/urllib/request.py",
> > line 367, in open
> >     req = meth(req)
> >   File
> >
> "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/urllib/request.py",
> > line 1066, in do_request_
> >     raise TypeError("POST data should be bytes"
> > TypeError: POST data should be bytes or an iterable of
> > bytes. It cannot be
> > str.
> > 
> > 
> > Nicolas Joannin, Ph.D.
> > Bioinformatics Center
> > Kyoto University, Uji campus, Japan
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> > 
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>