Hi David This is fixed now, and in CVS. The AttributeLists now appear as single attribute in XML and this applies to the query sent back to martservice as well. Furthermore, the reason attributelists are not exposed as individual attributes anymore is that order of attributes in an attributeList is strict for formatters and processing.
Should you need further help, please do write. Kind Regards Syed > I've constructed the following query by splitting the attribute lists > into single attributes. > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName="default" count="0" softwareVersion="0.5" > requestId="taverna"> > <Dataset name="compara_aaeg_lafr_orthologs"> > <Attribute name="aaeg_lafr_nonorientedrawsequence" /> > <Attribute name="aaeg_peptide_coor" /> > <Attribute name="lafr_peptide_coor" /> > <Attribute name="aaeg_strand_place" /> > <Attribute name="lafr_strand_place" /> > <Attribute name="aaeg_seq_edits" /> > <Attribute name="lafr_seq_edits" /> > <Attribute name="aaeg_chro_place" /> > <Attribute name="lafr_chro_place" /> > <Attribute name="aaeg_cigar_place" /> > <Attribute name="lafr_cigar_place" /> > <Attribute name="tagheader" /> > <Attribute name="subtype_place" /> > <Attribute name="subtype_place" /> > <Filter name="subtype" value="Bilateria" /> > <Filter name="homol_description" > value="apparent_ortholog_one2one" /> > </Dataset> > </Query> > > When I run the query I get the error: > > Query ERROR: caught BioMart::Exception::Usage: Attribute > aaeg_strand_place NOT FOUND > > If I construct the same query via the website the xml is: > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName = "default" Header = "1" count = "" > softwareVersion = "0.5" > > > <Dataset name = "compara_aaeg_lafr_orthologs" interface = "default" > > <Attribute name = "aaeg_lafr_nonorientedrawsequence" /> > <Attribute name = "aaeg_peptide_coor" /> > <Attribute name = "lafr_peptide_coor" /> > <Attribute name = "aaeg_transcript_chrom_strand" /> > <Attribute name = "lafr_transcript_chrom_strand" /> > <Attribute name = "aaeg_seq_edits" /> > <Attribute name = "lafr_seq_edits" /> > <Attribute name = "aaeg_chr_name" /> > <Attribute name = "lafr_chr_name" /> > <Attribute name = "aaeg_cigar_line" /> > <Attribute name = "lafr_cigar_line" /> > <Attribute name = "tag_header" /> > <Attribute name = "subtype" /> > <Attribute name = "subtype" /> > <Filter name = "subtype" value = "Bilateria"/> > <Filter name = "homol_description" value = > "apparent_ortholog_one2one"/> > </Dataset> > </Query> > > It seems that 'aaeg_strand_place' should be > 'aaeg_transcript_chrom_strand'. Are the dataset configurations incorrect > or have I missed something? > > David. > > -- > David Withers > School of Computer Science, University of Manchester, > Oxford Road, Manchester, M13 9PL, UK. > Tel: +44(0)161 275 0145 > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
