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LWP::Protocol::https required in test suite #313

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eserte opened this Issue Feb 23, 2019 · 2 comments

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eserte commented Feb 23, 2019

t/SeqFeature/Generic.t fails if LWP::Protocol::https is not installed:

...

--------------------- WARNING ---------------------
MSG: In attempting to join a remote location, sequence AF032048 was not in database. Will provide padding N's. Full exception 


------------- EXCEPTION: Bio::Root::Exception -------------
MSG: WebDBSeqI Request Error:
501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
Content-Type: text/plain
Client-Date: Sat, 23 Feb 2019 15:37:03 GMT
Client-Warning: Internal response

LWP will support https URLs if the LWP::Protocol::https module
is installed.

STACK: Error::throw
STACK: Bio::Root::Root::throw /home/cpansand/.cpan/build/2019022315/BioPerl-1.7.5-4/blib/lib/Bio/Root/Root.pm:449
STACK: Bio::DB::WebDBSeqI::_stream_request /home/cpansand/.cpan/build/2019022315/BioPerl-1.7.5-4/blib/lib/Bio/DB/WebDBSeqI.pm:783
STACK: Bio::DB::WebDBSeqI::get_seq_stream /home/cpansand/.cpan/build/2019022315/BioPerl-1.7.5-4/blib/lib/Bio/DB/WebDBSeqI.pm:476
STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /opt/perl-5.26.0t/lib/site_perl/5.26.0/Bio/DB/NCBIHelper.pm:502
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /home/cpansand/.cpan/build/2019022315/BioPerl-1.7.5-4/blib/lib/Bio/DB/WebDBSeqI.pm:194
STACK: Bio::SeqFeatureI::spliced_seq /home/cpansand/.cpan/build/2019022315/BioPerl-1.7.5-4/blib/lib/Bio/SeqFeatureI.pm:597
STACK: t/SeqFeature/Generic.t:221
-----------------------------------------------------------
... (etc) ...
#   Failed test at t/SeqFeature/Generic.t line 224.
#          got: 'MARFVVVALLALLSLSGLEAIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'
#     expected: 'MARFVVVALLALLSLSGLEAIQHAPKIQVYSRHPAENGKPNFLNCYVSGFHPSDIEVDLLKNGKKIEKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVSHVTFPTPKTVKWDRTM*'
# Looks like you failed 2 tests of 364.
t/SeqFeature/Generic.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
All 364 subtests passed 
...
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eserte commented Feb 23, 2019

Here's a similar fail report at CPAN Testers: http://www.cpantesters.org/cpan/report/102320629

cjfields added a commit that referenced this issue Feb 27, 2019

short-term fix for #313, but this test probably needs to conditionall…
…y check the case where Bio::DB::GenBank is not installed?
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cjfields commented Feb 27, 2019

For now we can skip this test if LWP::Protocol::https isn't present but I think any NCBI-related test will require HTTPS at some point, so Bio::DB::GenBank and related should make this requirement explicit; this is now in a separate repo so I'll link this bug there.

Also, the fact this does return a result despite the warnings suggests we should evaluate this accordingly in cases where Bio::DB::GenBank isn't installed (will have to see if a test exists for this). So, leaving open for now.

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