about pubmed plugin

Aurélien Naldi aurelien.naldi at gmail.com
Mon Mar 24 11:11:08 EDT 2008


Hi,

I have some scratching itches with the pubmed plugin:

* it does not fill the doi field
* it gets only the initials and not the full given name
* it does not work with doi directly (as it used to)

The attached patch solves the first two points but I don't understand
the last one: it finds the pubmed id thanks to the DOI and calls
properly the function to get pubmed data for a given pmdid, but the
the download fails.
The weird thing is that the same download works just fine when called
directly. I tried doing the doi -> pmid work twice in a row to check
if referencer.download can be launched twice and it also works.

Do other have the same problem ?

Here is the output I got (I just added a "print url" before
downloading the xml file from pubmed)::

[...]
Document::getMetaData: trying module 'pubmed'
Waiting...
Waiting...
Waiting...
Waiting...
Waiting...
Waiting...
Waiting...
Waiting...
openCB: result OK, opened
Done!
Waiting...
Woo, read 744 bytes
readCB: result OK
Waiting...
Woo, read 0 bytes
readCB: EOF
Done!
Waiting...
closeCB: result OK, closed
Done!
referencer_download: got 744 characters
DOI  10.1074/jbc.M608848200  has PubMed ID  17028180
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=Referencer&retmode=xml&db=pubmed&email=referencer%40icculus.org&id=17028180
pubmed.py:resolve_metadata: Got no metadata
>> referencer_document_dealloc


-- 
Aurélien Naldi
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