Arek Kasprzyk wrote: > > 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.
Hi Arek, Lots of our users want to use BioMart now so I need to try and get Taverna working with 0.4. I can construct query.xml for most of my tests, including ones with multiple datasets. My problems so far are: 1. linking datasets where none of the importables/exportables match 2. sequences - I use the datasetLink value specified by the sequence attribute but this gives me an error. Any examples you can give me on how to create query.xml will be very useful. I would also like the 0.5 spec so we can ready for when the 0.5 server is running. David. -- David Withers School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. Tel: +44(0)161 275 0145
