Database killed when I try to add the neosemantics plugin

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Colin Goldberg

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May 19, 2018, 7:17:55 AM5/19/18
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Hi,

On macosx 10.13.4, neo4j 3.3.5, I am trying to start up after adding the neosemantics plugin. Before starting, I downloaded the jar file neosemantics-3.3.0.2.jar from https://github.com/jbarrasa/neosemantics/releases and added two lines to the bottom of neo4j.conf

dbms.unmanaged_extension_classes=semantics.extension=/rdf

dbms.security.procedures.whitelist=semantics.*


Error message "Database killed ..." appears on the screen

The neo4j.log file shows:

Starting Neo4j.

2018-05-14 13:49:08.954+0000 INFO  ======== Neo4j 3.3.5 ========

2018-05-14 13:49:09.003+0000 INFO  Starting...

2018-05-14 13:49:10.410+0000 INFO  Bolt enabled on 127.0.0.1:7687.

2018-05-14 13:49:10.448+0000 INFO  Initiating metrics...

2018-05-14 13:49:15.475+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@3dc4ed6f' was successfully initialized, but failed to start. Please see the attached cause exception "class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@3dc4ed6f' was successfully initialized, but failed to start. Please see the attached cause exception "class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;".

org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@3dc4ed6f' was successfully initialized, but failed to start. Please see the attached cause exception "class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;".

        at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:68)

        at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:220)

        at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:111)

        at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:79)

        at com.neo4j.server.enterprise.CommercialEntryPoint.main(CommercialEntryPoint.java:22)

Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@3dc4ed6f' was successfully initialized, but failed to start. Please see the attached cause exception "class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;".

        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:466)

        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)

        at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:212)

        ... 3 more

Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory, /Users/colingoldberg/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-c4c8aad5-ff29-431c-8c33-0144b82bcf5a/installation-3.3.5/data/databases/graph.db

        at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:211)

        at org.neo4j.kernel.enterprise.EnterpriseGraphDatabase.<init>(EnterpriseGraphDatabase.java:36)

        at org.neo4j.server.enterprise.OpenEnterpriseNeoServer.lambda$static$1(OpenEnterpriseNeoServer.java:75)

        at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:88)

        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:445)

        ... 5 more

Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.impl.proc.Procedures@50dd1e3a' was successfully initialized, but failed to start. Please see the attached cause exception "class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;".

        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:466)

        at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)

        at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:207)

        ... 9 more

Caused by: java.lang.VerifyError: class com.fasterxml.jackson.databind.deser.SettableBeanProperty$Delegating overrides final method getDeclaringClass.()Ljava/lang/Class;

        at java.lang.ClassLoader.defineClass1(Native Method)

        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)

        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

        at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)

        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:368)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:362)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:361)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:411)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

        at org.neo4j.kernel.impl.proc.ProcedureJarLoader$1.fetchNextOrNull(ProcedureJarLoader.java:141)

        at org.neo4j.kernel.impl.proc.ProcedureJarLoader$1.fetchNextOrNull(ProcedureJarLoader.java:118)

        at org.neo4j.collection.PrefetchingRawIterator.peek(PrefetchingRawIterator.java:50)

        at org.neo4j.collection.PrefetchingRawIterator.hasNext(PrefetchingRawIterator.java:36)

        at org.neo4j.kernel.impl.proc.ProcedureJarLoader.loadProcedures(ProcedureJarLoader.java:91)

        at org.neo4j.kernel.impl.proc.ProcedureJarLoader.loadProceduresFromDir(ProcedureJarLoader.java:82)

        at org.neo4j.kernel.impl.proc.Procedures.start(Procedures.java:276)

        at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:445)

        ... 11 more

2018-05-14 13:49:15.477+0000 INFO  Neo4j Server shutdown initiated by request



I hope it's ok to ask this question here, even though the neosemantics plugin is (I think) not an official plugin.

Any help is appreciated.

Thanks

Colin Goldberg

J Barrasa (Neo4j)

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Jun 12, 2018, 8:02:03 PM6/12/18
to Neo4j
Hi Colin, 
This is a known issue in neosemantics-3.3.0.2 that was fixed some time ago. (see: https://github.com/jbarrasa/neosemantics/pull/44/commits/36488fb66328e6b93651ec47459a0b9604bd4b71)
I did not create a release for that so you'd need to rebuild from source to get a compatible jar.
Alternatively, if you can wait till next week I'm planning to publish a new release for Neo4j 3.4 that will include the fix.

FYI, the reason of the incompatibility was that  neosemantics-3.3.0.2 has an indirect dependency  (for the JSON-LD serialization parser) on a version of jackson that clashes with the one used by APOC.



Regards,

JB.

Colin Goldberg

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Jun 13, 2018, 11:17:47 AM6/13/18
to Neo4j
Thanks for the clarification. I will wait for the next version.

CG
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