[MOBY-dev] bug in MOBY::CommunSubs:getCrossReferences

[Sophie Durand]

Hello,

I have a problem while parsing the following moby output:

<?xml version='1.0' encoding='UTF-8'?><moby:MOBY
xmlns:moby='http://www.biomoby.org/moby'><moby:mobyContent
moby:authority='genoplante-info.infobiogen.fr'><moby:serviceNotes>GENOPLANTE 

PHYTOPROT. IDDN.FR.001.250004.000.S.P.2003.000.10300. This database, its
constitutive components and its documentation, are the intellectual
property of GENOPLANTE-VALOR.</moby:serviceNotes><moby:mobyData
moby:queryID='1'><moby:Collection
moby:articleName=''><moby:Simple><moby:Object
moby:namespace='AGI_LocusCode' moby:id='AT3G23130'
 ><CrossReference><moby:Object moby:namespace='PHYTOPROT_CLUSTER_Id' 
moby:id='148'
/></CrossReference></moby:Object></moby:Simple></moby:Collection></moby:mobyData></moby:mobyContent></moby:MOBY>

I'm using the Perl API with a genericServiceInputParser call and then a 
getCrossReferences call to obtain the cross reference. But in this case, 
I don't get any cross reference. If I delete the "moby:" namespaces like 
this :
<CrossReference><moby:Object namespace='PHYTOPROT_CLUSTER_Id'  id='148' 
/></CrossReference>
it works well.

So I looked in the code, and I modified the following function in 
MOBY::CommunSubs.pm, and then it works:

sub _makeObjectType {
     my ($xref) = @_;
     my $ns = $xref->getAttributeNode('namespace');
     $ns = $xref->getAttributeNode('moby:namespace') unless $ns;
     return undef unless $ns;
     my $id = $xref->getAttributeNode('id');
     $id = $xref->getAttributeNode('moby:id') unless $id;  # INSTEAD OF $ns
     return undef unless $id;
     my $XREF = MOBY::CrossReference->new(
         type => "object",
         namespace => $ns->getValue,
         id => $id->getValue,
      );
}

-- 
Sophie Durand
Ingénieure en Bioinformatique
INRA / URGI chez Infobiogen
523, place des Terrasses de l'Agora
91000 Evry - FRANCE