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

[Carnë Draug]

On 3 December 2016 at 15:32, Fields, Christopher J
<cjfields at illinois.edu> wrote:
>
> On 12/2/16, 3:25 PM, "carandraug at gmail.com on behalf of Carnë Draug" <carandraug at gmail.com on behalf of carandraug+dev at gmail.com> wrote:
>
>>On 2 December 2016 at 20:02, Fields, Christopher J
>><cjfields at illinois.edu> wrote:
>>> 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?).
>>
>>When did the switch over happened?  I found a planed date for 30/09/2016 [1]
>>but this still worked on October 30 [2] and I got the first failure report
>>from cpantests on November 24 [3].
>
> Sometime in November
>
>>I originally though the cause to be same but unless that happens on the
>>EBI servers, I don't know how.  I did notice that the code was making
>>requests using an undocumented [4] format "medlinexml".  Actually, all
>>formats are failing other than default (seems to be medlinefull),
>>medlinefull, and medlineref.
>>
>>  ## works
>>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=medlinefull
>>  ## fails
>>  https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=medline;id=2859121;format=pubmedxml
>>
>>Carnë
>>
>>[1] https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
>>[2] http://www.cpantesters.org/cpan/report/957a89f2-9ec4-11e6-a23c-a658b607aa42
>>[3] http://www.cpantesters.org/cpan/report/92af4674-b218-11e6-8dde-c5e727772ce6
>>[4] https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#medline
>
> Not sure, I’m hoping EBI can shed light on that.  But the timing is about right with the NCBI switch.
>
> chris

Here's the reply I got from them. Seems like there's nothing to do on
the bioperl side


---------- Forwarded message ----------
From: Rodrigo Lopez via RT <support at ebi.ac.uk>
Date: 5 December 2016 at 16:35
Subject: [Support #163271] dbfetch medlinedb errors when using
pubmedxml or medlinexml
To: carandraug+dev at gmail.com


Dear User,

Thank you for your feedback. We are aware there is a problem with some formats
for MEDLINE in dbfetch. An engineer is looking into this as we speak.

Apologies for the inconvenience.

support at ebi