Arek Kasprzyk wrote: > > On 17 May 2006, at 15:54, David Withers wrote: > >> Arek Kasprzyk wrote: >>> >>> On 17 May 2006, at 12:33, David Withers wrote: >>> >>>> Another question for you. When I send the following query to the >>>> martservice I get an error message returned. Can anyone tell me what >>>> I'm >>>> doing wrong? >>>> >>>> <?xml version="1.0" encoding="UTF-8"?> >>>> <!DOCTYPE Query> >>>> <Query virtualSchemaName="default" count="0"> >>>> <Dataset name="hsapiens_gene_ensembl"> >>>> <Filter name="gene_stable_id" value="ENSG00000100031" /> >>>> </Dataset> >>>> <Dataset name="hsapiens_genomic_sequence"> >>>> <Attribute name="coding_gene_flank" /> >>>> </Dataset> >>>> <Dataset name="hsapiens_gene_ensembl_structure"> >>>> <Attribute name="gene_stable_id" /> >>>> </Dataset> >>>> <Links source="hsapiens_gene_ensembl" >>>> target="hsapiens_gene_ensembl_structure" >>>> defaultLink="hsapiens_internal_transcript_id" /> >>>> <Links source="hsapiens_gene_ensembl_structure" >>>> target="hsapiens_genomic_sequence" defaultLink="coding_gene_flank" /> >>>> </Query> >>>> >>> >>> Hi David, >>> the error was actually thrown on the server side but not propagated to >>> you - sorry. >>> It says >>> >>> Wed May 17 13:44:10 2006] [error] -------------------- EXCEPTION >>> -------------------- >>> DATE: 17-MAY-2006 >>> MSG: Requests for flank sequence must be accompanied by an >>> upstream_flank or downstream_flank request >>> >>> you just need to add this to your query: >>> >>> <Filter name="upstream_flank" value="100" /> >> >> Hi Arek, >> >> Is it possible to work out from the config xml that you need to add this >> filter (and that its value is 100)? Or does it need to be a hard coded >> rule. >> > > Yes, It is yet another pointer attribute. For example look at > agambiae_gene_ensembl dataset > xml under attribute group 'sequence', attribute collection 'upstream' > and the filter > is called: agambiae_genomic_sequece.filter.upstream_flank > > The '100' value is user-defined. I could be anything from 1 to 9999. > Have a look > at > > > http://www.biomart.org/biomart/martview/NtLiZBboU5.mart > > > > This value is provided in the 'Upstream flank' box
The 'Upstream flank' box seems to have a default value of 100 but this doesn't seem to be specified anywhere in the config files. Other filters, such as 'gene_chrom_end', have a defaultValue attribute specified in the FilterDescription. I am still confused as to how you know that you need to add the upstream_flank filter if the user has selected the coding_gene_flank attribute. Is there a set of rules that I am missing? David. -- David Withers School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. Tel: +44(0)161 275 0145
