Thank you for the advice, I've put your piece of script into my
getDisplayNames subroutine of my formatter, but unfortunately the main
$option loop exists always on the first test (!$option->filter).
I've dive a little further into the BioMart code to see where my filters
disappeared, and it seems that's in the /execute/ subroutine of the
QueryRunner:
$self->executionPlan($query);
my $formatterName = $query->formatter() || 'TSV';
my $module = "BioMart::Formatter::$formatterName";
$self->loadModule($module);
my $formatter = $module->new();
* $query = $formatter->processQuery($query);
$self->executionPlan($query);# call again as formatter processQuery
can
# change plan
my $rtable = $self->_getResultTable($query);
* if ($query->count){
$self->set('count',$rtable);
}
else{
$formatter->resultTable($rtable);
$self->set('formatter',$formatter);
}
* they are still there when the processQuery of the formatter is called
* still there too just after when the executionPlan is call again on
the query
* but once the _getResultTable has been called, nothing more ... I
suspect something in the _processPath of the QueryRunner, but what ?
Thus, to make it works easily, I've modified my code and moved some
parts into the processQuery where the filters are still well defined,
and I store now values I need for the getDisplayNames into a formatter
object attribute created for this purpose.
Thanks
Patrice
On 12/03/2010 10:34 PM, Syed Haider wrote:
Hey Patrice,
look at this piece of code, hope this helps:
foreach my $option(@{$filter->getAllOptions}){
next if (!$option->filter);
my $options = $option->filter->getAllOptions;
my @vals;
foreach (@$options){
push @vals,$_->value;
}
my @filters = ($option->filter);
foreach my $filt (@filters) {
print $filt->name."\t".$filt->displayName;
}
}
On 30/11/2010 14:26, Patrice Dehais wrote:
Hello
I've a filter which defines a chromosomal region, thus in the marteditor
it has no field, tableConstraint, nor key but a filterList with
appropriate filter list (chr,start,end).
It works fine when I use Web interface of BioMart.
However, I need to retrieve the value of this filter in a homemade
Formatter.
I can retrieve values of all other filters (except this one) using this
script in the getDisplayNames subroutine of the formatter :
foreach my $f (@{$query->getAllFilters}) {
foreach my $row (@{$f->getTable->getRows}){
printf STDERR "filter name: %s value=
%s\n",$f->name,$row->[0];
}
}
Why doesn't it work for this special kind of filter ?
thanks
Patrice
--
Patrice Dehais : INRA - LCG - SIGENAE,
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
tel: +33(0)5.61.28.57.08 fax: +33(0)5.61.28.53.08
http://www.sigenae.org
