neo4j 3.2.3, tinkerpop 3.3.0. access previously created database.

[Bailey Glen]

So, I am trying to utilize tinkerpop 3.3.0 to access a neo4j database I created with in python with cypher (official neo4j-driver) in neo4j 3.2.3. I have worked through a lot of the details, but have now run into an error that I am uncertain how to get around. 

I have tried connecting from both the console and the server. Detailing the console below

:install org.apache.tinkerpop neo4j-gremlin 3.3.0

:install org.neo4j neo4j-tinkerpop-api-impl 0.7-3.2.3

graph = Neo4jGraph.open(pathtodb/graph.db);



Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, pathtodb/graph.db
Type ':help' or ':h' for help.
Display stack trace? [yN]y
java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, pathtodb/graph.db
 at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:143)
 at org.neo4j.kernel.impl.factory.CommunityFacadeFactory.newFacade(CommunityFacadeFactory.java:43)
 at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:108)
 at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:129)
 at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:117)
 at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:185)
 at org.neo4j.tinkerpop.api.impl.Neo4jFactoryImpl.newGraphDatabase(Neo4jFactoryImpl.java:45)
 at org.neo4j.tinkerpop.api.Neo4jFactory$Builder.open(Neo4jFactory.java:32)
 at org.apache.tinkerpop.gremlin.neo4j.structure.Neo4jGraph.<init>(Neo4jGraph.java:125)
 at org.apache.tinkerpop.gremlin.neo4j.structure.Neo4jGraph.open(Neo4jGraph.java:139)
 at org.apache.tinkerpop.gremlin.neo4j.structure.Neo4jGraph$open.call(Unknown Source)
 at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
 at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
 at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
 at groovysh_evaluate.run(groovysh_evaluate:3)
 at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:232)
 at org.codehaus.groovy.tools.shell.Interpreter.evaluate(Interpreter.groovy:70)
 at org.codehaus.groovy.tools.shell.Groovysh.execute(Groovysh.groovy:191)
 at org.apache.tinkerpop.gremlin.console.GremlinGroovysh.super$3$execute(GremlinGroovysh.groovy)
 at sun.reflect.GeneratedMethodAccessor14.invoke(Unknown Source)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
 at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
 at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1213)
 at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuperN(ScriptBytecodeAdapter.java:132)
 at org.apache.tinkerpop.gremlin.console.GremlinGroovysh.execute(GremlinGroovysh.groovy:72)
 at org.codehaus.groovy.tools.shell.Shell.leftShift(Shell.groovy:122)
 at org.codehaus.groovy.tools.shell.ShellRunner.work(ShellRunner.groovy:95)
 at org.codehaus.groovy.tools.shell.InteractiveShellRunner.super$2$work(InteractiveShellRunner.groovy)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
 at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
 at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1213)
 at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuperN(ScriptBytecodeAdapter.java:132)
 at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuper0(ScriptBytecodeAdapter.java:152)
 at org.codehaus.groovy.tools.shell.InteractiveShellRunner.work(InteractiveShellRunner.groovy:124)
 at org.codehaus.groovy.tools.shell.ShellRunner.run(ShellRunner.groovy:59)
 at org.codehaus.groovy.tools.shell.InteractiveShellRunner.super$2$run(InteractiveShellRunner.groovy)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
 at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
 at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1213)
 at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuperN(ScriptBytecodeAdapter.java:132)
 at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnSuper0(ScriptBytecodeAdapter.java:152)
 at org.codehaus.groovy.tools.shell.InteractiveShellRunner.run(InteractiveShellRunner.groovy:83)
 at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:232)
 at org.apache.tinkerpop.gremlin.console.Console.<init>(Console.groovy:143)
 at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:232)
 at org.apache.tinkerpop.gremlin.console.Console.main(Console.groovy:450)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.extension.KernelExtensions@29022a56' failed to initialize. Please see attached cause exception.
 at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:434)
 at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:66)
 at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:102)
 at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:139)
 ... 55 more
Caused by: java.lang.NoSuchMethodError: org.neo4j.kernel.api.impl.index.LuceneKernelExtensions.directoryFactory(ZLorg/neo4j/io/fs/FileSystemAbstraction;)Lorg/neo4j/kernel/api/impl/index/storage/DirectoryFactory;
 at org.neo4j.kernel.api.impl.labelscan.LuceneLabelScanStoreExtension.newInstance(LuceneLabelScanStoreExtension.java:78)
 at org.neo4j.kernel.api.impl.labelscan.LuceneLabelScanStoreExtension.newInstance(LuceneLabelScanStoreExtension.java:44)
 at org.neo4j.kernel.extension.KernelExtensions.init(KernelExtensions.java:69)
 at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:424)
 ... 58 more

I have tried with a  org.neo4j neo4j-tinkerpop-api-impl 0.3-2.3.2 and received an error that I needed to upgrade the version of the neo4j database. Enabling allow_store_upgrade led to an error indicating that it couldn't properly read in the db version.

