structr / neo4j Database corrupted -
i'm playing around structr in linux vm w/2g of ram. executed query , crashed system. attempts restart platform have failed, , embedded db has following error i'm looking hints might've happened.
2016-03-07 05:19:19.235+0000 info [org.neo4j]: recovery required log version 0 2016-03-07 05:19:36.119+0000 error [org.neo4j]: setting tm not ok. kernel has encountered problem, please perform necessary action (tx recovery/restart) null java.lang.nullpointerexception @ org.neo4j.index.impl.lucene.indextype.instantiatefield(indextype.java:318) @ org.neo4j.index.impl.lucene.indextype$1.addtodocument(indextype.java:63) @ org.neo4j.index.impl.lucene.lucenecommandapplier.visitindexaddrelationshipcommand(lucenecommandapplier.java:79) @ org.neo4j.kernel.impl.api.legacyindexapplier.visitindexaddrelationshipcommand(legacyindexapplier.java:143) @ org.neo4j.kernel.impl.api.commandapplierfacade.visitindexaddrelationshipcommand(commandapplierfacade.java:246) @ org.neo4j.kernel.impl.index.indexcommand$addrelationshipcommand.handle(indexcommand.java:236) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:82) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:45) @ org.neo4j.kernel.impl.transaction.log.physicaltransactionrepresentation.accept(physicaltransactionrepresentation.java:69) @ org.neo4j.kernel.impl.api.transactionrepresentationstoreapplier.apply(transactionrepresentationstoreapplier.java:111) @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:70) @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:36) @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:54) @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:32) @ org.neo4j.kernel.recovery.init(recovery.java:78) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:502) @ org.neo4j.kernel.lifecycle.lifesupport.init(lifesupport.java:72) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:106) @ org.neo4j.kernel.neostoredatasource.start(neostoredatasource.java:579) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.impl.transaction.state.datasourcemanager.start(datasourcemanager.java:117) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:330) @ org.neo4j.kernel.embeddedgraphdatabase.(embeddedgraphdatabase.java:59) @ org.neo4j.graphdb.factory.graphdatabasefactory.newdatabase(graphdatabasefactory.java:108) @ org.neo4j.graphdb.factory.graphdatabasefactory$1.newdatabase(graphdatabasefactory.java:95) @ org.neo4j.graphdb.factory.graphdatabasebuilder.newgraphdatabase(graphdatabasebuilder.java:185) @ org.structr.neo4j.neo4jdatabaseservice.initialize(neo4jdatabaseservice.java:130) @ org.structr.core.graph.nodeservice.initialize(nodeservice.java:115) @ org.structr.core.services.createservice(services.java:550) @ org.structr.core.services.initialize(services.java:325) @ org.structr.core.services.initialize(services.java:297) @ org.structr.core.services.getinstance(services.java:145) @ org.structr.server.main(server.java:36) 2016-03-07 05:19:36.300+0000 error [org.neo4j]: exception occurred while starting datasource. attempting close things down. component 'org.neo4j.kernel.recovery@245b6b85' failed initialize. please see attached cause exception. org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.recovery@245b6b85' failed initialize. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:508) @ org.neo4j.kernel.lifecycle.lifesupport.init(lifesupport.java:72) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:106) @ org.neo4j.kernel.neostoredatasource.start(neostoredatasource.java:579) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.impl.transaction.state.datasourcemanager.start(datasourcemanager.java:117) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:330) @ org.neo4j.kernel.embeddedgraphdatabase.(embeddedgraphdatabase.java:59) @ org.neo4j.graphdb.factory.graphdatabasefactory.newdatabase(graphdatabasefactory.java:108) @ org.neo4j.graphdb.factory.graphdatabasefactory$1.newdatabase(graphdatabasefactory.java:95) @ org.neo4j.graphdb.factory.graphdatabasebuilder.newgraphdatabase(graphdatabasebuilder.java:185) @ org.structr.neo4j.neo4jdatabaseservice.initialize(neo4jdatabaseservice.java:130) @ org.structr.core.graph.nodeservice.initialize(nodeservice.java:115) @ org.structr.core.services.createservice(services.java:550) @ org.structr.core.services.initialize(services.java:325) @ org.structr.core.services.initialize(services.java:297) @ org.structr.core.services.getinstance(services.java:145) @ org.structr.server.main(server.java:36) caused by: java.lang.nullpointerexception @ org.neo4j.index.impl.lucene.indextype.instantiatefield(indextype.java:318) @ org.neo4j.index.impl.lucene.indextype$1.addtodocument(indextype.java:63) @ org.neo4j.index.impl.lucene.lucenecommandapplier.visitindexaddrelationshipcommand(lucenecommandapplier.java:79) @ org.neo4j.kernel.impl.api.legacyindexapplier.visitindexaddrelationshipcommand(legacyindexapplier.java:143) @ org.neo4j.kernel.impl.api.commandapplierfacade.visitindexaddrelationshipcommand(commandapplierfacade.java:246) @ org.neo4j.kernel.impl.index.indexcommand$addrelationshipcommand.handle(indexcommand.java:236) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:82) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:45) @ org.neo4j.kernel.impl.transaction.log.physicaltransactionrepresentation.accept(physicaltransactionrepresentation.java:69) @ org.neo5j.kernel.impl.api.transactionrepresentationstoreapplier.apply(transactionrepresentationstoreapplier.java:111)
