Hi Rumi,
I did it again following your indications. Now, the message that come up
with the original query:
CL033: Connect failed to localhost:1111 = localhost:1111.
in lines 1-78 of Top-Level:
#line 1 "(console)"
sparql
define sql:log-enable 3
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX prv: <http://purl.org/net/provenance/ns#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX dctypes: <http://purl.org/dc/dcmitype/>
INSERT
{
GRAPH <http://rdf.disgenet.org/nanopub/test1>
{
?nanopub a np:Nanopublication .
?nanopub np:hasAssertion ?assertionGraph .
?assertionGraph a np:Assertion .
?nanopub np:hasProvenance ?provenanceGraph .
?provenanceGraph a np:Provenance .
?nanopub np:hasPublicationInfo ?publicationInfoGraph .
?publicationInfoGraph a np:PublicationInfo .
}
GRAPH ?assertionGraph
{
?association a sio:SIO_000983 .
?association sio:SIO_000628 ?gene .
?gene a ncit:C16612 .
?association sio:SIO_000628 ?disease .
?disease a ncit:C7057 .
}
GRAPH ?provenanceGraph
{
?assertionGraph sio:SIO_000772 ?pubmed .
?assertionGraph sio:SIO_000253 ?source .
?source rdfs:comment ?curation .
?assertionGraph dcterms:description ?sentence .
}
GRAPH ?publicationInfoGraph
{
?nanopub pav:authoredBy <http://orcid.org/0000-0003-0169-8159> ;
dcterms:created ?now ;
pav:createdBy <http://orcid.org/0000-0003-0169-8159> ;
dcterms:rights
<http://opendatacommons.org/licenses/odbl/1.0/> ;
dcterms:rightsHolder <http://ibi.imim.es/> ;
prv:usedData ?dgnTitle ;
pav:version ?dgnVersion .
}
}
USING <http://rdf.disgenet.org/>
WHERE
{
?type rdfs:subClassOf+ sio:SIO_000983 .
?association a ?type .
?association sio:SIO_000628 ?gene .
?gene a ncit:C16612 .
?association sio:SIO_000628 ?disease .
?disease a ncit:C7057 .
?association sio:SIO_000772 ?pubmed .
?association sio:SIO_000253 ?source .
?source rdfs:comment ?curation .
?association dcterms:description ?sentence .
?disgenet rdf:type dctypes:Dataset .
?disgenet dcterms:title ?dgnTitle .
filter regex(?dgnTitle, "^DisGeNET")
?disgenet pav:version ?dgnVersion .
BIND(iri(concat(str(?association),"_nanopub")) as ?nanopub)
BIND(iri(concat(str(?nanopub),"_assertion")) as ?assertionGraph)
BIND(iri(concat(str(?nanopub),"_provenance")) as ?provenanceGraph)
BIND(iri(concat(str(?nanopub),"_publicationInfo")) as
?publicationInfoGraph)
BIND(NOW() as ?now)
}
cheers,
n
On 09/05/2014 09:56 AM, Rumi wrote:
Hi Núria,
define part should be after sparql i.e.:
sparql
DEFINE sql:log-enable 3
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
etc.
Please let me know if that worked for you.
Best Regards,
Rumi Kocis
On 05-Sep-14 9:38 AM, Nuria Queralt Rosinach wrote:
Hi Rumi,
I did what you suggested querying from our sparql endpoint. Our
server did not understand the 'DEFINE' keyword:
Virtuoso 37000 Error SP030: SPARQL compiler, line 17: syntax error at 'DEFINE'
before 'sql:log-enable
So, i directly performed the query on the shell executing first
'log_enable(3)'. I'll send you the log output (query embedded):
*** Error 08S01: [Virtuoso Driver]CL065: Lost connection to server
in lines 2-78 of Top-Level:
#line 2 "(console)"
sparql
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX np: <http://www.nanopub.org/nschema#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX prv: <http://purl.org/net/provenance/ns#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX dctypes: <http://purl.org/dc/dcmitype/>
INSERT
{
GRAPH <http://rdf.disgenet.org/nanopub/test1>
{
?nanopub a np:Nanopublication .
?nanopub np:hasAssertion ?assertionGraph .
?assertionGraph a np:Assertion .
?nanopub np:hasProvenance ?provenanceGraph .
