Re: [Virtuoso-users] Fwd: Segmentation fault

Erick Antezana Wed, 06 Feb 2008 07:13:15 -0800

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, trythis: 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>>:


    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> Internal
    Commit transact 0x354ffcf890 0
    15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:11:52 LTRS_1 0 130.88.195.199 <http://130.88.195.199> Internal
    Commit transact 0x354ffcf890 0
    15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:14:38 LTRS_1 0 130.88.195.199 <http://130.88.195.199> Internal
    Commit transact 0x354ffcf890 0
    15:14:38 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Compile text:  isnull
    (sparql_to_sql_text (?))
    15:14:38 COMP_2 0 130.88.195.199 <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> Internal
    Commit transact 0x354ffcf890 0
    15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:11:52 LTRS_1 0 130.88.195.199 <http://130.88.195.199> Internal
    Commit transact 0x354ffcf890 0
    15:11:52 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:14:38 LTRS_1 0 130.88.195.199 <http://130.88.195.199> Internal
    Commit transact 0x354ffcf890 0
    15:14:38 LTRS_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Restart transact 0x354ffcf890
    15:14:38 COMP_2 0 130.88.195.199 <http://130.88.195.199> Internal
    Compile text:  isnull
    (sparql_to_sql_text (?))
    15:14:38 COMP_2 0 130.88.195.199 <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>


    -------------------------------------------------------------------------
    This SF.net email is sponsored by: Microsoft
    Defy all challenges. Microsoft(R) Visual Studio 2008.
    http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
    _______________________________________________
    Virtuoso-users mailing list
    Virtuoso-users@lists.sourceforge.net
    <mailto:Virtuoso-users@lists.sourceforge.net>
    https://lists.sourceforge.net/lists/listinfo/virtuoso-users

------------------------------------------------------------------------


-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
------------------------------------------------------------------------

_______________________________________________
Virtuoso-users mailing list
Virtuoso-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/virtuoso-users

Re: [Virtuoso-users] Fwd: Segmentation fault

Reply via email to