[referencer] about pubmed plugin

Aurélien Naldi aurelien.naldi at gmail.com
Mon Mar 24 12:09:08 EDT 2008


On Mon, Mar 24, 2008 at 4:48 PM, John Spray <jcspray at icculus.org> wrote:
>
>  On Mon, 2008-03-24 at 16:11 +0100, Aurélien Naldi wrote:
>  > 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
>
>  Committed your patch, with a little bit of extra error checking.

Thanks.

>
>  > * it does not work with doi directly (as it used to)
>
>  Still works for me.  I'm testing with 10.1093/bioinformatics/btm547.

ok, maybe the problem comes from hardy then...
Thanks for suggesting to remove the try/except, I should have done it
before... The error was:

Exception: <type 'exceptions.UnicodeDecodeError'>
Explication: 'ascii' codec can't decode byte 0xc3 in position 1:
ordinal not in range(128)


The following fixes it for me, I hope it doesn't create any other kind
of problem...


	print "DOI ", query, " has PubMed ID ", id

-	return get_citation_from_pmid (id)
+	return get_citation_from_pmid (id.encode("utf-8"))

 def get_citation_from_pmid (pmid, email='referencer at icculus.org',
tool='Referencer', database='pubmed'):


-- 
Aurélien Naldi


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