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

[Chris Fields]

Mauricio,

I'll try to take a look at it.  There may not be much we can do  
before the release candidate.  If it is a more complicated fix, we  
made need to file a bug to remind us of it's presence.

Chris

On Sep 24, 2006, at 3:59 PM, Mauricio Herrera Cuadra wrote:

> 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 make use of addresses that are no longer valid: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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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