[Bioperl-l] dbfetch medlinedb errors when using pubmedxml or medlinexml

[Carnë Draug]

For those who receive notifications from the CPAN test matrix, there's
been some tests failing on Bio::DB::Biblio::biofetch [1].  There seems
to be some changes on EBI's dbfetch or medlinedb.  Is anyone aware of
anything?

Even changing the URL on biofetch.pm to point to the correct place will
not work since Bio::Biblio::IO seems to only support pubmedxml and
medlinexml and none seems to be being served from EBI.

Example, biofetch is currently making this type of URLs

    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline&style=raw&format=medlinexml&id=10592273

But 'format=medlinexml' seems to be invalid.

For what is worth, I sent the email below to EBI support.

Carnë

[1] https://rt.cpan.org/Ticket/Display.html?id=119025

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This following query

    https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml

(which is one of the online examples [1] for the pubmedxml format) fails
with:

    ERROR 11 Unable to connect to database [medline].

On a related note, the format medlinexml is no longer listed on the
documentation although it worked until a few days ago [2].

Are this two formats no longer supported?

Thank you

Carnë

[1] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline
[2] https://rt.cpan.org/Ticket/Display.html?id=119025&results=c5f91ab4407b80140fad7409ff66a478