t/BioFetch.t started to fail

[eserte]

See subject. On my smoker systems:

...
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: BioFetch Error 11: Unable to connect to database [refseqn].
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/Root/Root.pm:447
STACK: Bio::DB::BioFetch::postprocess_data /home/cpansand/.cpan/build/2019052913/Bio-DB-BioFetch-1.7.3-0/blib/lib/Bio/DB/BioFetch.pm:450
STACK: Bio::DB::WebDBSeqI::_stream_request /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/DB/WebDBSeqI.pm:765
STACK: Bio::DB::WebDBSeqI::get_seq_stream /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/DB/WebDBSeqI.pm:472
STACK: Bio::DB::BioFetch::get_Stream_by_acc /home/cpansand/.cpan/build/2019052913/Bio-DB-BioFetch-1.7.3-0/blib/lib/Bio/DB/BioFetch.pm:525
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/DB/WebDBSeqI.pm:190
STACK: t/BioFetch.t:22
-----------------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: acc NM_006732.2 does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/Root/Root.pm:447
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/perl5.18.4p/lib/site_perl/5.18.4/Bio/DB/WebDBSeqI.pm:199
STACK: t/BioFetch.t:22
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 255 just after 2.
t/BioFetch.t ............. 
Dubious, test returned 255 (wstat 65280, 0xff00)
All 2 subtests passed 
...

[cement-head]

I'm seeing the same issue (I believe) as well.

[carandraug]

I can't reproduce the original issue (acc NM_006732.2 does not exist which would be an issue with the refseqn database --- https://www.ncbi.nlm.nih.gov/nuccore/NM_006732.2/ ). However, running the test now, it fails with:

$ prove -lr t
t/BioFetch.t .. 14/? 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: BioFetch Error 11: Unable to connect to database [unisave].
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
STACK: Bio::DB::BioFetch::postprocess_data /home/carandraug/src/bioperl/Bio-DB-BioFetch/lib/Bio/DB/BioFetch.pm:449
STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:769
STACK: Bio::DB::WebDBSeqI::get_seq_stream /usr/share/perl5/Bio/DB/WebDBSeqI.pm:476
STACK: Bio::DB::BioFetch::get_Stream_by_acc /home/carandraug/src/bioperl/Bio-DB-BioFetch/lib/Bio/DB/BioFetch.pm:524
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
STACK: t/BioFetch.t:101
-----------------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: acc P14733 does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
STACK: t/BioFetch.t:101

which is an issue with unisave which indeed is down at the moment https://www.ebi.ac.uk/uniprot/unisave/app

@cement-head do you really have the same problem as the original issue or is yours the same as me, .i.e., acc P14733 does not exist

It seems to me that BioFetch is just throwing an error about sequence not existing regardless of what caused the failure.

[carandraug]

which is an issue with unisave which indeed is down at the moment https://www.ebi.ac.uk/uniprot/unisave/app

I've contacted EMBL-EBI about this. UniSave is now back online. All the tests now pass so I can't reproduce this issue.