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

Chris Fields cjfields at uiuc.edu
Thu Sep 28 18:00:25 EDT 2006


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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