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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Sep 28 17:54:24 EDT 2006


Chris,

Did you got something from Lincoln about this? Shall I file a bug for 
tracking this?

Mauricio.

Chris Fields wrote:
> Mauricio,
> 
> I take that back!  After a quick look at your link, it looks like  
> XEMBL is essentially to be discontinued (well, merged with DBFetch).   
> I'm cc'ing this to Lincoln to get his thoughts (looks like he is the  
> designated maintainer in the POD), but I think they probably could be  
> deprecated if they have no function anymore.
> 
> Lincoln, in short, Mauricio has found that the XEMBL-related urls  
> with Bio::DB::XEMBL and Bio::DB::XEMBLServices no longer work.  Do  
> these modules have any value beyond their utility for accessing XEMBL?
> 
> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>> -- 
>> 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
> 
> 
> 
> 
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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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