I am currently using spring data neo4j 2.1.0 (community edition).
Occasionally I manage either to corrupt the database and/or database indexes.
I have gathered the following recovery step but would like to have a more definitive set for future use.
To recover a corrupt database. I currently delete the following files in the database data directory this process alone seems to work 90% of the time:
nioneo_logical.log.v* (wildcard for numbers)
nioneo_logical.log.active
I would like to know if any other files can be removed from the data directory to aid recovery and especially if any of the files in the data\index directory can be removed (without the necessity to rebuild indexes).
Help much appreciated.
messages.log
2013-12-16 10:41:40,516 ERROR [neo4j.index]: Failed to load index provider lucene
org.neo4j.graphdb.NotFoundException: Target file[lucene.log.v3] already exists
at org.neo4j.kernel.impl.util.FileUtils.renameFile(FileUtils.java:192) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.DefaultFileSystemAbstraction.renameFile(DefaultFileSystemAbstraction.java:77) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.renameLogFileToRightVersion(XaLogicalLog.java:683) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.renameIfExists(XaLogicalLog.java:181) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaLogicalLog.open(XaLogicalLog.java:150) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.impl.transaction.xaframework.XaContainer.openLogicalLog(XaContainer.java:64) ~[neo4j-kernel-1.8.jar:1.8]
at org.neo4j.index.impl.lucene.LuceneDataSource.<init>(LuceneDataSource.java:232) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.index.lucene.LuceneIndexProvider.load(LuceneIndexProvider.java:72) ~[neo4j-lucene-index-1.8.jar:1.8]
at org.neo4j.kernel.InternalAbstractGraphDatabase$DefaultKernelExtensionLoader.loadIndexImplementations(InternalAbstractGraphDatabase.java:1171) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.InternalAbstractGraphDatabase$DefaultKernelExtensionLoader.init(InternalAbstractGraphDatabase.java:1143) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:382) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:82) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:116) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:227) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:79) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:70) [neo4j-kernel-1.8.jar:1.8]
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:55) [neo4j-kernel-1.8.jar:1.8]
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.6.0_27]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) [na:1.6.0_27]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) [na:1.6.0_27]
at java.lang.reflect.Constructor.newInstance(Unknown Source) [na:1.6.0_27]
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:108) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1002) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:906) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:484) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1327) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1085) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:516) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:353) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:982) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:878) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.getSingletonFactoryBeanForTypeCheck(AbstractAutowireCapableBeanFactory.java:734) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.getTypeForFactoryBean(AbstractAutowireCapableBeanFactory.java:665) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.isTypeMatch(AbstractBeanFactory.java:518) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanNamesForType(DefaultListableBeanFactory.java:319) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.BeanFactoryUtils.beanNamesForTypeIncludingAncestors(BeanFactoryUtils.java:185) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:833) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:790) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:707) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:478) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:84) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:284) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1073) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:516) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585) [spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895) [spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425) [spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.context.support.FileSystemXmlApplicationContext.<init>(FileSystemXmlApplicationContext.java:140) [spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at org.springframework.context.support.FileSystemXmlApplicationContext.<init>(FileSystemXmlApplicationContext.java:84) [spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]
at com.ci.server.ContextManager.initSinkServer(ContextManager.java:120) [CiDataConverter-0.0.1-SNAPSHOT.jar:na]
at com.ci.server.Server.buildContext(Server.java:263) [CiDataConverter-0.0.1-SNAPSHOT.jar:na]
at com.ci.server.Server.runServer(Server.java:76) [CiDataConverter-0.0.1-SNAPSHOT.jar:na]
at com.ci.server.ServerMain.main(ServerMain.java:21) [CiDataConverter-0.0.1-SNAPSHOT.jar:na]
2013-12-16 10:41:40,524 DEBUG [neo4j.diagnostics]: --- SHUTDOWN diagnostics START ---
2013-12-16 10:41:40,524 DEBUG [neo4j.diagnostics]: --- SHUTDOWN diagnostics END ---
My Application Log file
SEVERE: Error initialising Neo4J context:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ciFinDomainServiceImpl': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private GelatoData.domainFinService.impl.FinancialRepository GelatoData.domainFinService.impl.CiFinDomainServiceImpl.financialRepository; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.data.neo4j.config.Neo4jConfiguration#0': Cannot resolve reference to bean 'graphDatabaseService' while setting bean property 'graphDatabaseService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'graphDatabaseService' defined in file [C:\app\Gelato\server\etc\GelatoServerData.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.neo4j.kernel.EmbeddedGraphDatabase]: Constructor threw exception; nested exception is org.neo4j.graphdb.NotFoundException: Target file[nioneo_logical.log.v2] already exists
Related cause: org.springframework.beans.factory.BeanCurrentlyInCreationException: Error creating bean with name 'mappingInfrastructure': Requested bean is currently in creation: Is there an unresolvable circular reference?
