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Getting "Problems when running partial commit. Partial transaction rolled back. " when loading a turtle file from local system

suyashs20
Node

I am facing this issue when loading a turtle file from the local system using n10s.onto.import.fetch

link to the turtle file in case anyone wants to replicate and help me with this issue.

https://archivo.dbpedia.org/info?o=http://purl.obolibrary.org/obo/foodon.owl

use file which has 79396 triples in it.

Thanks in advance. πŸ™‚

3 REPLIES 3

sameer_gijare14
Graph Buddy

Hi Suyash

Please show us log file so that someone can analyse the issue.

Thanking you
Sameer Sudhir G

orlandor
Node

Hello,

Was there ever a resolution to this issue? I'm having the same problem. Please see the logs below.

v/r

Rob

2022-01-20 23:36:33.887+0000 ERROR [o.n.k.a.p.GlobalProcedures] Problems when running partial commit. Partial transaction rolled back. 1306 triples lost.
com.google.common.cache.CacheLoader$InvalidCacheLoadException: CacheLoader returned null for key http://www.w3.org/2002/07/owl#Thing.
at com.google.common.cache.LocalCache$Segment.getAndRecordStats(LocalCache.java:2314) ~[apoc-4.4.0.1.jar:4.4.0.1]
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2278) ~[apoc-4.4.0.1.jar:4.4.0.1]
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2154) ~[apoc-4.4.0.1.jar:4.4.0.1]
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2044) ~[apoc-4.4.0.1.jar:4.4.0.1]
at com.google.common.cache.LocalCache.get(LocalCache.java:3952) ~[apoc-4.4.0.1.jar:4.4.0.1]
at com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4871) ~[apoc-4.4.0.1.jar:4.4.0.1]
at n10s.onto.OntologyImporter.processRestriction(OntologyImporter.java:450) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.onto.OntologyImporter.runPartialTx(OntologyImporter.java:368) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.onto.OntologyImporter.periodicOperation(OntologyImporter.java:78) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.onto.OntologyImporter.endRDF(OntologyImporter.java:111) ~[n10s-4.4.0.0.jar:4.4.0.0]
at org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:170) ~[n10s-4.4.0.0.jar:4.4.0.0]
at org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:125) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.CommonProcedures.instantiateAndKickOffParser(CommonProcedures.java:131) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.CommonProcedures.parseRDFPayloadOrFromUrl(CommonProcedures.java:119) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.onto.OntoProcedures.doOntoImport(OntoProcedures.java:62) ~[n10s-4.4.0.0.jar:4.4.0.0]
at n10s.onto.load.OntoLoadProcedures.fetch(OntoLoadProcedures.java:23) ~[n10s-4.4.0.0.jar:4.4.0.0]
at org.neo4j.kernel.impl.proc.GeneratedProcedure_fetch158190482190700.apply(Unknown Source) ~[?:?]
at org.neo4j.procedure.impl.ProcedureRegistry.callProcedure(ProcedureRegistry.java:235) ~[neo4j-procedure-4.4.0.jar:4.4.0]
at org.neo4j.procedure.impl.GlobalProceduresRegistry.callProcedure(GlobalProceduresRegistry.java:352) ~[neo4j-procedure-4.4.0.jar:4.4.0]
at org.neo4j.kernel.impl.newapi.AllStoreHolder.callProcedure(AllStoreHolder.java:1092) ~[neo4j-kernel-4.4.0.jar:4.4.0]
at org.neo4j.kernel.impl.newapi.AllStoreHolder.procedureCallWrite(AllStoreHolder.java:1011) ~[neo4j-kernel-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.$anonfun$callReadWriteProcedure$1(CallSupport.scala:51) ~[neo4j-cypher-interpreted-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callProcedure(CallSupport.scala:70) ~[neo4j-cypher-interpreted-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callReadWriteProcedure(CallSupport.scala:51) ~[neo4j-cypher-interpreted-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.interpreted.TransactionBoundReadQueryContext.callReadWriteProcedure(TransactionBoundQueryContext.scala:1138) ~[neo4j-cypher-interpreted-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.planning.ExceptionTranslatingReadQueryContext.callReadWriteProcedure(ExceptionTranslatingQueryContext.scala:229) ~[neo4j-cypher-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.EagerReadWriteCallMode$.callProcedure(ProcedureCallMode.scala:65) ~[neo4j-cypher-runtime-util-4.4.0.jar:4.4.0]
at org.neo4j.codegen.OperatorTaskPipeline0_296.compiledOperate(Unknown Source) ~[?:?]
at org.neo4j.cypher.internal.runtime.pipelined.operators.CompiledTask.operateWithProfile(OperatorCodeGenBaseTemplates.scala:451) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.pipelined.PipelineTask.executeOperators(PipelineTask.scala:62) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.pipelined.PipelineTask.executeWorkUnit(PipelineTask.scala:51) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.pipelined.Worker.executeTask(Worker.scala:144) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.pipelined.Worker.workOnQuery(Worker.scala:97) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.runtime.pipelined.execution.CallingThreadExecutingQuery.request(CallingThreadExecutingQuery.scala:40) ~[neo4j-cypher-pipelined-runtime-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.PipelinedRuntimeResult.request(PipelinedRuntime.scala:502) ~[neo4j-enterprise-cypher-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.result.StandardInternalExecutionResult.request(StandardInternalExecutionResult.scala:90) ~[neo4j-cypher-4.4.0.jar:4.4.0]