Am I using incompatible versions? Do I need to recreate the indexes in an alternative method to avoid Lucene? Do I need to update something else?

[Bailey Glen]

I tried removing all of the neo4j indices but this did not impact the problem

[Robert Dale]

The supported version of Neo4j is tightly coupled to the TinkerPop version.. TinkerPop 3.3.0 supports only Neo4j 2.3.3.  See also http://tinkerpop.apache.org/docs/current/reference/#neo4j-gremlin

TinkerPop 3.3.1 will update to Neo4j 3.2.3.  It would be fantastic if you could try out that upgrade path and provide any feedback!

Upgrade Neo4j

^^^^^^^^^^^^^

See Neo4j's https://neo4j.com/guides/upgrade/   3.2 Upgrade FAQ for a complete guide on how to upgrade from the previous 2.3.3 version. Also note that many of the configuration settings have https://neo4j.com/developer/kb/manually-migrating-configuration-settings-from-neo4j-2x-to-neo4j-3x/  changed from neo4j 2x to 3x

In particular, these properties referenced in TinkerPop documentation and configuration were renamed:

|=========================================================
|Neo4j 2.3 (TinkerPop \<= 3.3.0) |Neo4j 3.2 (TinkerPop 3.3.1)
|node_auto_indexing              |dbms.auto_index.nodes.enabled
|relationship_auto_indexing      |dbms.auto_index.relationships.enabled
|ha.cluster_server               |ha.host.coordination
|ha.server                       |ha.host.data
|=========================================================

Robert Dale

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[Bailey Glen]

So, just to be clear, the two reasonable options at this point seem to be...

rebuild my db in neo4j 2.3.3 with tp 3.3.0

OR

upgrade tp to 3.3.1 AND upgrade/rebuild my neo4j databaase to 3.2.3

I'm inclined to tackle the first option as it seems like it will be much more straightforward/better supported, and I have yet to attempt building TP from source. However, if it would be helpful for you, I would be happy to try option 2 as well, but will need some pointers on exactly which version of the source I should start with to build tp 3.3.1. Or are binaries available somewhere?

Robert Dale

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[Bailey Glen]

First off, at some point in this thread I got confused about my neo4j server version. It was build from scratch with 3.2.3, which as I understand it is the correct version for 3.0.1. Also, since I couldn't seem to find the documentation for neo4j 2.3.3, I decided to take a crack at building 3.3.1. I did the following.

>docker run -it maven /bin/bash

then from the docker

>git clone https://github.com/apache/tinkerpop.git  # (it looks like master is 3.3.1-SNAPSHOT)

created the ~/.groovy/groovy.xml from the 3.0.0 docs

>mvn clean install -pl neo4j-gremlin/ 

>mvn clean install -pl neo4j-gremlin/ 

>./gremlin-console/target/apache-tinkerpop-gremlin-console-3.3.1-SNAPSHOT-standalone/bin/gremlin.sh

then from the console

>:install org.apache.tinkerpop neo4j-gremlin 3.3.1-SNAPSHOT

restart console

>conf = new BaseConfiguration()

>conf.setProperty('gremlin.neo4j.directory','pathtodb/graph.db/');

>conf.setProperty('gremlin.neo4j.conf.allow_store_upgrade', 'true');

>graph = Neo4jGraph.open(conf);

>g = graph.traversal()

>g.V().count()

0

so. I got no errors, and was able to seemingly connect to the neo4j database, but it appears empty from the console. 

If I spin up a 3.2.3 server, I can still see all my graph content.

Thoughts?

[Bailey Glen]

A few edits, and also got it to work.

The graph was blank because I forgot to mount to volume to the docker, so it was simply creating a new blank graph.

i also didn't need the goovy xml, had a dupliucate command in the build, and left out activating the plugin

docker run -it --mount type=bind,source=/path/to/data,target=/path/to/data maven /bin/bash

>git clone https://github.com/apache/tinkerpop.git  # (it looks like master is 3.3.1-SNAPSHOT)

>cd tinkerpop

>mvn clean install -pl gremlin-console/ 

>mvn clean install -pl neo4j-gremlin/ 

>./gremlin-console/target/apache-tinkerpop-gremlin-console-3.3.1-SNAPSHOT-standalone/bin/gremlin.sh

then from the console

>:install org.apache.tinkerpop neo4j-gremlin 3.3.1-SNAPSHOT

restart console

>:plugin use tinkerpop.neo4j

>conf = new BaseConfiguration()

>conf.setProperty('gremlin.neo4j.directory','/path/to/data/databases/graph.db/');

>conf.setProperty('gremlin.neo4j.conf.allow_store_upgrade', 'true');

>graph = Neo4jGraph.open(conf);

>g = graph.traversal()

>g.V().count()

57258

All seems to be working at the moment. Now going to try embedding in gremlin server and connecting via gremlin-python