Re: [Virtuoso-users] Transaction aborted because it's log after image size went above the limit

Thu, 18 Sep 2014 05:34:21 -0700 

Hi Rumi,

In the end, that worked fine! thanks a lot.

Cheers,
Núria

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/
********************************************************************


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