Hi all,
I continued debugging and as far as I see, the biomart.pm module is now
working fine. I copy-pasted the changes I made to the build_features
method below. There seemed to be an issue with the attributes given to
the 'new' method of the BioMart::Query and to the 'getResultTable'
method of BioMart::QueryPlanner but that should be fixed now.
Have fun!
Regards,
ELS
sub build_features
{
my ($self, $opts) = @_;
my $segment = $opts->{'segment'} || return ( );
my $segment_start = $opts->{'start'};
my $segment_end = $opts->{'end'};
# Use $segment and, if they are defined, $segment_start and
# $segment_end, to fetch the appropriate data from the mart.
my $virtual_schema_name;
if (defined($self->{'BioMart'}->{'virtualSchema'})) {
$virtual_schema_name =
($self->{'BioMart'}->{'virtualSchema'});
}else {
$virtual_schema_name = DEFAULTVSCHEMA;
}
### modified by EV ###
my $query = BioMart::Query->new( 'registry' =>
$self->{'BioMart'}->{'registry'},
'virtualSchemaName'=>$virtual_schema_name);
my $atts = $self->{'BioMart'}->{'attributes'};
foreach my $att (@{$atts}) {
$query->addAttribute($att);
}
my $segFilter = $self->{'BioMart'}->{'filters'}->[0]->new();#clone
my $segTable = BioMart::AttributeTable->new();
$segTable->addRow( [ $segment ] );
$segFilter->setTable($segTable);
$query->addFilter($segFilter);
if ($segment_start && $segment_end) {
my $startFilter =
$self->{'BioMart'}->{'filters'}->[1]->new();#clone
my $startTable = BioMart::AttributeTable->new();
$startTable->addRow( [ $segment_start ] );
$startFilter->setTable($startTable);
$query->addFilter($startFilter);
my $endFilter = $self->{'BioMart'}->{'filters'}->[2]->new();#clone
my $endTable = BioMart::AttributeTable->new();
$endTable->addRow( [ $segment_end ] );
$endFilter->setTable($endTable);
$query->addFilter($endFilter);
}
my $reqKeys = REQUIREDKEYS;
my $defaults = DEFAULTS;
my @features = ( );
my $query_planner = BioMart::QueryPlanner->new();
### modified by EV ###
my $rtable = $query_planner->getResultTable($query);
#,
#$self->{'BioMart'}->{'registry'},
#undef,
#INIT_BATCHSIZE);
ROW: while ($rtable->hasMoreRows) {
my $row = $rtable->nextRow;
my $href = {};
#skip this feature unless all keys in REQUIREDKEYS are defined
my $good = 0;
KEY: foreach my $reqKey (@{$reqKeys}) {
my $pos = $self->{'BioMart'}->{'required_keys'}->{$reqKey};
next KEY unless ($row->[$pos]);
$good++;
}
next ROW unless($good);
my $i = 0;
while ($i < @{$row}) {
my $key = $self->{'BioMart'}->{'feature_keys'}->[$i];
$href->{$key} = $row->[$i] || $defaults->{$key}; #may be
either default, or undef
$i++;
}
push @features, $href;
}
return @features;
}
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: dinsdag 11 juli 2006 12:12
To: Els Vanbleu
Cc: [email protected]
Subject: Re: Biomart as DAS server
On 11 Jul 2006, at 08:28, Els Vanbleu wrote:
> Dear all,
>
> We are trying to implement BioMart as DAS server. Therefore we
> followed
> the instructions as mentioned in the README file of the /das folder,
> i.e. install ProServer, make an Importable/Exportable in the mart and
> write a biomart.ini file. All dependencies were correctly established
> and the ProServer was successfully launched using our biomart.ini file
> (we get a pid.file and output is directed to a log.file).
>
> With the url (pidserver/das/dsn/) we retrieve the available data
> sources
> but when trying to catch some features (e.g.
> pidserver/das/mymart1/features?segment=B0222.1), the system failed
> (giving a source error).
>
> After intensive debugging, we already think we solved a few bugs,
> namely
> in the das/biomart.pm module
>
> use constant DEFAULTVSCHEMA => "defaultSchema";
>
> should be
>
> use constant DEFAULTVSCHEMA => "default";
>
> in order to have compliant virtualSchemas when no virtualSchema is
> specifically set in the mart (and so the mart uses the 'default'
> virtualSchema).
>
> Secondly, it turned out to us that the Location->getDatasetByName
> method
> was case sensitive (BioMart::Configuration::Location), so for our
> purposes we made it case insensitive.
>
> sub getDatasetByName {
> my ($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
------------------------------------------------------------------------
-------
