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

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Sep 28 22:33:55 EDT 2006


Done. Added you in the CC list.

Cheers,
Mauricio.

Chris Fields wrote:
> I haven't heard anything from Lincoln yet, so filing a bug would be a  
> great idea, at least to have as a reminder.
> 
> Chris
> 
> On Sep 28, 2006, at 4:54 PM, Mauricio Herrera Cuadra wrote:
> 
>> 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
>>> _______________________________________________
>>> 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
>>
> 
> 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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