On Mon Nov 28 17:19:56 2016, CDRAUG wrote:
Show quoted text> On Mon Nov 28 16:58:22 2016, SREZIC wrote:
> > The test suite fails since some days:
> >
> > ...
> > syntax error at line 1, column 0, byte 0 at /opt/perl-
> > 5.20.1/lib/site_perl/5.20.1/x86_64-linux/XML/Parser.pm line 187.
> > # Looks like your test exited with 255 just after 2.
> > t/biofetch.t ..............
> > Dubious, test returned 255 (wstat 65280, 0xff00)
> > Failed 8/10 subtests
> > ...
> >
> > Looking with strace at the failing test script it seems that an
> > external resource is not available anymore:
> >
> > ...
> > 19069 07:12:39.312848 read(3, "ERROR 11 Unable to connect to database
> > [medline].\r\n", 8192) = 51 <0.000010>
> > ...
>
>
> Thank you for reporting back. NCBI transitioned to https, so all the http
> connections are failing.
Digging deep, the tests were connecting to EBI servers and not NCBI servers.
The timing matches the change on the NCBI so they might be related but EBI
did not gave us any details. They are trying to fix but looks like
there's nothing else to do other than wait for them to fix it. Here's
the reply I got from them:
Show quoted text---------- Forwarded message ----------
From: Rodrigo Lopez via RT <support@ebi.ac.uk>
Date: 5 December 2016 at 16:35
Subject: [Support #163271] dbfetch medlinedb errors when using pubmedxml or medlinexml
To: carandraug+dev@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@ebi
