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

[Fields, Christopher J]

That error does make me think it has to do with the recent NCBI switch-over to HTTPS; the issue may be primarily on the EBI dbfetch though (maybe a redirect to grab the appropriate format directly from NCBI, which is now failing?).  



Chris

On 12/2/16, 1:29 PM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org on behalf of carandraug+dev at gmail.com> wrote:

>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=	 <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
>
>---
>
>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
>
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