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

[suyashs20]

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. 🙂

[sameer_gijare14]

Hi Suyash

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

Thanking you
Sameer Sudhir G

[orlandor]

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]

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