the structr log has this:
mar 07, 2016 12:19:16 org.structr.core.services initialize info: starting services mar 07, 2016 12:19:16 org.structr.neo4j.neo4jdatabaseservice initialize info: relationship cache size set 10,000 mar 07, 2016 12:19:16 org.structr.neo4j.neo4jdatabaseservice initialize info: node cache size set 10,000 mar 07, 2016 12:19:16 org.structr.neo4j.neo4jdatabaseservice initialize info: initializing database (./db) ... java.lang.runtimeexception: error starting org.neo4j.kernel.embeddedgraphdatabase, /usr/local/download/structr/binaries/structr-ui-2.0-snapshot-201603060822.5403e4/./db @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:334) @ org.neo4j.kernel.embeddedgraphdatabase.(embeddedgraphdatabase.java:59) @ org.neo4j.graphdb.factory.graphdatabasefactory.newdatabase(graphdatabasefactory.java:108) @ org.neo4j.graphdb.factory.graphdatabasefactory$1.newdatabase(graphdatabasefactory.java:95) @ org.neo4j.graphdb.factory.graphdatabasebuilder.newgraphdatabase(graphdatabasebuilder.java:185) @ org.structr.neo4j.neo4jdatabaseservice.initialize(neo4jdatabaseservice.java:130) @ org.structr.core.graph.nodeservice.initialize(nodeservice.java:115) @ org.structr.core.services.createservice(services.java:550) @ org.structr.core.services.initialize(services.java:325) @ org.structr.core.services.initialize(services.java:297) @ org.structr.core.services.getinstance(services.java:145) @ org.structr.server.main(server.java:36) caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.impl.transaction.state.datasourcemanager@162be846' initialized, failed start. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:532) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:330) ... 11 more caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.neostoredatasource@191a8997' initialized, failed start. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:532) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) @ org.neo4j.kernel.impl.transaction.state.datasourcemanager.start(datasourcemanager.java:117) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) ... 13 more caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.recovery@245b6b85' failed initialize. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:508) @ org.neo4j.kernel.lifecycle.lifesupport.init(lifesupport.java:72) @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:106) @ org.neo4j.kernel.neostoredatasource.start(neostoredatasource.java:579) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) ... 16 more caused by: java.lang.nullpointerexception @ org.neo4j.index.impl.lucene.indextype.instantiatefield(indextype.java:318) @ org.neo4j.index.impl.lucene.indextype$1.addtodocument(indextype.java:63) @ org.neo4j.index.impl.lucene.lucenecommandapplier.visitindexaddrelationshipcommand(lucenecommandapplier.java:79) @ org.neo4j.kernel.impl.api.legacyindexapplier.visitindexaddrelationshipcommand(legacyindexapplier.java:143) @ org.neo4j.kernel.impl.api.commandapplierfacade.visitindexaddrelationshipcommand(commandapplierfacade.java:246) @ org.neo4j.kernel.impl.index.indexcommand$addrelationshipcommand.handle(indexcommand.java:236) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:82) @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:45) @ org.neo4j.kernel.impl.transaction.log.physicaltransactionrepresentation.accept(physicaltransactionrepresentation.java:69) @ org.neo4j.kernel.impl.api.transactionrepresentationstoreapplier.apply(transactionrepresentationstoreapplier.java:111) @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:70) @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:36) @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:54) @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:32) @ org.neo4j.kernel.recovery.init(recovery.java:78) @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:502) ... 20 more mar 07, 2016 12:19:36 org.structr.core.services createservice severe: vital service nodeservice failed start: error starting org.neo4j.kernel.embeddedgraphdatabase, /usr/local/download/structr/binaries/structr-ui-2.0-snapshot-201603060822.5403e4/./db. aborting
this when try start db using 2.2.8 neo4j community program. in both cases failing on 'null pointer' of sort.
