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Error while loading the ontology (XML/RDF)

onto_poc
Node

‎02-01-2023 05:43 AM

Hi, I am trying to import an ontology:

https://bioportal.bioontology.org/ontologies/OAE#:~:text=The%20Ontology%20of%20Adverse%20Events,foll... 

Here's what I'm doing:

CALL n10s.graphconfig.init();

I read that it might be related to memory allocation of neo4j. To test that, I tried an even bigger ontology and it was loaded successfully. However this ontology (link attached), is throwing exception (also attached).

CALL n10s.onto.import.fetch("<path_to_file>","RDF/XML",{commitSize: 100000, nodeCacheSize: 20000})

This is the error I'm getting:

onto_poc_0-1675258961688.png

2023-02-01 13:42:27.670+0000 ERROR [o.n.k.a.p.GlobalProcedures] Problems when running partial commit. Partial transaction rolled back. 53203 triples lost.
java.lang.IllegalStateException: null
	at java.util.HashMap$Ha**bleep**erator.remove(HashMap.java:1609) ~[?:?]
	at n10s.onto.OntologyImporter.runPartialTx(OntologyImporter.java:390) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.onto.OntologyImporter.periodicOperation(OntologyImporter.java:78) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.onto.OntologyImporter.endRDF(OntologyImporter.java:111) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.endDocument(RDFXMLParser.java:299) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at org.eclipse.rdf4j.rio.rdfxml.SAXFilter.endDocument(SAXFilter.java:192) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endDocument(AbstractSAXParser.java:754) ~[?:?]
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:547) ~[?:?]
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:889) ~[?:?]
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:825) ~[?:?]
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) ~[?:?]
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1224) ~[?:?]
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:637) ~[?:?]
	at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:228) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:195) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.CommonProcedures.instantiateAndKickOffParser(CommonProcedures.java:131) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.CommonProcedures.parseRDFPayloadOrFromUrl(CommonProcedures.java:119) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.onto.OntoProcedures.doOntoImport(OntoProcedures.java:62) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at n10s.onto.load.OntoLoadProcedures.fetch(OntoLoadProcedures.java:23) ~[n10s-5.1.0.0.jar:5.1.0.0]
	at org.neo4j.kernel.impl.proc.GeneratedProcedure_fetch3793396182387.apply(Unknown Source) ~[?:?]
	at org.neo4j.procedure.impl.ProcedureRegistry.callProcedure(ProcedureRegistry.java:217) ~[neo4j-procedure-5.3.0.jar:5.3.0]
	at org.neo4j.procedure.impl.GlobalProceduresRegistry.callProcedure(GlobalProceduresRegistry.java:322) ~[neo4j-procedure-5.3.0.jar:5.3.0]
	at org.neo4j.kernel.impl.newapi.ProcedureCaller$ForTransactionScope.callProcedure(ProcedureCaller.java:277) ~[neo4j-kernel-5.3.0.jar:5.3.0]
	at org.neo4j.kernel.impl.newapi.AllStoreHolder.procedureCallWrite(AllStoreHolder.java:918) ~[neo4j-kernel-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.$anonfun$callReadWriteProcedure$1(CallSupport.scala:58) ~[neo4j-cypher-interpreted-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callProcedure(CallSupport.scala:85) ~[neo4j-cypher-interpreted-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callReadWriteProcedure(CallSupport.scala:58) ~[neo4j-cypher-interpreted-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.interpreted.TransactionBoundReadQueryContext.callReadWriteProcedure(TransactionBoundQueryContext.scala:1437) ~[neo4j-cypher-interpreted-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.planning.ExceptionTranslatingReadQueryContext.callReadWriteProcedure(ExceptionTranslatingQueryContext.scala:273) ~[neo4j-cypher-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.EagerReadWriteCallMode$.callProcedure(ProcedureCallMode.scala:82) ~[neo4j-cypher-runtime-util-5.3.0.jar:5.3.0]
	at org.neo4j.codegen.OperatorTaskPipeline0_107.compiledOperate(Unknown Source) ~[?:?]
