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.
Hi,
All attribute which end by "something"_place are placeholders.
I had, at some point, to use place holders for the attribute lists.
Here aaeg_strand_place is a placeholder of aaeg_transcript_chrom_strand
and so on :
aaeg_chro_place -> aaeg_chr_name
aaeg_cigar_place -> aaeg_cigar_line
Also, we use attribute lists here because the formatters have to receive
a bunch of attributes in a certain order, in order to work.
Hope this helps
Ben
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
-------------------------------------------------------------------------------
--
Benoit Ballester, PhD
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom
