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. The config for upstream_flank says that it's of type list, but doesn't specify any options and I can't find anywhere where a value of 100 is specified. David. -- David Withers School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. Tel: +44(0)161 275 0145
