Eric, I've fixed this bug in the commercial version and the fix is now on its way to Virtuoso Open Source CVS. I guess that in few hours you'll get either updated version at SourceForge or a diff with 5.0.4 or both.
The query you've provided returns empty result set for me, but it's due to inappropriate constant or due to inaccurate loading of the data. But I can now get SQL> sparql define input:default-graph-uri <http://www.cellcycleontology.org/ontology/rdf/CCO> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#> SELECT ?prot WHERE{ <http://www.cellcycleontology.org/ontology/rdf/CCO_B0000005> cco:is_a ?ortholog_cluster . ?prot cco:is_a ?ortholog_cluster . FILTER(! sameTerm(?prot,<http://www.cellcycleontology.org/ontology/rdf/CCO_B0000005>)) } limit 10; prot VARCHAR _______________________________________________________________________________ http://www.cellcycleontology.org/ontology/rdf/CCO_B0000001 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000002 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000003 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000004 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000006 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000007 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000008 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000010 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000011 http://www.cellcycleontology.org/ontology/rdf/CCO_B0000012 10 Rows. -- 4 msec. after loading data that way: DB.DBA.RDF_LOAD_RDFXML (file_to_string_output('EricAntezana/cco.rdf'), 'http://www.cellcycleontology.org/ontology/rdf/CCO', 'http://www.cellcycleontology.org/ontology/rdf/CCO'); Best Regards, Ivan Mikhailov, OpenLink Software. On Wed, 2008-02-06 at 14:19 +0000, Erick Antezana wrote: > Hi, > > we're running 5.0.3 on a linux box. So far everything was going > perfectly until we tested the following query which is very simple > against a huge graph (that could be found here: > http://www.cellcycleontology.org/ontology/rdf/cco.rdf): > > PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> > PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#> > > SELECT ?prot > WHERE{ > cco:CCO_B0001243 cco:is_a ?ortholog_cluster . > ?prot cco:is_a ?ortholog_cluster . > FILTER(!sameTerm(?prot,cco:CCO_B0001243)) > } > > the endpoint is: http://crunch.fvms.ugent.be:8890/sparql > > It seems that the "sameTerm" is causing this problem. I tried to play > with the parameters int he INI file by increasing the buffers, etc, etc > but no success...Any hints would be appreciated. > > In the logs, we got: > > 15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:14:38 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:14:38 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:14:38 COMP_2 0 130.88.195.199 Internal Compile text: isnull > (sparql_to_sql_text (?)) > 15:14:38 COMP_2 0 130.88.195.199 Internal Compile text: sparql define > output:valmode "LONG" define input:default-graph-uri > <http://www.cellcycleontology.org/ontology/rdf/CCO> PREFIX > rdfs:<http://www.w3.org/2000/01/rdf-schema#> > PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#> > > SELECT ?prot > WHERE{ > cco:CCO_B0001243 cco:is_a ?ortholog_cluster . > ?prot cco:is_a ?ortholog_cluster . > FILTER(!sameTerm(?prot,cco:CCO_B0001243)) > } > > and we also got: > > 15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:14:38 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0 > 15:14:38 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890 > 15:14:38 COMP_2 0 130.88.195.199 Internal Compile text: isnull > (sparql_to_sql_text (?)) > 15:14:38 COMP_2 0 130.88.195.199 Internal Compile text: sparql define > output:valmode "LONG" define input:default-graph-uri > <http://www.cellcycleontology.org/ontology/rdf/CCO> PREFIX > rdfs:<http://www.w3.org/2000/01/rdf-schema#> > PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#> > > SELECT ?prot > WHERE{ > cco:CCO_B0001243 cco:is_a ?ortholog_cluster . > ?prot cco:is_a ?ortholog_cluster . > FILTER(!sameTerm(?prot,cco:CCO_B0001243)) > } > > thanks, > Erick > p.s. Here it is the HTTP line: > http://crunch.fvms.ugent.be:8890/sparql?default-graph-uri=http%3A%2F%2Fwww.cellcycleontology.org%2Fontology%2Frdf%2FCCO&query=PREFIX+rdfs%3A%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+cco%3A%3Chttp%3A%2F%2Fwww.cellcycleontology.org%2Fontology%2Frdf%2FCCO%23%3E%0D%0A%0D%0ASELECT+%3Fprot%0D%0AWHERE%7B%0D%0A+++cco%3ACCO_B0001243+cco%3Ais_a+%3Fortholog_cluster+.%0D%0A+++%3Fprot+cco%3Ais_a+%3Fortholog_cluster+.%0D%0A+++FILTER%28%21sameTerm%28%3Fprot%2Ccco%3ACCO_B0001243%29%29%0D%0A%7D&format=text%2Fhtml&debug=on > >