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:287)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1073)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:516)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.context.support.FileSystemXmlApplicationContext.<init>(FileSystemXmlApplicationContext.java:140)
at org.springframework.context.support.FileSystemXmlApplicationContext.<init>(FileSystemXmlApplicationContext.java:84)
at com.ci.server.ContextManager.initSinkServer(ContextManager.java:120)
at com.ci.server.Server.buildContext(Server.java:263)
at com.ci.server.Server.runServer(Server.java:76)
at com.ci.server.ServerMain.main(ServerMain.java:21)
Caused by: org.springframework.beans.factory.BeanCreationException: Could not autowire field: private GelatoData.domainFinService.impl.FinancialRepository GelatoData.domainFinService.impl.CiFinDomainServiceImpl.financialRepository; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.data.neo4j.config.Neo4jConfiguration#0': Cannot resolve reference to bean 'graphDatabaseService' while setting bean property 'graphDatabaseService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'graphDatabaseService' defined in file [C:\app\Gelato\server\etc\GelatoServerData.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.neo4j.kernel.EmbeddedGraphDatabase]: Constructor threw exception; nested exception is org.neo4j.graphdb.NotFoundException: Target file[nioneo_logical.log.v2] already exists
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:506)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:84)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:284)
... 16 more
Neo4j data directory contents
Volume in drive C is OS
Volume Serial Number is 8861-7230
Directory of C:\app_data\gelato\data
16/12/2013 10:49 <DIR> .
16/12/2013 10:49 <DIR> ..
25/11/2013 13:12 11 active_tx_log
16/12/2013 10:38 <DIR> index
25/11/2013 13:42 1,571 index.db
25/11/2013 13:14 0 lock
16/12/2013 10:41 289,837 messages.log
16/12/2013 10:41 54 neostore
16/12/2013 10:41 9 neostore.id
10/12/2013 17:32 25,164 neostore.nodestore.db
16/12/2013 10:41 9 neostore.nodestore.db.id
16/12/2013 10:41 5,535,000 neostore.propertystore.db
25/11/2013 13:14 128 neostore.propertystore.db.arrays
16/12/2013 10:41 9 neostore.propertystore.db.arrays.id
16/12/2013 10:41 9 neostore.propertystore.db.id
10/12/2013 17:32 1,044 neostore.propertystore.db.index
16/12/2013 10:41 9 neostore.propertystore.db.index.id
10/12/2013 17:32 1,026 neostore.propertystore.db.index.keys
16/12/2013 10:41 9 neostore.propertystore.db.index.keys.id
10/12/2013 17:32 3,379,456 neostore.propertystore.db.strings
16/12/2013 10:41 9 neostore.propertystore.db.strings.id
10/12/2013 17:32 1,132,461 neostore.relationshipstore.db
16/12/2013 10:41 9 neostore.relationshipstore.db.id
16/12/2013 10:41 10 neostore.relationshiptypestore.db
16/12/2013 10:41 9 neostore.relationshiptypestore.db.id
10/12/2013 17:32 114 neostore.relationshiptypestore.db.names
16/12/2013 10:41 9 neostore.relationshiptypestore.db.names.id
16/12/2013 10:42 612 nioneo_logical.log.2
16/12/2013 10:41 4 nioneo_logical.log.active
10/12/2013 14:32 353,479 nioneo_logical.log.v0
10/12/2013 17:32 14,659,211 nioneo_logical.log.v1
10/12/2013 17:18 26,214,477 nioneo_logical.log.v2
25/11/2013 13:12 2,022,220 rrd
16/12/2013 10:40 176 tm_tx_log.1
32 File(s) 53,616,145 bytes
3 Dir(s) 881,749,417,984 bytes free
Neo4j Index contents
Volume in drive C is OS
Volume Serial Number is 8861-7230
Directory of C:\app_data\gelato\data\index
16/12/2013 10:49 <DIR> .
16/12/2013 10:49 <DIR> ..
16/12/2013 10:38 <DIR> lucene
16/12/2013 10:41 40 lucene-store.db
16/12/2013 10:41 16 lucene.log.1
16/12/2013 10:40 4 lucene.log.active
25/11/2013 13:13 382 lucene.log.v0
25/11/2013 13:44 26,945,214 lucene.log.v1
10/12/2013 17:32 392,983 lucene.log.v2
10/12/2013 17:18 26,214,420 lucene.log.v3
10/12/2013 17:18 26,214,553 lucene.log.v4
9 File(s) 79,767,612 bytes
3 Dir(s) 881,749,921,792 bytes free
