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

[Carnë Draug]

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].


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