at org.neo4j.cypher.internal.result.ClosingExecutionResult.request(ClosingExecutionResult.scala:144) ~[neo4j-cypher-4.4.0.jar:4.4.0]
at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.doRequest(QuerySubject.java:184) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.request(QuerySubject.java:167) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.Operators$MultiSubscriptionSubscriber.request(Operators.java:2158) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.StrictSubscriber.request(StrictSubscriber.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at org.neo4j.fabric.stream.Rx2SyncStream$RecordSubscriber.request(Rx2SyncStream.java:129) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at org.neo4j.fabric.stream.Rx2SyncStream.maybeRequest(Rx2SyncStream.java:91) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at org.neo4j.fabric.stream.Rx2SyncStream.readRecord(Rx2SyncStream.java:50) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at org.neo4j.fabric.bolt.BoltQueryExecutionImpl$QueryExecutionImpl.request(BoltQueryExecutionImpl.java:179) ~[neo4j-fabric-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.AbstractCypherAdapterStream.handleRecords(AbstractCypherAdapterStream.java:105) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v3.messaging.ResultHandler.onPullRecords(ResultHandler.java:41) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v4.messaging.PullResultConsumer.consume(PullResultConsumer.java:42) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine$State.consumeResult(TransactionStateMachine.java:507) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine$State$2.streamResult(TransactionStateMachine.java:351) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine.streamResult(TransactionStateMachine.java:99) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.transaction.StatementProcessorTxManager.streamResults(StatementProcessorTxManager.java:249) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.transaction.StatementProcessorTxManager.pullData(StatementProcessorTxManager.java:111) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v4.runtime.InTransactionState.processStreamPullResultMessage(InTransactionState.java:78) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v4.runtime.AbstractStreamingState.processUnsafe(AbstractStreamingState.java:51) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v4.runtime.InTransactionState.processUnsafe(InTransactionState.java:64) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.v3.runtime.FailSafeBoltStateMachineState.process(FailSafeBoltStateMachineState.java:48) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.statemachine.impl.AbstractBoltStateMachine.nextState(AbstractBoltStateMachine.java:154) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.statemachine.impl.AbstractBoltStateMachine.process(AbstractBoltStateMachine.java:102) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.messaging.BoltRequestMessageReader.lambda$doRead$1(BoltRequestMessageReader.java:93) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.DefaultBoltConnection.lambda$enqueue$0(DefaultBoltConnection.java:156) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatchInternal(DefaultBoltConnection.java:252) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatch(DefaultBoltConnection.java:187) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatch(DefaultBoltConnection.java:177) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.scheduling.ExecutorBoltScheduler.executeBatch(ExecutorBoltScheduler.java:257) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at org.neo4j.bolt.runtime.scheduling.ExecutorBoltScheduler.lambda$scheduleBatchOrHandleError$3(ExecutorBoltScheduler.java:240) ~[neo4j-bolt-4.4.0.jar:4.4.0]
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1700) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) [netty-common-4.1.69.Final.jar:4.1.69.Final]
at java.lang.Thread.run(Thread.java:834) [?:?]

sameer_gijare14
Graph Buddy

Hello

I suspect it is a part of memory tuning and capacity error on neo4j server.Please use memrec tool for reconfiguring memory.Also check if drivers are upgraded and compatible with your graph engine component assembly.
Please let us know after you are done with upgrades.

Many thanks
Mr Sameer Sudhir G

Nodes 2022
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