Hi Andy:
Thank you for the answer. I can query my database from the tdb before I use
the sprql update. I believe the problem is coming from the sparql update
itself.
here is the code for sparql update:
System.out.println(" ... offsides Sparql Updates AFTER ...");
data.startQuery();
String query3 = data.loadQuery("src/offisdesTripleSparqlafterUpdates.tql"
);
data.endQuery();
UpdateAction.parseExecute(query3, data.tdb);
and here is the sparql update:
DELETE { ?s ?p ?o .}
INSERT{ ?dse ?p ?o .}
WHERE {
?s ?p ?o .
FILTER (contains(str(?s), "http://bio2rdf.org/offsides:";))
BIND(uri(CONCAT("
https://csel.cs.colorado.edu/~noor/Drug_Disease_ontology/DDID.rdf#os_";,
replace(str(?s), "http://bio2rdf.org/offsides:"; , ""))) AS ?dse)};
What do you think ? also, would you provide me with an example of using
sync().
Thanks
On Mon, Feb 10, 2014 at 9:26 AM, Andy Seaborne <[email protected]> wrote:
> On 09/02/14 21:42, Adeeb Noor wrote:
>
>> Hi All:
>>
>> I have a tdb dataset with almost 1g. I am trying to modify with using
>> Sparql update, however I get this error:
>>
>> ERROR TDB ::
>> ObjectFileStorage.read[nodes.dat](65419578)[filesize=
>> 103476978][file.size()=103476978]:
>> Impossibly large object : 893792824 bytes >
>> filesize-(loc+SizeOfInt)=38057396
>>
>> 14:33:42 ERROR BindingTDB :: get1(?s)
>>
>> com.hp.hpl.jena.tdb.base.file.FileException:
>> ObjectFileStorage.read[nodes.dat](65419578)[filesize=
>> 103476978][file.size()=103476978]:
>> Impossibly large object : 893792824 bytes >
>> filesize-(loc+SizeOfInt)=38057396
>>
>
> I'm afraid it looks like the dataset is corrupt. This happened sometime
> in the past, probably due to the JVM crash or exiting without a sync()
> being called.
>
> From the stacktrace, I don't see any sign you are using transactions. One
> of things transactions gives you is resistance to crashes. Used directly,
> the code assumes you will cleanly exit the JVM - no crashes, no exit
> without calling sync().
>
> Andy
>
>
>> at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(
>>
>> ObjectFileStorage.java:346)
>>
>> at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(
>> NodeTableNative.java:178)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(
>> NodeTableNative.java:103)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(
>> NodeTableNative.java:74)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(
>> NodeTableCache.java:103)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(
>> NodeTableCache.java:74)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(
>> NodeTableWrapper.java:55)
>>
>> at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(
>> NodeTableInline.java:67)
>>
>> at com.hp.hpl.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:123)
>>
>> at com.hp.hpl.jena.sparql.engine.binding.BindingBase.get(
>> BindingBase.java:123)
>>
>> at com.hp.hpl.jena.sparql.core.Var.lookup(Var.java:84)
>>
>> at com.hp.hpl.jena.sparql.core.Var.lookup(Var.java:79)
>>
>> at com.hp.hpl.jena.sparql.core.Substitute.substitute(Substitute.java:123)
>>
>> at com.hp.hpl.jena.sparql.core.Substitute.substitute(Substitute.java:110)
>>
>> at com.hp.hpl.jena.sparql.modify.TemplateLib.subst(TemplateLib.java:158)
>>
>> at com.hp.hpl.jena.sparql.modify.TemplateLib$3.convert(
>> TemplateLib.java:115)
>>
>> at com.hp.hpl.jena.sparql.modify.TemplateLib$3.convert(
>> TemplateLib.java:104)
>>
>> at org.apache.jena.atlas.iterator.Iter$5.hasNext(Iter.java:337)
>>
>> at com.hp.hpl.jena.sparql.modify.UpdateEngineWorker.execDelete(
>> UpdateEngineWorker.java:496)
>>
>> at com.hp.hpl.jena.sparql.modify.UpdateEngineWorker.visit(
>> UpdateEngineWorker.java:418)
>>
>> at com.hp.hpl.jena.sparql.modify.request.UpdateModify.visit(
>> UpdateModify.java:97)
>>
>> at com.hp.hpl.jena.sparql.modify.UpdateVisitorSink.send(
>> UpdateVisitorSink.java:46)
>>
>> at com.hp.hpl.jena.sparql.modify.UpdateVisitorSink.send(
>> UpdateVisitorSink.java:26)
>>
>> at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:578)
>>
>> at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:586)
>>
>> at com.hp.hpl.jena.sparql.modify.UpdateProcessorBase.execute(
>> UpdateProcessorBase.java:57)
>>
>> at com.hp.hpl.jena.update.UpdateAction.execute$(UpdateAction.java:190)
>>
>> at com.hp.hpl.jena.update.UpdateAction.execute(UpdateAction.java:181)
>>
>> at com.hp.hpl.jena.update.UpdateAction.parseExecute(
>> UpdateAction.java:135)
>>
>> at com.hp.hpl.jena.update.UpdateAction.parseExecute(
>> UpdateAction.java:106)
>>
>> What should I do ?
>>
>>
>
--
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: [email protected]
