-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Actually this one's quite straightforward (thankfully!).
The attribute list you are using refers internally to a bunch of placeholder attributes (in this case they're easy to spot because Ben has given them names ending in _place). Those placeholder attributes in turn resolve to real attributes. When using XML queries you need to name the resolved real attributes, not the placeholder ones that pointed to them. I'm not sure if this is a bug or a feature. The MartView web code is aware of it and behaves appropriately, but the requirement to use resolved attributes is not immediately obvious to non-MartView users. cheers, Richard Arek Kasprzyk wrote: > > On 24 Jan 2007, at 16:38, David Withers wrote: > >> 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? >> > > We need Ben's opinion on this. Ben which one is the correct attribute? > a. > > > >> David. >> >> -- David Withers >> School of Computer Science, University of Manchester, >> Oxford Road, Manchester, M13 9PL, UK. >> Tel: +44(0)161 275 0145 >> > > > ------------------------------------------------------------------------------- > > 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 > ------------------------------------------------------------------------------- > > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFt4/r4C5LeMEKA/QRAi23AKCKUi0v8m9HKDDPKh+qVHg5IK4HygCfRbWC XsQbt4YVzAYGjKdfdOFb7F0= =XxdT -----END PGP SIGNATURE-----
