[Biopython] Eftech and db='bioproject'... DTD problem?

[Nicolas Joannin]

Hi Michiel,

Thanks for the suggestion. Will do so and post any response I'll get!

Best regards,
Nicolas




On Thu, Jun 13, 2013 at 12:32 AM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:

> The XML returned by Entrez for this query starts like this:
> <?xml version="1.0"?>
> <RecordSet><DocumentSummary>
>     <Project>
>         <ProjectID>
> ...
> so it does not contain any information regarding the relevant DTD needed
> to parse this XML.
> I would suggest to check with NCBI to find out what to appropriate way is
> to access the bioproject database through Entrez.
>
> Best,
> -Michiel.
>
>
>   ------------------------------
>  *From:* Nicolas Joannin <nicolas.joannin at gmail.com>
> *To:* Biopython Mailing List <biopython at lists.open-bio.org>
> *Sent:* Wednesday, June 12, 2013 12:04 PM
> *Subject:* [Biopython] Eftech and db='bioproject'... DTD problem?
>
> Hello,
>
> I'm trying to use Entrez.efetch to retrieve info about a BioProject.
> However, I get DTD error (see ouput below).
> Using "validate=False" avoids the error, but results in an empty string
> output..
>
> Any idea as to how I can read BioProject data from Entrez?
>
> Best regards,
> Nicolas
>
> Example output:
>
> >>> h=Entrez.efetch(db='bioproject', id='20431')
> >>> p=Entrez.read(h)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
>
> "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/__init__.py",
> line 368, in read
>     record = handler.read(handle)
>   File
>
> "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
> line 184, in read
>     self.parser.ParseFile(handle)
>   File
>
> "/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
> line 300, in startElementHandler
>     raise ValidationError(name)
> Bio.Entrez.Parser.ValidationError: Failed to find tag 'RecordSet' in the
> DTD. To skip all tags that are not represented in the DTD, please call
> Bio.Entrez.read or Bio.Entrez.parse with validate=False.
>
>
> 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
>
>
>