Hi Arek,
The XML says:
tableConstraint="ox_EntrezGene__dm" type="text"/>
The error message says it is looking for this table:
ERROR: caught BioMart::Exception::Database: Error during query
execution: Table 'metazoa_mart_3.ox_EntrezGene__dm' doesn't exist
but the table in your mart is called:
dmelanogaster_eg_gene__ox_EntrezGene__dm;
Yes, that was puzzling me, but I thought that it'd pick up the dataset
name to qualify it with. Or am I getting confused with the template
mechanism? My template looks like this before marteditor exports it:
<Option checkForNulls="true" displayName="EntrezGene ID(s)"
displayType="text" field="dbprimary_acc_1074" internalName="entrezgene"
isSelectable="true" key="gen\
e_id_1020_key" legal_qualifiers="=,in" multipleValues="1" qualifier="="
tableConstraint="ox_EntrezGene__dm" type="text">
<SpecificOptionContent field="dbprimary_acc_1074"
internalName="dmelanogaster_eg_gene" key="translation_id_1068_key"
tableConstraint="ox_EntrezGene__dm"/>
If I understand you, am I correct in thinking that this should actually
be much simpler in order to work:
<Option checkForNulls="true" displayName="EntrezGene ID(s)"
displayType="text" field="dbprimary_acc_1074" internalName="entrezgene"
isSelectable="true" key="gen\
e_id_1020_key" legal_qualifiers="=,in" multipleValues="1" qualifier="="
tableConstraint="ox_EntrezGene__dm" type="text">
<SpecificOptionContent internalName="dmelanogaster_eg_gene"
key="translation_id_1068_key"/>
Cheers,
Dan.
--
Dan Staines, PhD Ensembl Genomes Technical Coordinator
EMBL-EBI Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