	at org.neo4j.cypher.internal.runtime.pipelined.operators.CompiledTask.operateWithProfile(OperatorCodeGenBaseTemplates.scala:679) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.PipelineTask.executeOperators(PipelineTask.scala:82) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.PipelineTask.executeWorkUnit(PipelineTask.scala:66) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.Worker$.executeTask(Worker.scala:1080) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.Worker.executeTask(Worker.scala:135) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.Worker$.workOnQuery(Worker.scala:986) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.Worker$.workOnQuery(Worker.scala:401) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.runtime.pipelined.execution.CallingThreadExecutingQuery.request(CallingThreadExecutingQuery.scala:44) ~[neo4j-cypher-pipelined-runtime-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.PipelinedRuntimeResult.request(PipelinedRuntimeResult.scala:87) ~[neo4j-enterprise-cypher-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.result.StandardInternalExecutionResult.request(StandardInternalExecutionResult.scala:103) ~[neo4j-cypher-5.3.0.jar:5.3.0]
	at org.neo4j.cypher.internal.result.ClosingExecutionResult.request(ClosingExecutionResult.scala:149) ~[neo4j-cypher-5.3.0.jar:5.3.0]
	at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.doRequest(QuerySubject.java:155) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.request(QuerySubject.java:143) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.Operators$MultiSubscriptionSubscriber.request(Operators.java:2158) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at reactor.core.publisher.StrictSubscriber.request(StrictSubscriber.java:138) ~[reactor-core-3.4.24.jar:3.4.24]
	at org.neo4j.fabric.stream.Rx2SyncStream$RecordSubscriber.request(Rx2SyncStream.java:109) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at org.neo4j.fabric.stream.Rx2SyncStream.maybeRequest(Rx2SyncStream.java:77) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at org.neo4j.fabric.stream.Rx2SyncStream.readRecord(Rx2SyncStream.java:45) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at org.neo4j.fabric.bolt.BoltQueryExecutionImpl$QueryExecutionImpl.request(BoltQueryExecutionImpl.java:151) ~[neo4j-fabric-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.transaction.AbstractCypherAdapterStream.handleRecords(AbstractCypherAdapterStream.java:96) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.transaction.result.ResultHandler.onPullRecords(ResultHandler.java:64) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.v40.messaging.result.PullResultConsumer.consume(PullResultConsumer.java:39) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.transaction.TransactionStateMachine$State.consumeResult(TransactionStateMachine.java:517) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.transaction.TransactionStateMachine$State$2.streamResult(TransactionStateMachine.java:370) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.transaction.TransactionStateMachine.streamResult(TransactionStateMachine.java:107) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.transaction.StatementProcessorTxManager.streamResults(StatementProcessorTxManager.java:226) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.transaction.StatementProcessorTxManager.pullData(StatementProcessorTxManager.java:117) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.v40.fsm.InTransactionState.processStreamPullResultMessage(InTransactionState.java:73) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.v40.fsm.AbstractStreamingState.processUnsafe(AbstractStreamingState.java:47) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.v40.fsm.InTransactionState.processUnsafe(InTransactionState.java:60) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.v40.fsm.FailSafeState.process(FailSafeState.java:44) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.fsm.AbstractStateMachine.nextState(AbstractStateMachine.java:136) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.fsm.AbstractStateMachine.process(AbstractStateMachine.java:96) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.connector.connection.AtomicSchedulingConnection.lambda$submit$4(AtomicSchedulingConnection.java:113) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.connector.connection.AtomicSchedulingConnection.executeJob(AtomicSchedulingConnection.java:336) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.connector.connection.AtomicSchedulingConnection.doExecuteJobs(AtomicSchedulingConnection.java:270) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at org.neo4j.bolt.protocol.common.connector.connection.AtomicSchedulingConnection.executeJobs(AtomicSchedulingConnection.java:212) ~[neo4j-bolt-5.3.0.jar:5.3.0]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539) ~[?:?]
	at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) ~[?:?]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) ~[?:?]
	at java.lang.Thread.run(Thread.java:833) ~[?:?]

 

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