[Biopython-dev] Parsing efetch results from the Journals database through Bio.Entrez

[Michiel de Hoon]

Thanks for letting me know.
Could you try with the latest version in the Python 2.6 series? This DeprecationWarning seems to be a bug in Python itself. I haven't seen this deprecation warning with either Python 2.6.5 or Python 2.7.

--Michiel.

--- On Mon, 9/20/10, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython-dev] Parsing efetch results from the Journals database through Bio.Entrez
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: biopython-dev at biopython.org
> Date: Monday, September 20, 2010, 6:09 AM
> On Fri, Sep 3, 2010 at 6:26 PM,
> Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> > Hi everybody,
> >
> > The parser in Bio.Entrez can parse any XML returned by
> the Entrez E-utilities
> > as long as the corresponding DTD is available ...
> > The advantage of removing these hacks is that it will
> allow us to validate all
> > XML against the DTD, and to raise an error (if the
> user requests so) if any
> > elements are found in the XML that don't validate
> against the DTD.
> 
> Hi Michiel,
> 
> All the tests look fine but there is a deprecation warning
> from your new
> exception classes (I'm running it with Python 2.6 on the
> Mac):
> 
> $ python test_Entrez.py
> Test error handling when presented with Fasta non-XML data
> ...
> /Library/Python/2.6/site-packages/Bio/Entrez/Parser.py:114:
> DeprecationWarning: BaseException.message has been
> deprecated as of
> Python 2.6
>   self.message = message
> ok
> Test error handling when presented with GenBank non-XML
> data ... ok
> Test parsing XML returned by EFetch, Nucleotide database
> (first test) ... ok
> Test parsing XML returned by EFetch, Protein database ...
> ok
> Test parsing XML returned by EFetch, OMIM database ... ok
> Test parsing XML returned by EFetch, PubMed database (first
> test) ... ok
> Test parsing XML returned by EFetch, PubMed database
> (second test) ... ok
> Test parsing XML returned by EFetch, Taxonomy database ...
> ok
> Test parsing XML output returned by EGQuery (first test)
> ... ok
> Test parsing XML output returned by EGQuery (second test)
> ... ok
> Test if corrupted XML is handled correctly ...
> /Library/Python/2.6/site-packages/Bio/Entrez/Parser.py:121:
> DeprecationWarning: BaseException.message has been
> deprecated as of
> Python 2.6
>   self.message = message
> ok
> 
> 
> Peter
>