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问题：

structr/neo4j数据库已损坏

杨海
2023-03-14

我在一个Linux的虚拟机上玩结构器，它有2G的内存。我执行了一个查询，导致系统崩溃。重启平台的尝试失败了，嵌入式数据库有以下错误，所以我在寻找可能发生的事情的提示。

2016-03-07 05:19:19.235+0000 INFO  [org.neo4j]: Recovery required for log with version 0
2016-03-07 05:19:36.119+0000 ERROR [org.neo4j]: setting TM not OK. Kernel has encountered some problem, please perform necessary action (tx recovery/restart) null
java.lang.NullPointerException
        at org.neo4j.index.impl.lucene.IndexType.instantiateField(IndexType.java:318)
        at org.neo4j.index.impl.lucene.IndexType$1.addToDocument(IndexType.java:63)
        at org.neo4j.index.impl.lucene.LuceneCommandApplier.visitIndexAddRelationshipCommand(LuceneCommandApplier.java:79)
        at org.neo4j.kernel.impl.api.LegacyIndexApplier.visitIndexAddRelationshipCommand(LegacyIndexApplier.java:143)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visitIndexAddRelationshipCommand(CommandApplierFacade.java:246)
        at org.neo4j.kernel.impl.index.IndexCommand$AddRelationshipCommand.handle(IndexCommand.java:236)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:82)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:45)
        at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
        at org.neo4j.kernel.impl.api.TransactionRepresentationStoreApplier.apply(TransactionRepresentationStoreApplier.java:111)
        at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:70)
        at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:36)
        at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:54)
        at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:32)
        at org.neo4j.kernel.Recovery.init(Recovery.java:78)
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:502)
        at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:72)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:106)
        at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:579)
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
        at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:117)
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
        at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330)
        at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:59)
        at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:108)
        at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:95)
        at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:185)
        at org.structr.neo4j.Neo4jDatabaseService.initialize(Neo4jDatabaseService.java:130)
        at org.structr.core.graph.NodeService.initialize(NodeService.java:115)
        at org.structr.core.Services.createService(Services.java:550)
        at org.structr.core.Services.initialize(Services.java:325)
        at org.structr.core.Services.initialize(Services.java:297)
        at org.structr.core.Services.getInstance(Services.java:145)
        at org.structr.Server.main(Server.java:36)
2016-03-07 05:19:36.300+0000 ERROR [org.neo4j]: Exception occurred while starting the datasource. Attempting to close things down. Component 'org.neo4j.kernel.Recovery@245b6b85' failed to initialize. Please see attached cause exception.
org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.Recovery@245b6b85' failed to initialize. Please see attached cause exception.
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:508)
        at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:72)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:106)
        at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:579)
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
        at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:117)
        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
        at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330)
        at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:59)
        at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:108)
        at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:95)
        at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:185)
        at org.structr.neo4j.Neo4jDatabaseService.initialize(Neo4jDatabaseService.java:130)
        at org.structr.core.graph.NodeService.initialize(NodeService.java:115)
        at org.structr.core.Services.createService(Services.java:550)
        at org.structr.core.Services.initialize(Services.java:325)
        at org.structr.core.Services.initialize(Services.java:297)
        at org.structr.core.Services.getInstance(Services.java:145)
        at org.structr.Server.main(Server.java:36)
Caused by: java.lang.NullPointerException
        at org.neo4j.index.impl.lucene.IndexType.instantiateField(IndexType.java:318)
        at org.neo4j.index.impl.lucene.IndexType$1.addToDocument(IndexType.java:63)
        at org.neo4j.index.impl.lucene.LuceneCommandApplier.visitIndexAddRelationshipCommand(LuceneCommandApplier.java:79)
        at org.neo4j.kernel.impl.api.LegacyIndexApplier.visitIndexAddRelationshipCommand(LegacyIndexApplier.java:143)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visitIndexAddRelationshipCommand(CommandApplierFacade.java:246)
        at org.neo4j.kernel.impl.index.IndexCommand$AddRelationshipCommand.handle(IndexCommand.java:236)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:82)
        at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:45)
        at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
        at org.neo5j.kernel.impl.api.TransactionRepresentationStoreApplier.apply(TransactionRepresentationStoreApplier.java:111)