starting neo4j server console-mode... using additional jvm arguments: -server -xx:+disableexplicitgc -dorg.neo4j.server.properties=conf/neo4j-server.properties -djava.util.logging.config.file=conf/logging.properties -xx:+useconcmarksweepgc -xx:+cmsclassunloadingenabled -xx:-omitstacktraceinfastthrow -xx:hashcode=5 -dneo4j.ext.udc.source=tarball 2016-03-07 13:18:44.618+0000 info [api] setting startup timeout to: 120000ms based on 120000 detected incorrectly shut down database, performing recovery.. 2016-03-07 13:19:01.274+0000 info [api] shutdown neo4j server. 2016-03-07 13:19:01.275+0000 error [api] failed start neo server on port [7474] org.neo4j.server.serverstartupexception: starting neo4j server failed: error starting org.neo4j.kernel.embeddedgraphdatabase, /usr/local/download/structr/binaries/structr-ui-2.0-snapshot-201603060822.5403e4/db @ org.neo4j.server.abstractneoserver.start(abstractneoserver.java:258) ~[neo4j-server-2.2.8.jar:2.2.8] @ org.neo4j.server.bootstrapper.start(bootstrapper.java:117) [neo4j-server-2.2.8.jar:2.2.8] @ org.neo4j.server.bootstrapper.main(bootstrapper.java:69) [neo4j-server-2.2.8.jar:2.2.8] caused by: java.lang.runtimeexception: error starting org.neo4j.kernel.embeddedgraphdatabase, /usr/local/download/structr/binaries/structr-ui-2.0-snapshot-201603060822.5403e4/db @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:334) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.embeddedgraphdatabase.(embeddedgraphdatabase.java:59) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.recovery.storerecoverer.recover(storerecoverer.java:96) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.server.preflight.performrecoveryifnecessary.run(performrecoveryifnecessary.java:65) ~[neo4j-server-2.2.8.jar:2.2.8] @ org.neo4j.server.preflight.preflighttasks.run(preflighttasks.java:71) ~[neo4j-server-2.2.8.jar:2.2.8] @ org.neo4j.server.abstractneoserver.runpreflighttasks(abstractneoserver.java:399) ~[neo4j-server-2.2.8.jar:2.2.8] @ org.neo4j.server.abstractneoserver.start(abstractneoserver.java:195) ~[neo4j-server-2.2.8.jar:2.2.8] ... 2 common frames omitted caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.impl.transaction.state.datasourcemanager@2de4d378' initialized, failed start. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:532) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.internalabstractgraphdatabase.run(internalabstractgraphdatabase.java:330) ~[neo4j-kernel-2.2.8.jar:2.2.8] ... 8 common frames omitted caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.neostoredatasource@4b9b15' initialized, failed start. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:532) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:115) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.state.datasourcemanager.start(datasourcemanager.java:117) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) ~[neo4j-kernel-2.2.8.jar:2.2.8] ... 10 common frames omitted caused by: org.neo4j.kernel.lifecycle.lifecycleexception: component 'org.neo4j.kernel.recovery@3016120' failed initialize. please see attached cause exception. @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:508) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport.init(lifesupport.java:72) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport.start(lifesupport.java:106) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.neostoredatasource.start(neostoredatasource.java:579) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.start(lifesupport.java:526) ~[neo4j-kernel-2.2.8.jar:2.2.8] ... 13 common frames omitted caused by: java.lang.nullpointerexception: null @ org.neo4j.index.impl.lucene.indextype.instantiatefield(indextype.java:318) ~[neo4j-lucene-index-2.2.8.jar:2.2.8] @ org.neo4j.index.impl.lucene.indextype$1.addtodocument(indextype.java:63) ~[neo4j-lucene-index-2.2.8.jar:2.2.8] @ org.neo4j.index.impl.lucene.lucenecommandapplier.visitindexaddrelationshipcommand(lucenecommandapplier.java:79) ~[neo4j-lucene-index-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.api.legacyindexapplier.visitindexaddrelationshipcommand(legacyindexapplier.java:143) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.api.commandapplierfacade.visitindexaddrelationshipcommand(commandapplierfacade.java:246) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.index.indexcommand$addrelationshipcommand.handle(indexcommand.java:236) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:82) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.api.commandapplierfacade.visit(commandapplierfacade.java:45) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.log.physicaltransactionrepresentation.accept(physicaltransactionrepresentation.java:69) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.api.transactionrepresentationstoreapplier.apply(transactionrepresentationstoreapplier.java:111) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:70) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.state.recoveryvisitor.visit(recoveryvisitor.java:36) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:54) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.impl.transaction.log.logfilerecoverer.visit(logfilerecoverer.java:32) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.recovery.init(recovery.java:78) ~[neo4j-kernel-2.2.8.jar:2.2.8] @ org.neo4j.kernel.lifecycle.lifesupport$lifecycleinstance.init(lifesupport.java:502) ~[neo4j-kernel-2.2.8.jar:2.2.8] ... 17 common frames omitted
the root cause structr tries index object tostring() method returns null. there's no filter such objects in neither lucene nor neo4j, leads database crash , unrecoverable database store.
we'll provide fix structr possible, , filed issue neo4j: https://github.com/neo4j/neo4j/issues/6685
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