On 17 May 2006, at 17:15, David Withers wrote:
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.
Hi David,
apologies, I misunderstood your question first time round. You are
right.
This value indeed should be specified in the config file if the
'default'
is to be displayed. We'll add this to the config.
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?
probably not. I simply pointed you to where these things live but
it is possible that this particular bit is hardcoded in our client
somewhere
in which case it is an oversight on our part. It is probably better is
someone
more familiar with MartView could comment and disprove my 'theories' if
necessary.
Unless you hear to the contrary from someone else you can assume for
now that in 0.4
this is a hardcoded set of rules for this particular filter. In this
indeed is the case this
will be better formalized for 0.5
a.
David.
--
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
Tel: +44(0)161 275 0145
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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
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