Re: [Refdb-users] med2ris failure

[Markus H. <mar...@mh...>]

Hi Bruce,

Quoting Bruce Hayward <b.h...@le...>:

> Recently I've been getting lots of failures when I try to convert a
> Pubmed xml file to ris format.

I can feel your pain, brother :-( This time it's not me but Pubmed who =20
screwed up things. They have introduced a couple of changes lately =20
which create invalid XML.

> junk after document element at line 216, column 4, byte 11204 at
> /usr/local/lib/perl5/site_perl/5.8.8/mach/XML/Parser.pm line 187
>
> In this case the ris file contains only the first reference

This is because the XML file contains consecutive top-level =20
PubmedArticle elements. In a valid XML file these should be wrapped in =20
a PubmedArticleSet element as they used to be until a few weeks ago. A =20
workaround is to request the datasets individually.

> not well-formed (invalid token) at line 3, column 27, byte 44 at
> /usr/local/lib/perl5/site_perl/5.8.8/mach/XML/Parser.pm line 187
>
> In this case the ris file is empty.

This is because Pubmed no longer correctly exports attribute values. =20
Compare the second element of a valid (until mid last week) and a =20
recent entry:

<MedlineCitation Owner=3D"NLM" Status=3D"MEDLINE">

vs.

<MedlineCitation Owner Status>

This again is invalid XML which the expat parser used by med2ris =20
rightfully barfs at.

One workaround is to copy the pretty-printed version (which happens to =20
be valid) to your editor and save that to a file, instead of using the =20
built-in "File" or "Text" tools in the drop-down box of the Pubmed =20
interface.

I have encountered additional XML problems in the last week or so. =20
E.g. the author name "O'Brien" is no longer exported as is, but as =20
"O&apos;Brien" which again is invalid XML as the non-standard entity =20
isn't declared anywhere.

I've complained at the help desk about the latter two issues (I didn't =20
know about the first one yet), and they told me they were working at a =20
fix. But I think it won't hurt if you go ahead and contact them as =20
well to tighten the thumb screws a bit further.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de