?provenanceGraph a np:Provenance .
?nanopub np:hasPublicationInfo ?publicationInfoGraph .
?publicationInfoGraph a np:PublicationInfo .
}
GRAPH ?assertionGraph
{
?association a sio:SIO_000983 .
?association sio:SIO_000628 ?gene .
?gene a ncit:C16612 .
?association sio:SIO_000628 ?disease .
?disease a ncit:C7057 .
}
GRAPH ?provenanceGraph
{
?assertionGraph sio:SIO_000772 ?pubmed .
?assertionGraph sio:SIO_000253 ?source .
?source rdfs:comment ?curation .
?assertionGraph dcterms:description ?sentence .
}
GRAPH ?publicationInfoGraph
{
?nanopub pav:authoredBy <http://orcid.org/0000-0003-0169-8159> ;
dcterms:created ?now ;
pav:createdBy <http://orcid.org/0000-0003-0169-8159> ;
dcterms:rights
<http://opendatacommons.org/licenses/odbl/1.0/> ;
dcterms:rightsHolder <http://ibi.imim.es/> ;
prv:usedData ?dgnTitle ;
pav:version ?dgnVersion .
}
}
USING <http://rdf.disgenet.org/>
WHERE
{
?type rdfs:subClassOf+ sio:SIO_000983 .
?association a ?type .
?association sio:SIO_000628 ?gene .
?gene a ncit:C16612 .
?association sio:SIO_000628 ?disease .
?disease a ncit:C7057 .
?association sio:SIO_000772 ?pubmed .
?association sio:SIO_000253 ?source .
?source rdfs:comment ?curation .
?association dcterms:description ?sentence .
?disgenet rdf:type dctypes:Dataset .
?disgenet dcterms:title ?dgnTitle .
filter regex(?dgnTitle, "^DisGeNET")
?disgenet pav:version ?dgnVersion .
BIND(iri(concat(str(?association),"_nanopub")) as ?nanopub)
BIND(iri(concat(str(?nanopub),"_assertion")) as ?assertionGraph)
BIND(iri(concat(str(?nanopub),"_provenance")) as ?provenanceGraph)
BIND(iri(concat(str(?nanopub),"_publicationInfo")) as
?publicationInfoGraph)
BIND(NOW() as ?now)
}
Cheers,
Núria
On 09/04/2014 01:28 PM, Rumi wrote:
Hi Nuria,
On 04-Sep-14 1:00 PM, Nuria Queralt Rosinach wrote:
Dear all,
I am trying to insert new quads into our virtuoso server
constructed via a query pattern. The query is performed against a
graph that contains 14.722.231 triples. The following message come up:
Virtuoso 40005 Error SR325: Transaction aborted because it's log after image
size went above the limit
The virtuoso instance is the open source:
* Version: 07.10.3207
* Build: Mar 24 2014
Is there any solution to this issue? Many thanks in advance.
Please try the following:
1) Add to your query:
DEFINE sql:log-enable 3
2) Execute the query.
3) Send us the query and the log output
Best Regards,
Rumi Kocis
Cheers,
n
--
********************************************************************
Núria Queralt Rosinach
Research Programme on Biomedical Informatics (GRIB)
Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
C/Dr. Aiguader 88, 08003
Barcelona, Spain
Tel.: +34 93 316 0536 (1536)
E-mail:nquer...@imim.es
Skype IM: nuriaqr76
http://ibi.imim.es/
********************************************************************
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--
********************************************************************
Núria Queralt Rosinach
Research Programme on Biomedical Informatics (GRIB)
Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
C/Dr. Aiguader 88, 08003
Barcelona, Spain
Tel.: +34 93 316 0536 (1536)
E-mail:nquer...@imim.es
Skype IM: nuriaqr76
http://ibi.imim.es/
********************************************************************
--
********************************************************************
Núria Queralt Rosinach
Research Programme on Biomedical Informatics (GRIB)
Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
C/Dr. Aiguader 88, 08003
Barcelona, Spain
Tel.: +34 93 316 0536 (1536)
E-mail: nquer...@imim.es
Skype IM: nuriaqr76
http://ibi.imim.es/
********************************************************************
------------------------------------------------------------------------------
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
_______________________________________________
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Virtuoso-users@lists.sourceforge.net
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