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

Chris Fields cjfields at uiuc.edu
Mon Sep 25 00:31:38 EDT 2006


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
>>
>>
>>
>>
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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






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