bug #8393
Updated by Andreas Kohlbecker over 4 years ago
This happens after changing the last updated timestamp of the '/etc/jetty8/contexts/eubon-utis-1.3.xml'
~~~
java.nio.channels.OverlappingFileLockException
at sun.nio.ch.SharedFileLockTable.checkList(FileLockTable.java:255)
at sun.nio.ch.SharedFileLockTable.add(FileLockTable.java:152)
at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1089)
at java.nio.channels.FileChannel.tryLock(FileChannel.java:1154)
at org.neo4j.kernel.impl.nioneo.store.StoreFileChannel.tryLock(StoreFileChannel.java:113)
at org.neo4j.kernel.impl.nioneo.store.FileLock.wrapFileChannelLock(FileLock.java:35)
at org.neo4j.kernel.impl.nioneo.store.FileLock.getOsSpecificFileLock(FileLock.java:93)
at org.neo4j.kernel.DefaultFileSystemAbstraction.tryLock(DefaultFileSystemAbstraction.java:93)
at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:74)
at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:328)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:56)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:90)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:199)
at com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Graph.<init>(Neo4j2Graph.java:154)
at com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Graph.<init>(Neo4j2Graph.java:136)
at org.cybertaxonomy.utis.store.Neo4jStore.initStoreEngine(Neo4jStore.java:61)
at org.cybertaxonomy.utis.store.Store.<init>(Store.java:78)
at org.cybertaxonomy.utis.store.Neo4jStore.<init>(Neo4jStore.java:50)
at org.cybertaxonomy.utis.store.Neo4jStoreManager.provideStoreFor(Neo4jStoreManager.java:45)
at org.cybertaxonomy.utis.checklist.EUNIS_Client.initQueryClient(EUNIS_Client.java:173)
~~~~
doing a
~~~
rm /var/lib/utis/1.3/neo4j/eunis/store_lock
~~~
does not help, after removing the lock file the webapp restart still fails but with another exception:
~~~
java.lang.IllegalStateException: Unable to lock store [/var/lib/utis/1.3/neo4j/eunis/neostore.relationshiptypestore.db.names], this is usually caused by another Neo4j kernel already running in this JVM for this particular store
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.checkStorage(CommonAbstractStore.java:170)
at org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.<init>(CommonAbstractStore.java:108)
at org.neo4j.kernel.impl.nioneo.store.AbstractDynamicStore.<init>(AbstractDynamicStore.java:78)
at org.neo4j.kernel.impl.nioneo.store.DynamicStringStore.<init>(DynamicStringStore.java:43)
at org.neo4j.kernel.impl.nioneo.store.StoreFactory.newDynamicStringStore(StoreFactory.java:158)
at org.neo4j.kernel.impl.nioneo.store.StoreFactory.newRelationshipTypeTokenStore(StoreFactory.java:164)
at org.neo4j.kernel.impl.nioneo.store.StoreFactory.attemptNewNeoStore(StoreFactory.java:130)
at org.neo4j.kernel.impl.nioneo.store.StoreFactory.newNeoStore(StoreFactory.java:114)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.start(NeoStoreXaDataSource.java:328)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.impl.transaction.XaDataSourceManager.start(XaDataSourceManager.java:164)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:328)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:56)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:90)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:199)
at com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Graph.<init>(Neo4j2Graph.java:154)
at com.tinkerpop.blueprints.impls.neo4j2.Neo4j2Graph.<init>(Neo4j2Graph.java:136)
at org.cybertaxonomy.utis.store.Neo4jStore.initStoreEngine(Neo4jStore.java:61)
at org.cybertaxonomy.utis.store.Store.<init>(Store.java:78)
at org.cybertaxonomy.utis.store.Neo4jStore.<init>(Neo4jStore.java:50)
at org.cybertaxonomy.utis.store.Neo4jStoreManager.provideStoreFor(Neo4jStoreManager.java:45)
at org.cybertaxonomy.utis.checklist.EUNIS_Client.initQueryClient(EUNIS_Client.java:173)
at org.cybertaxonomy.utis.client.AbstractClient.<init>(AbstractClient.java:22)
at org.cybertaxonomy.utis.checklist.BaseChecklistClient.<init>(BaseChecklistClient.java:31)
at org.cybertaxonomy.utis.checklist.AggregateChecklistClient.<init>(AggregateChecklistClient.java:10)
at org.cybertaxonomy.utis.checklist.TinkerPopChecklistClient.<init>(TinkerPopChecklistClient.java:49)
at org.cybertaxonomy.utis.checklist.EUNIS_Client.<init>(EUNIS_Client.java:129)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at java.lang.Class.newInstance(Class.java:383)
at org.bgbm.utis.controller.UtisController.initProviderMap(UtisController.java:146)
at org.bgbm.utis.controller.UtisController.<init>(UtisController.java:106)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:148)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1030)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:983)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:487)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:296)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:628)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:932)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:651)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:602)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:665)
at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:521)
at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:462)
at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:136)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.eclipse.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:532)
at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64)
at org.eclipse.jetty.servlet.ServletHandler.initialize(ServletHandler.java:791)
at org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:265)
at org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1270)
at org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:719)
at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:522)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64)
at org.eclipse.jetty.deploy.bindings.StandardStarter.processBinding(StandardStarter.java:39)
at org.eclipse.jetty.deploy.AppLifeCycle.runBindings(AppLifeCycle.java:186)
at org.eclipse.jetty.deploy.DeploymentManager.requestAppGoal(DeploymentManager.java:494)
at org.eclipse.jetty.deploy.DeploymentManager.addApp(DeploymentManager.java:141)
at org.eclipse.jetty.deploy.providers.ScanningAppProvider.fileChanged(ScanningAppProvider.java:163)
at org.eclipse.jetty.deploy.providers.ScanningAppProvider$1.fileChanged(ScanningAppProvider.java:61)
at org.eclipse.jetty.util.Scanner.reportChange(Scanner.java:669)
at org.eclipse.jetty.util.Scanner.reportDifferences(Scanner.java:543)
at org.eclipse.jetty.util.Scanner.scan(Scanner.java:403)
at org.eclipse.jetty.util.Scanner$1.run(Scanner.java:353)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
~~~