[Biopython-dev] Type vs type in Entrez.esummary XML (via BioStar)

[Peter Cock]

On Mon, Aug 22, 2011 at 7:53 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> On Sun, Aug 21, 2011 at 8:48 AM, Feed My Inbox <updates at feedmyinbox.com> wrote:
>> // Error using Entrez.esummary from biopython
>> // August 16, 2011 at 8:47 AM
>>
>> http://biostar.stackexchange.com/questions/11232/error-using-entrez-esummary-from-biopython
>> Can someone please explain this error?
>>
>> I hava a smal script that tries to fetch information from the a
>> NCBI BioAssay using the Entrez module form Bipython. I get
>> an error I do not understand. I try to run:
>>
>> from Bio import Entrez
>> Entrez.email="yourname at mail.se"
>>
>> handle_esummary=Entrez.esummary(db='pcassay',id='1337')
>> record_esummary=Entrez.read(handle_esummary)
>>
>>
>> I get the error:
>>
>> File "smaltest.py", line 5, in <module>
>>    record_esummary=Entrez.read(handle_esummary)
>>  File "/usr/common/schrodinger/mmshare-v20109/lib/Linux-x86_64/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 297, in read
>>    record = handler.run(handle)
>>  File "/usr/common/schrodinger/mmshare-v20109/lib/Linux-x86_64/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 90, in run
>>    self.parser.ParseFile(handle)
>>  File "/usr/common/schrodinger/mmshare-v20109/lib/Linux-x86_64/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 105, in startElement
>>    itemtype = str(attrs["Type"]) # convert from Unicode
>> KeyError: 'Type'
>>
>
> I can reproduce this and The cause is the NCBI using
> lowercase in one tag's attribute:
>
> <Item Name="SourceNameList" type="List">
>
> We're expecting the attributes to be Name and Type, and
> that is the case for all the other <Item> tags in this file.
>
> Michiel - do you think we should just add a fallback for
> type if we get a KeyError on Type? Do you think we should
> report this inconsistency/bug to the NCBI?

Actually it clearly violates the DTD, and thus fails XML
validation - so it is clearly a NCBI bug.

Peter