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

[Rumi <rts...@op...>]

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:nqu...@im...
>>> Skype IM: nuriaqr76
>>> http://ibi.imim.es/
>>> ********************************************************************
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Slashdot TV.
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>>>
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>>> 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:nqu...@im...
> Skype IM: nuriaqr76
> http://ibi.imim.es/
> ********************************************************************