Re: [Virtuoso-devel] SERVICE calls to Virtuoso 7 from Sesame 2.8

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Hi Simon,

We are looking into the cause of the error with the query containing the "VALUES" clause and will report back ...

Best Regards
Hugh Williams
Professional Services
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On 28 Apr 2014, at 23:31, Simon Jupp <ju...@eb...> wrote:

> 
> I can abstract away from my data a bit using dbpedia to illustrate the problem. Can anyone tell me if the following is valid SPARQL 1.1? (dbpedia sparql endpoint seems down now, so I couldn't check). It seems sesame is ok with this syntax, but virtuoso isn't.
> 
> SELECT  ?__rowIdx ?subject
> WHERE
>   {  ?subject a ?type  }
> LIMIT 10
> VALUES ( ?__rowIdx ?type ) {
>   ( "0" <http://umbel.org/umbel#PresidentOfOrganization> )
> }
> 
> I can do a similar query on the uniprot sparql endpoint (http://beta.sparql.uniprot.org) that works fine
> 
> SELECT  ?__rowIdx ?subject
> WHERE
>   {  ?subject a ?type  }
> LIMIT 10
> VALUES ( ?__rowIdx ?type ) {
>   ( "0" <http://purl.uniprot.org/core/Taxon> )
> }
> 
> It seems sesame is ok with this syntax, but virtuoso isn't.
> 
> Peter, just to clarify the original query to my local Sesame server was
> 
> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
> PREFIX mydata:<http://www.mydomain.com/mydata#>
> PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
> 
> SELECT ?geneid ?probe WHERE {
>   ?result mydata:dbXref ?geneid . 
>    SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
>       ?probe atlasterms:dbXref ?geneid . 
>     }
> }
> 
> If I look in the logs of http://www.ebi.ac.uk/rdf/services/atlas/sparql, the query that actually gets sent from sesame 2.7.11 is
> 
> SELECT ?geneid ?probe WHERE {
>       ?probe atlasterms:dbXref ?geneid . 
> }
> 
> This works fine, it looks like sesame gets the full solution from the atlas endpoint, and then does the binding with my local data after. However, same data and same query doesn't work with sesame 2.8, instead the query I see coming into the atlas endpoint uses the VALUES clause, so something has changed in sesame 2.8 as far as I can see.
> 
> Cheers
> Simon
> 
> On 28 Apr 2014, at 22:20, Peter Ansell wrote:
> 
>> Hi Simon,
>> 
>> Sesame-2.8 is still in beta, but I am fairly sure that we haven't modified the SPARQL code much since 2.7. Can you test that it also sends a similar query with 2.7.11?
>> 
>> It doesn't look like a SPARQL-1.1 Federated Query by the way. It looks like a fairly normal SPARQL-1.1 Query.
>> 
>> Thanks,
>> 
>> Peter
>> 
>> On Tuesday, 29 April 2014 1:58 AM, Hugh Williams <hwi...@op...> wrote:
>> Hi Simon,
>> 
>> So you are saying the Sesame server is executing the SPARQL-FED query targeting a Virtuoso 7.1 endpoint and the query below is what is then being executed against the Virtuoso Server and failing ?
>> 
>> Is there a publicly available endpoint this query can be run against to see the error, or are the datasets used available for download so it could be setup locally ?
>> 
>> Best Regards
>> Hugh Williams
>> Professional Services
>> OpenLink Software, Inc.      //              http://www.openlinksw.com/
>> Weblog   -- http://www.openlinksw.com/blogs/
>> LinkedIn -- http://www.linkedin.com/company/openlink-software/
>> Twitter  -- http://twitter.com/OpenLink
>> Google+  -- http://plus.google.com/100570109519069333827/
>> Facebook -- http://www.facebook.com/OpenLinkSoftware
>> Universal Data Access, Integration, and Management Technology Providers
>> 
>> On 28 Apr 2014, at 16:07, Simon Jupp <ju...@eb...> wrote:
>> 
>>> Hi, 
>>> 
>>> We are having a problem with federated queries coming into our virtuoso 7.1 endpoint from a Sesame server running sesame 2.8. 
>>> 
>>> Sesame sends queries using the VALUES keyword, but the query will not parse in virtuoso. This is an example of a query coming in from Sesame  
>>> 
>>> PREFIX  atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
>>> PREFIX  sesame: <http://www.openrdf.org/schema/sesame#>
>>> PREFIX  fn:   <http://www.w3.org/2005/xpath-functions#>
>>> 
>>> SELECT  ?__rowIdx ?probe
>>> WHERE
>>>   { ?probe atlasterms:dbXref ?geneid }
>>> LIMIT   100000
>>> VALUES ( ?__rowIdx ?geneid ) {
>>>   ( "0" <http://identifiers.org/ensembl/ENSMUSG00000024673> )
>>>   ( "2" <http://identifiers.org/ensembl/ENSMUSG00000028158> )
>>>   ( "4" <http://identifiers.org/ensembl/ENSMUSG00000033715> )
>>> }
>>> The Virtuoso error message is
>>> Virtuoso 37000 Error SP031: SPARQL compiler: Variable name 'geneid' is used in the BINDINGS clause but not in the query result set
>>> This SPARQL syntax looks ok to me. 
>>> 
>>> Cheers
>>> Simon
>>> 
>>> ---------------------------------------------------
>>> Simon Jupp
>>> Samples Phenotypes and Ontologies Team
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>> 
>>> Web: http://www.ebi.ac.uk/~jupp
>>> E-mail: ju...@eb...
>>> Tel: + 44 (0) 1223 494 664
>>> 
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>> 
>> 
>> ------------------------------------------------------------------------------
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>> 
>> 
> 
> ------------------------------------------------------------------------------
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> Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
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