Hi Pierre, Hugh,
thanks for your support. We will wait then some news from you (release
5.0.5).
cheers,
Erick
Pierre De Wilde wrote:
It was a possible workaround. I have used FILTER(isIRI(?o) =
false) instead of FILTER(!isIRI(?o)) in 5.0.3, but it doesn't seem to
work with sameTerm().
Regarding 5.0.4, it may be safer to wait the 'official' confirmation
that your problem is solved.
Pierre
2008/2/6, Erick Antezana <er...@psb.ugent.be
<mailto:er...@psb.ugent.be>>:
Hi Pierre,
I tried out the line:
FILTER(sameTerm(?prot,cco:CCO_B0001243) = false)
and some variants like:
FILTER(sameTerm(?prot,cco:CCO_B0001243) = 'false')
I've got the following message:
37000 Error SQ074: Line 9: syntax error at '=' before 'isnull'
SPARQL query:
define sql:signal-void-variables 1 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)=false)
}
We will probably then install 5.0.4, unless you have any other
suggestion?
thanks,
Erick
Pierre De Wilde wrote:
> Hi Erick,
>
>
> In 5.0.3, FILTER(!...) may not work properly. Instead, try
> this: FILTER(sameTerm(?prot,cco:CCO_B0001243) = false)
> In 5.0.4, FILTER(!...) seems to work properly.
>
>
> Pierre
>
> 2008/2/6, Erick Antezana <er...@psb.ugent.be
<mailto:er...@psb.ugent.be>
> <mailto:er...@psb.ugent.be <mailto:er...@psb.ugent.be>>>:
>
> 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 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:11:52 LTRS_1 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:14:38 LTRS_1 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:14:38 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Compile text: isnull
> (sparql_to_sql_text (?))
> 15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199>
<http://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 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:11:52 LTRS_1 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:14:38 LTRS_1 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Commit transact 0x354ffcf890 0
> 15:14:38 LTRS_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Restart transact 0x354ffcf890
> 15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199>
<http://130.88.195.199> Internal
> Compile text: isnull
> (sparql_to_sql_text (?))
> 15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199>
<http://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
<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>
>
<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
<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>>
>
>
>
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