Integrate Neo4j DB with Java and Apache Tomcat

sd...@njit.edu

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Sep 3, 2014, 9:52:28 PM9/3/14

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Hello,

My name is Shashank. I am currently a Masters student. I am trying to explore new technologies and new to Neo4j. I have basic idea on nodes, relationships and querying the database. I have developed a small database in my laptop. I want to integrate it with Java and implement few algorithms on the data (like apriori algorithm) for my data mining project.

Is it a good idea to use Neo4j for data mining. If so, please let me know any example that can fetch data from Neo4j server using Java. Also, I was wondering whether we can use Tomcat instead of Maven.

Your help is very much appreciated.

Thanks,

Shashank

Sukaant Chaudhary

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Sep 4, 2014, 5:17:22 AM9/4/14

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Hi Shashank,
Use the code in the following link, it is cypher-jdbc, it will help you to integrate with Java:
http://docs.neo4j.org/chunked/stable/tutorials-cypher-java.html

You need the following dependency:
<dependency>
        <groupId>org.neo4j</groupId>
        <artifactId>neo4j-kernel</artifactId>
        <version>${neo4j.version}</version>
</dependency>

About Tomcat and Maven

Tomcat is a Server whereas Maven is a build tool both are different things.

Hope this will help.

If you have any further queries please feel free to ask.

-Sukaant Chaudhary

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sd...@njit.edu

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Sep 4, 2014, 3:37:03 PM9/4/14

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Hi Sukaant,

I tried integrating my database with Java. I created a small java application, added neo4j dependency in pom.xml.

Below is the code I wrote.

GraphDatabaseService db = new GraphDatabaseFactory().newEmbeddedDatabase("path of my db");

ExecutionEngine engine = new ExecutionEngine(db, StringLogger.SYSTEM );

ExecutionResult result;

try ( Transaction ignored = db.beginTx() )

{

result = engine.execute( "match (n) return n" );

}

System.out.print(result);

db.shutdown();

This is throwing the below error. I tried looking for the solution, but that was not successful. Below is the error i received.

Exception in thread "main" org.neo4j.graphdb.TransactionFailureException: Failed to mark transaction as rollback only.

at org.neo4j.kernel.TopLevelTransaction.markAsRollbackOnly(TopLevelTransaction.java:97)

at org.neo4j.kernel.TopLevelTransaction.failure(TopLevelTransaction.java:86)

at org.neo4j.cypher.internal.spi.v2_1.TransactionBoundQueryContext.close(TransactionBoundQueryContext.scala:65)

at org.neo4j.cypher.internal.compiler.v2_1.spi.DelegatingQueryContext.close(DelegatingQueryContext.scala:38)

at org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext.org$neo4j$cypher$internal$compiler$v2_1$spi$ExceptionTranslatingQueryContext$$super$close(ExceptionTranslatingQueryContext.scala:34)

at org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$$anonfun$close$1.apply$mcV$sp(ExceptionTranslatingQueryContext.scala:34)

at org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext$$anonfun$close$1.apply(ExceptionTranslatingQueryContext.scala:34)

at org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext.org$neo4j$cypher$internal$compiler$v2_1$spi$ExceptionTranslatingQueryContext$$translateException(ExceptionTranslatingQueryContext.scala:152)

at org.neo4j.cypher.internal.compiler.v2_1.spi.ExceptionTranslatingQueryContext.close(ExceptionTranslatingQueryContext.scala:34)

at org.neo4j.cypher.internal.compiler.v2_1.spi.DelegatingQueryContext.close(DelegatingQueryContext.scala:38)

at org.neo4j.cypher.internal.compiler.v2_1.executionplan.ExecutionWorkflowBuilder$$anonfun$runWithQueryState$1.apply(ExecutionPlanBuilder.scala:164)

at org.neo4j.cypher.internal.compiler.v2_1.TaskCloser$$anonfun$1.apply(TaskCloser.scala:43)

at org.neo4j.cypher.internal.compiler.v2_1.TaskCloser$$anonfun$1.apply(TaskCloser.scala:41)

at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:251)

at scala.collection.immutable.List.foreach(List.scala:318)

at scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:251)

at scala.collection.AbstractTraversable.flatMap(Traversable.scala:105)

