Neo4j org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out after CDI migration - jsf

Question

I migrated a JavaEE JSF application running over GlassFish server from using Managed Beans to using CDI.
Everything works fine, all pages display correctly except a page which uses Neo4j which now returns a
org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out
I chased the problem down to a specific git commit where I change my class LibraryController from being:
#ManagedBean
#SessionScoped
public class LibraryController
{
private GraphStorage graphStorage;
public LibraryController()
{
graphStorage = new GraphStorage();
graphStorage.setUp();
}
}
to
#Named
#SessionScoped
public class LibraryController
{
private GraphStorage graphStorage;
public LibraryController()
{
graphStorage = new GraphStorage();
graphStorage.setUp();
}
}
the timeout error happens when the neo4j changes are committed with tx.finish inside the setUp() method of GraphStorage:
public class GraphStorage
{
private void createNodespace()
{
Transaction tx = graphDb.beginTx();
try
{
Node rootNode = graphDb.createNode();
setGraphRootUUIDString(java.util.UUID.randomUUID().toString());
rootNode.setProperty("uuid", getGraphRootUUIDString());
index.add(rootNode, "uuid", rootNode.getProperty("uuid"));
tx.success();
}
finally
{
tx.finish();
}
}
public void setUp()
{
graphDb = new GraphDatabaseFactory().newEmbeddedDatabase(FILESYSTEM_DB);
indexManager = graphDb.index();
index = indexManager.forNodes("indexNodes");
registerShutdownHook();
createNodespace();
}
}
Notice I have a main method inside GraphStorage which calls the same setUp() and creates the same nodes which runs fine, it seems the CDI somehow breaks the way Neo4j works.
Any hint at how to fix this please?
EDIT:
Ok found out that the main method inside GraphStorage correctly works because it calls the constructor once, while JavaEE CDI calls the constructor of GraphStorage multiple times
due apparently to how CDI is implemented (i.e. proxies). Still dont' know how to fix this
TRACE LOG:
Schwerwiegend: Error Rendering View[documents.xhtml]
javax.el.ELException: documents.xhtml #47,61 value="#{libraryController.root}": org.neo4j.graphdb.TransactionFailureException: Unable to commit transaction
at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:114)
at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:194)
at org.primefaces.component.api.UITree.getValue(UITree.java:118)
at org.primefaces.component.tree.TreeRenderer.encodeMarkup(TreeRenderer.java:228)
at org.primefaces.component.tree.TreeRenderer.encodeEnd(TreeRenderer.java:185)
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:924)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1863)
at javax.faces.render.Renderer.encodeChildren(Renderer.java:176)
at javax.faces.component.UIComponentBase.encodeChildren(UIComponentBase.java:894)
at org.primefaces.renderkit.CoreRenderer.renderChild(CoreRenderer.java:70)
at org.primefaces.renderkit.CoreRenderer.renderChildren(CoreRenderer.java:57)
at org.primefaces.component.panel.PanelRenderer.encodeContent(PanelRenderer.java:204)
at org.primefaces.component.panel.PanelRenderer.encodeMarkup(PanelRenderer.java:121)
at org.primefaces.component.panel.PanelRenderer.encodeEnd(PanelRenderer.java:58)
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:924)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1863)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
at com.sun.faces.application.view.FaceletViewHandlingStrategy.renderView(FaceletViewHandlingStrategy.java:443)
at com.sun.faces.application.view.MultiViewHandler.renderView(MultiViewHandler.java:131)
at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:120)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.primefaces.webapp.filter.FileUploadFilter.doFilter(FileUploadFilter.java:70)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at com.example.common.utils.AuthenticationFilter.doFilter(AuthenticationFilter.java:59)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:357)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:191)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:168)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
at java.lang.Thread.run(Thread.java:744)
Caused by: javax.el.ELException: org.neo4j.graphdb.TransactionFailureException: Unable to commit transaction
at javax.el.BeanELResolver.getValue(BeanELResolver.java:368)
at com.sun.faces.el.DemuxCompositeELResolver._getValue(DemuxCompositeELResolver.java:176)
at com.sun.faces.el.DemuxCompositeELResolver.getValue(DemuxCompositeELResolver.java:203)
at com.sun.el.parser.AstValue.getValue(AstValue.java:140)
