Hi Núria, On 05-Sep-14 2:50 PM, Nuria Queralt Rosinach wrote:
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.
From where are you trying to execute the sparql statement against the Virtuoso server:
1) iSQL 2) Virtuoso Conductor Ui 3) sparql endpoint? as the error from above indicates the Virtuoso SQL Server port 1111 is down? Best Regards, Rumi
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-enableSo, 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 KocisCheers, 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/ ******************************************************************** ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Virtuoso-users mailing list Virtuoso-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/virtuoso-users-- ******************************************************************** 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/ ********************************************************************
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