at org.neo4j.cypher.internal.compiler.v2_1.TaskCloser.close(TaskCloser.scala:40)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator$$anonfun$close$1.apply$mcV$sp(ClosingIterator.scala:67)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator$$anonfun$close$1.apply(ClosingIterator.scala:67)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator$$anonfun$translateException$1.apply(ClosingIterator.scala:72)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.decoratedCypherException(ClosingIterator.scala:102)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.translateException(ClosingIterator.scala:70)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.close(ClosingIterator.scala:66)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator$$anonfun$failIfThrows$1.apply(ClosingIterator.scala:96)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.decoratedCypherException(ClosingIterator.scala:102)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.failIfThrows(ClosingIterator.scala:91)

at org.neo4j.cypher.internal.compiler.v2_1.ClosingIterator.hasNext(ClosingIterator.scala:34)

at org.neo4j.cypher.internal.compiler.v2_1.PipeExecutionResult.hasNext(PipeExecutionResult.scala:167)

at scala.collection.Iterator$class.toString(Iterator.scala:1153)

at org.neo4j.cypher.internal.compiler.v2_1.PipeExecutionResult.toString(PipeExecutionResult.scala:35)

at java.lang.String.valueOf(String.java:2854)

at java.io.PrintStream.print(PrintStream.java:683)

at cricketFun.main(cricketFun.java:25)

Caused by: java.lang.NullPointerException

at org.neo4j.kernel.TopLevelTransaction.markAsRollbackOnly(TopLevelTransaction.java:93)

... 37 more

Why is it failing to fetch the data? Am I doing anything wrong? Also, if I tried running the application second time, it throws me this error.

Exception in thread "main" java.lang.RuntimeException: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, C:\Users\sd482\Documents\Neo4j\default.graphdb

at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:362)

at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:59)

at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:90)

at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:199)

at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:70)

at cricketFun.main(cricketFun.java:16)

Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.StoreLockerLifecycleAdapter@f1bb79c' was successfully initialized, but failed to start. Please see attached cause exception.

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:513)

at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)

at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:339)

... 5 more

Caused by: org.neo4j.kernel.StoreLockException: Unable to obtain lock on store lock file: C:\Users\sd482\Documents\Neo4j\default.graphdb\store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)

at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:82)

at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44)

at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507)

... 7 more

Caused by: java.io.IOException: Couldn't lock lock file C:\Users\sd482\Documents\Neo4j\default.graphdb\lock because another process already holds the lock.

at org.neo4j.kernel.impl.nioneo.store.FileLock.getLockFileBasedFileLock(FileLock.java:120)

at org.neo4j.kernel.impl.nioneo.store.FileLock.getOsSpecificFileLock(FileLock.java:64)

at org.neo4j.kernel.DefaultFileSystemAbstraction.tryLock(DefaultFileSystemAbstraction.java:93)

at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:74)

... 9 more

I know this is due to the locking issue. Though I'm using "db.shutdown();" in my code, it is not unlocking the database when the application is terminated. I had to close the IDE everytime to unlock it. Please let me know where I am making the mistake.

Sorry for the very long question, and thank you so much for your help. :)

Thanks,

Shashank

Michael Hunger

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Sep 4, 2014, 3:44:38 PM9/4/14

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You have the wrong execution-engine, you need the javacompat one.

Your results contain nodes to access them (for printing) you need a transaction.

There is a result.dumpToString() method which you can use within your transaction.

Or just return attributes of the nodes from your query.

Michael

Saishashank Devannagari

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Sep 4, 2014, 5:43:10 PM9/4/14

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Hi Michael,

Thank you for the quick response. It is working now as expected. :)

Milton Yutaka Nishiyama Junior

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Jan 22, 2015, 12:37:13 AM1/22/15

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Hi Everyone,

I have a plataform in Java running with Tomcat, and I want to create a simple interface to access and make some queries in the neo4j graphdb, and I would like to know if there is any simple example on how to create a web interface to acess graphdb based on java and tomcat.
I gave a look in the Spring website, but I didn't find an easy example, and I don't have experience with Spring.

Thank You,

Milton

Sukaant Chaudhary

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Jan 22, 2015, 1:21:56 AM1/22/15

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Hi Milton,
There are multiple methods to use Neo4J with Java.
Please go through the following URL:

JDBC Example:
http://www.markhneedham.com/blog/2013/06/20/neo4j-a-simple-example-using-the-jdbc-driver/

Cypher Example:
http://neo4j.com/docs/stable/tutorials-cypher-java.html

REST Example:
http://neo4j.com/docs/stable/server-java-rest-client-example.html

Please let me know if you need any further help in this.

-Sukaant Chaudhary

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