at com.sun.el.parser.AstValue.getValue(AstValue.java:204)
at com.sun.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:226)
at org.jboss.weld.el.WeldValueExpression.getValue(WeldValueExpression.java:50)
at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:109)
... 59 more
Caused by: org.neo4j.graphdb.TransactionFailureException: Unable to commit transaction
at org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:143)
at com.example.dms.GraphStorage.createNodespace(GraphStorage.java:190)
at com.example.dms.GraphStorage.setUp(GraphStorage.java:405)
at com.example.controllers.LibraryController.<init>(LibraryController.java:94)
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.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:79)
at org.jboss.weld.injection.ConstructorInjectionPoint.newInstance(ConstructorInjectionPoint.java:63)
at org.jboss.weld.injection.producer.AbstractInstantiator.newInstance(AbstractInstantiator.java:29)
at org.jboss.weld.injection.producer.DefaultInstantiator.newInstance(DefaultInstantiator.java:90)
at org.jboss.weld.injection.producer.BasicInjectionTarget.produce(BasicInjectionTarget.java:86)
at org.jboss.weld.injection.producer.BeanInjectionTarget.produce(BeanInjectionTarget.java:172)
at org.jboss.weld.bean.ManagedBean.create(ManagedBean.java:157)
at org.jboss.weld.context.ForwardingContextual.create(ForwardingContextual.java:27)
at org.jboss.weld.context.AbstractContext.get(AbstractContext.java:103)
at org.jboss.weld.context.PassivatingContextWrapper$AbstractPassivatingContextWrapper.get(PassivatingContextWrapper.java:64)
at org.jboss.weld.bean.proxy.ContextBeanInstance.getInstance(ContextBeanInstance.java:93)
at org.jboss.weld.bean.proxy.ProxyMethodHandler.invoke(ProxyMethodHandler.java:79)
at com.example.controllers.LibraryController$Proxy$_$$_WeldClientProxy.getRoot(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at javax.el.BeanELResolver.getValue(BeanELResolver.java:363)
... 66 more
Caused by: org.neo4j.graphdb.TransactionFailureException: commit threw exception
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:432)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:344)
at org.neo4j.kernel.impl.transaction.TransactionImpl.commit(TransactionImpl.java:134)
at org.neo4j.kernel.TopLevelTransaction.finish(TopLevelTransaction.java:127)
... 91 more
Caused by: javax.transaction.xa.XAException
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:576)
at org.neo4j.kernel.impl.transaction.TxManager.commit(TxManager.java:394)
... 94 more
Caused by: java.lang.RuntimeException: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock#/home/antonio.test/glassfish-4.0/glassfish/domains/domain1/config/target/dms-db/index/lucene/node/indexNodes/write.lock
at org.neo4j.index.impl.lucene.LuceneDataSource.newIndexWriter(LuceneDataSource.java:718)
at org.neo4j.index.impl.lucene.LuceneDataSource.syncGetIndexSearcher(LuceneDataSource.java:596)
at org.neo4j.index.impl.lucene.LuceneDataSource.getIndexSearcher(LuceneDataSource.java:560)
at org.neo4j.index.impl.lucene.CommitContext.ensureWriterInstantiated(CommitContext.java:58)
at org.neo4j.index.impl.lucene.LuceneCommand$AddCommand.perform(LuceneCommand.java:188)
at org.neo4j.index.impl.lucene.LuceneTransaction.doCommit(LuceneTransaction.java:286)
at org.neo4j.kernel.impl.transaction.xaframework.XaTransaction.commit(XaTransaction.java:322)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceManager.commit(XaResourceManager.java:489)
at org.neo4j.kernel.impl.transaction.xaframework.XaResourceHelpImpl.commit(XaResourceHelpImpl.java:64)
at org.neo4j.kernel.impl.transaction.TransactionImpl.doCommit(TransactionImpl.java:570)
... 95 more
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock#/home/antonio.test/glassfish-4.0/glassfish/domains/domain1/config/target/dms-db/index/lucene/node/indexNodes/write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:84)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:1098)
at org.neo4j.index.impl.lucene.LuceneDataSource.newIndexWriter(LuceneDataSource.java:707)
... 104 more

Answer 1

Beans called twice as you found out is normal behaviour, the first creation is the Weld container creating a scoped proxy of the bean so that the scoped proxy, which extends your bean, gets injected whenever some other component needs your bean.
Now for the solution you should avoid putting logic in the constructor and put it instead in a PostConstructor which behaves as you would expect it to, so you would change your code to look something like:
#PostConstruct
void postConstruct()
{
graphStorage = new GraphStorage();
graphStorage.setUp();
}