Hi All,
My fallback query, which uses rdfs:subClassOf/ to a depth of 25 and
unions them, does not seem to produce results but does use near 100%
single thread CPU.
The graph this runs on has about 55548 triples in it.
status('rhck')
gives
Running Statements:
Time (msec) Text
1028035 sparql
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> CONSTRUCT {?sub rdfs
15 #line 1 "(console)"
status('rhck')
Index Usage:
Table Index Touches Reads %Miss Locks Waits
%W n-dead
DB.DBA.RDF_QUAD RDF_QUAD 72931116 21 0% 1842692
0 0% 0
DB.DBA.RDF_QUAD RDF_QUAD_SP 57266334 1 0% 306655
0 0% 0
DB.DBA.RDF_QUAD RDF_QUAD_POGS 2847786305 12 0% 6743708
0 0% 0
DB.DBA.RDF_QUAD RDF_QUAD_OP 22068653 2 0% 239990
0 0% 0
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
CONSTRUCT
{ ?sub rdfs:subClassOf ?super .}
FROM <http://purl.uniprot.org/enzymes/>
WHERE
{ { ?sub
((((((((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
(((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf
?super }
UNION
{ ?sub
((rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf)/rdfs:subClassOf ?super }
UNION
{ ?sub (rdfs:subClassOf/rdfs:subClassOf)/rdfs:subClassOf ?super }
UNION
{ ?sub rdfs:subClassOf/rdfs:subClassOf ?super }
UNION
{ ?sub rdfs:subClassOf ?super }
}
Regards,
Jerven
On 14/05/13 10:16, Jerven Bolleman wrote:
> Hi All,
>
> When executing
>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
>
> CONSTRUCT
> { ?sub rdfs:subClassOf ?super .}
> FROM <http://purl.uniprot.org/go/>
> WHERE
> { ?sub (rdfs:subClassOf)* ?super }
>
> I get the following exception.
>
> Query evaluation failed:PREFIX
> rdfs:<http://www.w3.org/2000/01/rdf-schema#> CONSTRUCT {?sub
> rdfs:subClassOf ?super} FROM <http://purl.uniprot.org/go/> WHERE {?sub
> rdfs:subClassOf* ?super}
> org.openrdf.query.QueryEvaluationException: : SPARQL execute
> failed:[PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> CONSTRUCT
> {?sub rdfs:subClassOf ?super} FROM <http://purl.uniprot.org/go/> WHERE
> {?sub rdfs:subClassOf* ?super}]
> Exception:virtuoso.jdbc3.VirtuosoException: TR...: transitive start
> not given
> at
> virtuoso.sesame2.driver.VirtuosoRepositoryConnection.executeSPARQLForHandler(Unknown
> Source)
>
>
> Regards,
> Jerven
--
-------------------------------------------------------------------
Jerven Bolleman [email protected]
SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
1211 Geneve 4,
Switzerland www.isb-sib.ch - www.uniprot.org
Follow us at https://twitter.com/#!/uniprot
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