On 11 May 2006, at 17:14, David Withers wrote:
Hi Arek,
I'm trying to run the following query:
<?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_genomic_sequence"
target="hsapiens_gene_ensembl" defaultLink="coding_gene_flank" />
<Links source="hsapiens_gene_ensembl_structure"
target="hsapiens_gene_ensembl" defaultLink="" />
</Query>
but I don't know how to work out the link between
hsapiens_gene_ensembl_structure and hsapiens_gene_ensembl.
Do I need to specify links between all the datasets?
Hi David,
I am afraid so. The current 0.4 implementation for web services
and API query handling is rather complicated as it requires people
to deal with visible and invisible datasets, placeholders, links and
in more complex cases
pretty much the execution path of the query.
All of it will be removed in 0.5 which will not require for clients to
deal with any of it
explicitly and instead will be dealt with by the library on the server
side. The query xml
will only require to specify visible datasets and their attributes and
filters. This is going
to be very straightforward.
Since you are developing a client which is supposed to work against 0.5
you have two choices
here. You can either follow a few examples that we can provide on how
to create query.xml in
cases involving more than one dataset and test it against the 0.4
server (www.biomart.org/biomart/martservice)
or wait for a couple of weeks when we have a new 0.5 test server
running with much simpler spec of query.xml
(alternatively we can provide you the spec for 0.5 query right now and
you can develop against
it until it becomes 'testable' in a couple of weeks or so with the
arrival of a new test server so it does not hold back your development)
Please let us know what your preference is
a.
PS. I am cc-ing this answer to mart-dev list as 'complicated 0.4
query' is the thread of the day today :)
Hope you don't mind.
Thanks,
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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