On 11 Jul 2006, at 08:28, Els Vanbleu wrote:
Dear all,
We are trying to implement BioMart as DAS server. Therefore we
followed
the instructions as mentioned in the README file of the /das folder,
i.e. install ProServer, make an Importable/Exportable in the mart and
write a biomart.ini file. All dependencies were correctly established
and the ProServer was successfully launched using our biomart.ini file
(we get a pid.file and output is directed to a log.file).
With the url (pidserver/das/dsn/) we retrieve the available data
sources
but when trying to catch some features (e.g.
pidserver/das/mymart1/features?segment=B0222.1), the system failed
(giving a source error).
After intensive debugging, we already think we solved a few bugs,
namely
in the das/biomart.pm module
use constant DEFAULTVSCHEMA => "defaultSchema";
should be
use constant DEFAULTVSCHEMA => "default";
in order to have compliant virtualSchemas when no virtualSchema is
specifically set in the mart (and so the mart uses the 'default'
virtualSchema).
Secondly, it turned out to us that the Location->getDatasetByName
method
was case sensitive (BioMart::Configuration::Location), so for our
purposes we made it case insensitive.
sub getDatasetByName {
my ($self,$dataSetName) = @_;
$dataSetName = uc $dataSetName;
my $dataSetHash = $self->get('datasets');
my $dataSetEntry = $dataSetHash->{$dataSetName};
return $dataSetEntry;
}
But still, no luck. The remaining error message now is:
Hi Els,
DAS server functionality clearly slipped through
our release testing procedure - apologies. You identified all the
problems correctly.
Let us investigate and we'll get back to you with the advice on this
soon
a.
-------------------- EXCEPTION --------------------
DATE: 10-JUL-2006
MSG: You need to define virtual schema name in order to create a Query
object
STACK BioMart::Query::_new
/var/www/biomart-web/biomart-plib//BioMart/Query.pm:92
STACK BioMart::RootI::new
/var/www/biomart-web/biomart-plib//BioMart/RootI.pm:54
STACK Bio::Das::ProServer::SourceAdaptor::biomart::build_features
../lib/Bio/Das/ProServer/SourceAdaptor/biomart.pm:146
STACK (eval) ./proserver:467
STACK poeserver::client_got_request ./proserver:459
STACK (eval) ./proserver:357
STACK poeserver::__ANON__ ./proserver:357
STACK POE::Session::_invoke_state
/usr/lib/perl5/site_perl/5.8.0/POE/Session.pm:484
STACK POE::Kernel::call
/usr/lib/perl5/site_perl/5.8.0/POE/Kernel.pm:1656
STACK POE::Wheel::ReadWrite::__ANON__
/usr/lib/perl5/site_perl/5.8.0/POE/Wheel/ReadWrite.pm:309
STACK POE::Session::_invoke_state
/usr/lib/perl5/site_perl/5.8.0/POE/Session.pm:484
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/POE/Kernel.pm:983
STACK POE::Kernel::_dispatch_event
/usr/lib/perl5/site_perl/5.8.0/POE/Kernel.pm:969
STACK POE::Kernel::_data_ev_dispatch_due
/usr/lib/perl5/site_perl/5.8.0/POE/Resource/Events.pm:256
STACK POE::Kernel::loop_do_timeslice
/usr/lib/perl5/site_perl/5.8.0/POE/Loop/Select.pm:315
STACK POE::Kernel::loop_run
/usr/lib/perl5/site_perl/5.8.0/POE/Loop/Select.pm:323
STACK POE::Kernel::run
/usr/lib/perl5/site_perl/5.8.0/POE/Kernel.pm:1218
STACK toplevel ./proserver:185
-------------------------------------------
at ../lib/Bio/Das/ProServer/SourceAdaptor/biomart.pm line 146
It seems to us that the ProServer got stuck when applying the
das_features method from the Bio/Das/ProServer/SourceAdaptor.pm module.
Can anyone still follow? Any ideas how to proceed?
Thanks in advance.
Els Vanbleu
------------------------------------------------------------------------
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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