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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Sun Sep 24 16:59:53 EDT 2006


Chris,

I have the same opinion about the testing for these type of modules. My 
point here actually was that the XEMBL modules *could be* no longer 
compatible with the new XEMBL service and should be audited to see if 
they need changes.

Cheers,
Mauricio.

Chris Fields wrote:
> 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 make use of addresses that are no longer valid: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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> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM


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