structr日志包含以下内容：

Mar 07, 2016 12:19:16 AM org.structr.core.Services initialize
INFO: Starting services
Mar 07, 2016 12:19:16 AM org.structr.neo4j.Neo4jDatabaseService initialize
INFO: Relationship cache size set to 10,000
Mar 07, 2016 12:19:16 AM org.structr.neo4j.Neo4jDatabaseService initialize
INFO: Node cache size set to 10,000
Mar 07, 2016 12:19:16 AM 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
    at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:334)
    at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:59)
    at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:108)
    at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:95)
    at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:185)
    at org.structr.neo4j.Neo4jDatabaseService.initialize(Neo4jDatabaseService.java:130)
    at org.structr.core.graph.NodeService.initialize(NodeService.java:115)
    at org.structr.core.Services.createService(Services.java:550)
    at org.structr.core.Services.initialize(Services.java:325)
    at org.structr.core.Services.initialize(Services.java:297)
    at org.structr.core.Services.getInstance(Services.java:145)
    at org.structr.Server.main(Server.java:36)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.impl.transaction.state.DataSourceManager@162be846' was successfully initialized, but failed to start. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:532)
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
    at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330)
    ... 11 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@191a8997' was successfully initialized, but failed to start. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:532)
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
    at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:117)
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
    ... 13 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.Recovery@245b6b85' failed to initialize. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:508)
    at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:72)
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:106)
    at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:579)
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526)
    ... 16 more
Caused by: java.lang.NullPointerException
    at org.neo4j.index.impl.lucene.IndexType.instantiateField(IndexType.java:318)
    at org.neo4j.index.impl.lucene.IndexType$1.addToDocument(IndexType.java:63)
    at org.neo4j.index.impl.lucene.LuceneCommandApplier.visitIndexAddRelationshipCommand(LuceneCommandApplier.java:79)
    at org.neo4j.kernel.impl.api.LegacyIndexApplier.visitIndexAddRelationshipCommand(LegacyIndexApplier.java:143)
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visitIndexAddRelationshipCommand(CommandApplierFacade.java:246)
    at org.neo4j.kernel.impl.index.IndexCommand$AddRelationshipCommand.handle(IndexCommand.java:236)
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:82)
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:45)
    at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69)
    at org.neo4j.kernel.impl.api.TransactionRepresentationStoreApplier.apply(TransactionRepresentationStoreApplier.java:111)
    at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:70)
    at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:36)
    at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:54)
    at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:32)
    at org.neo4j.kernel.Recovery.init(Recovery.java:78)
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:502)
    ... 20 more
Mar 07, 2016 12:19:36 AM org.structr.core.Services createService
SEVERE: Vital service NodeService failed to start: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /usr/local/download/structr/binaries/structr-ui-2.0-SNAPSHOT-201603060822.5403e4/./db. Aborting

这是我尝试使用2.2.8 Neo4j社区程序启动db时得到的结果。在这两种情况下，它在某种类型的“空指针”上失败。

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] Successfully shutdown Neo4j Server.
2016-03-07 13:19:01.275+0000 ERROR [API] Failed to 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
    at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:258) ~[neo4j-server-2.2.8.jar:2.2.8]
    at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:117) [neo4j-server-2.2.8.jar:2.2.8]
    at 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
    at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:334) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:59) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.recovery.StoreRecoverer.recover(StoreRecoverer.java:96) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.server.preflight.PerformRecoveryIfNecessary.run(PerformRecoveryIfNecessary.java:65) ~[neo4j-server-2.2.8.jar:2.2.8]
    at org.neo4j.server.preflight.PreFlightTasks.run(PreFlightTasks.java:71) ~[neo4j-server-2.2.8.jar:2.2.8]
    at org.neo4j.server.AbstractNeoServer.runPreflightTasks(AbstractNeoServer.java:399) ~[neo4j-server-2.2.8.jar:2.2.8]
    at 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' was successfully initialized, but failed to start. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:532) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    ... 8 common frames omitted
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@4b9b15' was successfully initialized, but failed to start. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:532) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:117) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:526) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    ... 10 common frames omitted
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.Recovery@3016120' failed to initialize. Please see attached cause exception.
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:508) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:72) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:106) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:579) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at 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
    at org.neo4j.index.impl.lucene.IndexType.instantiateField(IndexType.java:318) ~[neo4j-lucene-index-2.2.8.jar:2.2.8]
    at org.neo4j.index.impl.lucene.IndexType$1.addToDocument(IndexType.java:63) ~[neo4j-lucene-index-2.2.8.jar:2.2.8]
    at org.neo4j.index.impl.lucene.LuceneCommandApplier.visitIndexAddRelationshipCommand(LuceneCommandApplier.java:79) ~[neo4j-lucene-index-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.api.LegacyIndexApplier.visitIndexAddRelationshipCommand(LegacyIndexApplier.java:143) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visitIndexAddRelationshipCommand(CommandApplierFacade.java:246) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.index.IndexCommand$AddRelationshipCommand.handle(IndexCommand.java:236) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:82) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.api.CommandApplierFacade.visit(CommandApplierFacade.java:45) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.log.PhysicalTransactionRepresentation.accept(PhysicalTransactionRepresentation.java:69) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.api.TransactionRepresentationStoreApplier.apply(TransactionRepresentationStoreApplier.java:111) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:70) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.state.RecoveryVisitor.visit(RecoveryVisitor.java:36) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:54) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.impl.transaction.log.LogFileRecoverer.visit(LogFileRecoverer.java:32) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.Recovery.init(Recovery.java:78) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:502) ~[neo4j-kernel-2.2.8.jar:2.2.8]
    ... 17 common frames omitted

共有1个答案

邹俊友
2023-03-14

根本原因是structr试图索引一个toString（）方法返回null的对象。由于Lucene和Neo4j中都没有针对此类对象的过滤器，这会导致数据库崩溃和无法恢复的数据库存储。

我们将尽快为Structr提供修复，我向Neo4j提交了一个问题：https://github.com/neo4j/neo4j/issues/6685

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