Neo4j 2.1.6: Fixing corrupted relationships and nodes - neo4j

Question

I realize the db is old and this is a long shot...
I've got an older project that has been running on Neo4j 2.1.6 with no issues. Yesterday I started getting [{Neo.DatabaseError.Statement.ExecutionFailure }] errors when I try to make updates to the graph using Cypher via the transaction endpoint.
I finally tracked down the problem to a couple of relationships attached to a couple of nodes that seem to be corrupted/invalid. Trying to delete them on the console just returns 'null' and trying to delete them via the transaction endpoint leads to:
{"code":"Neo.DatabaseError.Statement.ExecutionFailure","message":null,"stackTrace":"java.lang.NullPointerException
org.neo4j.kernel.impl.nioneo.xa.RelationshipDeleter.updateNodesForDeletedRelationship(RelationshipDeleter.java:187)
org.neo4j.kernel.impl.nioneo.xa.RelationshipDeleter.relDelete(RelationshipDeleter.java:67)
org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransactionContext.relationshipDelete(NeoStoreTransactionContext.java:85)
org.neo4j.kernel.impl.nioneo.xa.NeoStoreTransaction.relDelete(NeoStoreTransaction.java:818)
org.neo4j.kernel.impl.persistence.PersistenceManager.relDelete(PersistenceManager.java:140)
org.neo4j.kernel.impl.core.NodeManager.deleteRelationship(NodeManager.java:780)
org.neo4j.kernel.impl.api.state.OldTxStateBridgeImpl.deleteRelationship(OldTxStateBridgeImpl.java:164)
org.neo4j.kernel.impl.api.state.TxStateImpl.relationshipDoDelete(TxStateImpl.java:439)
org.neo4j.kernel.impl.api.StateHandlingStatementOperations$1.visit(StateHandlingStatementOperations.java:138)
org.neo4j.kernel.impl.api.store.CacheLayer.visit(CacheLayer.java:476)
org.neo4j.kernel.impl.api.StateHandlingStatementOperations.relationshipDelete(StateHandlingStatementOperations.java:133)
org.neo4j.kernel.impl.api.ConstraintEnforcingEntityOperations.relationshipDelete(ConstraintEnforcingEntityOperations.java:159)
org.neo4j.kernel.impl.api.LockingStatementOperations.relationshipDelete(LockingStatementOperations.java:231)
org.neo4j.kernel.impl.api.OperationsFacade.relationshipDelete(OperationsFacade.java:528)
org.neo4j.cypher.internal.spi.v2_1.TransactionBoundQueryContext$RelationshipOperations.delete(TransactionBoundQueryContext.scala:180)
org.neo4j.cypher.internal.spi.v2_1.TransactionBoundQueryContext$RelationshipOperations.delete(TransactionBoundQueryContext.scala:178)
org.neo4j.cypher.internal.compiler.v2_1.spi.DelegatingOperations.delete(DelegatingQueryContext.scala:110)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$ExceptionTranslatingOperations.org$neo4j$cypher$internal$compiler$v2_1$spi$ExceptionTranslatingQueryContext$ExceptionTranslatingOperations$$super$delete(ExceptionTranslatingQueryContext.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$ExceptionTranslatingOperations$$anonfun$delete$1.apply$mcV$sp(ExceptionTranslatingQueryContext.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$ExceptionTranslatingOperations$$anonfun$delete$1.apply(ExceptionTranslatingQueryContext.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$ExceptionTranslatingOperations$$anonfun$delete$1.apply(ExceptionTranslatingQueryContext.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext.org$neo4j$cypher$internal$compiler$v2_1$spi$ExceptionTranslatingQueryContext$$translateException(ExceptionTranslatingQueryContext.scala:152)
org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$ExceptionTranslatingOperations.delete(ExceptionTranslatingQueryContext.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.spi.UpdateCountingQueryContext$CountingOps.delete(UpdateCountingQueryContext.scala:120)
org.neo4j.cypher.internal.compiler.v2_1.mutation.DeleteEntityAction.org$neo4j$cypher$internal$compiler$v2_1$mutation$DeleteEntityAction$$delete(DeleteEntityAction.scala:51)
org.neo4j.cypher.internal.compiler.v2_1.mutation.DeleteEntityAction.exec(DeleteEntityAction.scala:37)
org.neo4j.cypher.internal.compiler.v2_1.pipes.ExecuteUpdateCommandsPipe.org$neo4j$cypher$internal$compiler$v2_1$pipes$ExecuteUpdateCommandsPipe$$exec(ExecuteUpdateCommandsPipe.scala:57)
org.neo4j.cypher.internal.compiler.v2_1.pipes.ExecuteUpdateCommandsPi$$$$1019fdff8b266d7d9d5647386930b3d8$$$$ands$1$$anonfun$apply$2.apply(ExecuteUpdateCommandsPipe.scala:46)
org.neo4j.cypher.internal.compiler.v2_1.pipes.ExecuteUpdateCommandsPi$$$$1019fdff8b266d7d9d5647386930b3d8$$$$ands$1$$anonfun$apply$2.apply(ExecuteUpdateCommandsPipe.scala:46)
scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
org.neo4j.cypher.internal.compiler.v2_1.pipes.EmptyResultPipe.internalCreateResults(EmptyResultPipe.scala:29)
org.neo4j.cypher.internal.compiler.v2_1.pipes.PipeWithSource.createResults(Pipe.scala:105)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anonfun$getExecutionPlanFunction$1$$anonfun$apply$2.apply(ExecutionPlanBuilder.scala:120)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anonfun$getExecutionPlanFunction$1$$anonfun$apply$2.apply(ExecutionPlanBuilder.scala:119)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionWorkflowBuilder.runWithQueryState(ExecutionPlanBuilder.scala:168)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anonfun$getExecutionPlanFunction$1.apply(ExecutionPlanBuilder.scala:118)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anonfun$getExecutionPlanFunction$1.apply(ExecutionPlanBuilder.scala:103)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anon$1.execute(ExecutionPlanBuilder.scala:68)
org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionPlanBuilder$$anon$1.execute(ExecutionPlanBuilder.scala:67)
org.neo4j.cypher.internal.ExecutionPlanWrapperForV2_1.execute(CypherCompiler.scala:159)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:76)
org.neo4j.cypher.ExecutionEngine.execute(ExecutionEngine.scala:71)
org.neo4j.cypher.javacompat.ExecutionEngine.execute(ExecutionEngine.java:84)
org.neo4j.server.rest.transactional.TransactionHandle.executeStatements(TransactionHandle.java:277)
org.neo4j.server.rest.transactional.TransactionHandle.commit(TransactionHandle.java:139)
org.neo4j.server.rest.web.TransactionalService$2.write(TransactionalService.java:194)
com.sun.jersey.core.impl.provider.entity.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:71)
com.sun.jersey.core.impl.provider.entity.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:57)
com.sun.jersey.spi.container.ContainerResponse.write(ContainerResponse.java:306)
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1437)
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349)
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339)
com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537)
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:699)
javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:698)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1506)
org.neo4j.server.guard.GuardingRequestFilter.doFilter(GuardingRequestFilter.java:68)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1477)
ch.qos.logback.access.servlet.TeeFilter.doFilter(TeeFilter.java:55)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1477)
org.neo4j.server.guard.GuardingRequestFilter.doFilter(GuardingRequestFilter.java:68)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1477)
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:211)
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1096)
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:432)
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:175)
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1030)
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136)
org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52)
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
org.eclipse.jetty.server.handler.RequestLogHandler.handle(RequestLogHandler.java:92)
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
org.eclipse.jetty.server.Server.handle(Server.java:445)
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:268)
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:229)
org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:358)
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:601)
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:532)
java.lang.Thread.run(Thread.java:745)\n"
Is there anyway to nuke these relationships? Looks like the first one was corrupted two days ago and I'd prefer not to lose two days of data if at all possible.

Answer 1

Just in case anybody else finds their way here, Michael Hunger wrote a tool that will copy a database and skip anything that is broken which is exactly what I needed. You can find it at https://github.com/jexp/store-utils/tree/21.
Turns out all of my issues were due to one relationship attached to a NULL node... Ran the tool, copied over the fixed up database and everything is working perfectly again.