Re: [Taverna-users] [mart-admin] BioMart broken in Taverna

[David W. <dav...@ma...>]

Syed Haider wrote:
> Mainly David,
> 
> Just a thought based on my limited understanding about how taverna
> works, guess you retrieve the dataset configurations via webservice and
> your request is like:
> 
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=hsapiens_gene_ensembl
> 
> and the response you are getting now is :
> 
> Dataset name conflict for hsapiens_gene_ensembl. Need to further qualify
> with the virtualSchemaName as well
> 
> however for other datasets, you do receive the XML like always. The
> above response is generated when you have more than one datasets with
> same name, effectively you must specify the virtualschema=NAME
> 
> so in our case, the above request would be:
> 
> http://www.biomart.org/biomart/martservice?type=configuration&virtualschema=default&dataset=hsapiens_gene_ensembl
> 
> 
> The other Mart on Biomart central server which contains a dataset with
> same name i-e 'hsapiens_gene_ensembl' is in virtualschema
> 'pancrease_expression_db', so its request would be
> 
> http://www.biomart.org/biomart/martservice?type=configuration&virtualschema=pancreas_expression_db&dataset=hsapiens_gene_ensembl

Hi Syed

I do specify the virtualschema in the queries. This problem has been 
fixed in lastest version of Taverna (1.5.2.1); the main problem was that 
I was specifying the interface and some marts specify incorrect 
interface names (e.g. pepseekerGOLD_mart has an interface of 
'default,default').

David.


-- 
David Withers
School of Computer Science, University of Manchester,
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Tel: +44(0)161 275 0145