On 11/02/14 01:19, Adeeb Noor wrote:
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.
Sorry - it's not. The symptom and the cause are in different places.
The update is touching (because of the WHERE { ?s ?p ?o }) and
materializing every subject in the database and that happens to include
a node that has not touched since the crash. The cause is the crash/JVM
exit.
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().
dataset.begin(ReadWrite.WRITE) ;
try {
....
dataset.commit() ;
} finally {
dataset.end() ;
}
http://jena.apache.org/documentation/tdb/tdb_transactions.html
Andy
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 ?
