[Bioperl-l] Are Bio::DB::XEMBL and Bio::DB::XEMBLService still valid?

Chris Fields cjfields at uiuc.edu
Sat Sep 23 16:26:12 EDT 2006


Mauricio,

There were similar issues with the Biblio_biofetch.t tests recently,  
which Brian fixed.  It has to do with the way testing for remote  
databases is set up for most test cases, which requires BIOPERLDEBUG=1.

We should probably have tests in the suite that check the URL, have  
the test actually fail if the URL can't be found, then skip  
subsequent tests that rely on the returned results.  You can do this  
with Test::More relatively easily by using skip blocks, which allow  
you to conditionally skip tests if something bad happens.  You could  
do something like this:

SKIP:{
     my $db = Bio::DB::GenBank->new();
     my $seq;
     eval { $seq = $db->get_Seq_by_acc('ABC123')};
     ok(!$@, 'get_Seq_by_acc() URL passes');
     skip('Bio::DB::GenBank failure', 4) if $@;
     ... # four more tests based on $seq
}

This way you could run sets of tests that may rely on different URLs  
in the same test suite; just wrap each one in a skip block and test  
using eval{};.  All of this, however, relies on the fact that an  
error is actually thrown by the module being tested.  Tests could be  
run or skipped based on what setting BIOPERLDEBUG has early on, maybe  
in BEGIN{}.

I plan on adding similar tests to EUtilities.t at some point.

Chris

On Sep 23, 2006, at 2:41 PM, Mauricio Herrera Cuadra wrote:

> Folks,
>
> While validating URLs in the source tree I've found that these 2  
> modules
> make use of addresses that are no longer valid:
>
> http://www.ebi.ac.uk/XEMBL
> http://www.ebi.ac.uk:80/cgi-bin/xembl/XEMBL-SOAP.pl
>
> Searching for the XEMBL service to update them, I've noticed that the
> service itself has been changed to offer new functionality:
>
> http://www.ebi.ac.uk/xembl/
> http://www.ebi.ac.uk/xembl/oldindex.html
>
> Browsing through the commit history for this 2 modules, I've found  
> that
> the last *real* changes for them were made 3-4 years ago. Its test
> output confirms my idea that this modules no longer work:
>
> [bioperl at nordwand] ~/src/bioperl-live % perl -I. -w t/XEMBL_DB.t
> 1..9
> ok 1
> ok 2 # server may be down
> ok 3 # Cannot run XEMBL_DB tests
> ok 4 # Cannot run XEMBL_DB tests
> ok 5 # Cannot run XEMBL_DB tests
> ok 6 # Cannot run XEMBL_DB tests
> ok 7 # Cannot run XEMBL_DB tests
> ok 8 # Cannot run XEMBL_DB tests
> ok 9 # Cannot run XEMBL_DB tests
>
> I've searched through the mailing lists archives and nobody has  
> reported
> them as non functional. Does anybody have the time to look into this?
>
> Regards,
> Mauricio.
>
> -- 
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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