Issues in connecting to Neo4j from linux - neo4j

Trying to connect to Neo4j from java I get the following error:
Exception in thread "main" java.lang.RuntimeException: Error starting
org.neo4j.kernel.EmbeddedGraphDatabase, /data/graph.db
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:323)
at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:100)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:92)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:197)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:69)
at .....
Caused by: org.neo4j.kernel.lifecycle.LifecycleException:
Component
'org.neo4j.kernel.impl.transaction.XaDataSourceManager#4514ba77' was
successfully initialized, but failed to start. Please see attached
cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:504)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:300)
... 7 more Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component
'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#2c86c977' was
successfully initialized, but failed to start. Please see attached
cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:504)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.impl.transaction.XaDataSourceManager.start(XaDataSourceManager.java:165)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:498)
... 9 more Caused by: java.lang.IllegalArgumentException: No schema index provider org.neo4j.kernel.api.index.SchemaIndexProvider
found. Kernel extensions available on classpath:
Class path entries: /...../java/....xyz.jar
at org.neo4j.kernel.api.index.SchemaIndexProvider$2.select(SchemaIndexProvider.java:136)
at org.neo4j.kernel.api.index.SchemaIndexProvider$2.select(SchemaIndexProvider.java:128)
at org.neo4j.kernel.extension.KernelExtensions.resolveDependency(KernelExtensions.java:207)
at org.neo4j.kernel.InternalAbstractGraphDatabase$DependencyResolverImpl.resolveDependency(InternalAbstractGraphDatabase.java:1403)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.start(NeoStoreXaDataSource.java:311)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:498)
... 12 more
I am using Ne04j-2.0.0-M05 version, running the java code under Java 7 in a linux machine. The same jar files and java code works good though in a windows machine. The web admin interface works well (hence path to db may not be a issue since I ve given the same path in org.neo4j.server.database.location and org.neo4j.server.webadmin.data.uri),
The java code I used to connect is :
String dbpath = "/NEO4J_HOME/data/graph.db/";
graphdb = new GraphDatabaseFactory().newEmbeddedDatabase(dbpath);
Can you tell what might cause the java.lang.IllegalArgumentException: No schema index provider org.neo4j.kernel.api.index.SchemaIndexProvider found

Looks like you're lacking neo4j-lucene-index on your classpath. If that hint does not help provide a list of jars being on the classpath.

Keep Neo4j related jars seperate, i.e do not bundle them inside the jar you create. Instead just make use of class path option to point Neo4j libraries in run time.

I got the same error, and finally fount it's the different version of neo4j and neo4j-lucene-index which caused the error. They need to keep in the same version. Still not sure which version of lucene it depends on, but 3.6.2 can survive the compile. Thanks Stefan. It's hard to find the latest version of everything neo4j depends on.
compile "org.neo4j:neo4j-kernel:2.0.0-RC1"
compile "org.apache.lucene:lucene-core:3.6.2"
compile "org.neo4j:neo4j-lucene-index:2.0.0-RC1"
This fixed my error.

Related

cannot enable fabric on Neo4j

I'm trying to enable fabric on neo4j 4.1.3 enterprise but getting the below error.
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer#17fede14' was successfully initialized, but failed to start. Please see the attached cause exception "The specified database 'fabric' already exists.".
#fabric config
fabric.database.name=fabric
fabric.graph.0.uri=neo4j://localhost:7687
fabric.graph.0.database=client1
fabric.graph.0.name=client1
fabric.graph.1.uri=neo4j://localhost:7687
fabric.graph.1.database=client2
fabric.graph.1.name=client2
I deleted everything under /data and restarted and it seems to have resolved it.

Neo.TransientError.Database.DatabaseUnavailable | Database 'graph.db' is unavailable

I am trying to import the Hetionet into the Neo4j and I follow the guidiance below:
https://github.com/hetio/hetionet/tree/master/hetnet/neo4j
While using the command
curl --insecure --location https://github.com/hetio/hetionet/raw/master/hetnet/neo4j/hetionet-v1.0.db.tar.bz2 | tar --extract --bzip2
The error “curl: (23) Failure writing output to destination” has been thrown.
Therefore I just downloaded the file directly and moved to the directory ".Neo4jDesktop\relate-data\dbmss\dbms-0d0d3324-d1a6-4d3e-b82c-0c4451a8c880\data\databases"
After I started the database, It showed that this database is currently offline. When I trying to do some operations to it, the error "Neo.TransientError.Database.DatabaseUnavailable" has been shown.
Some valuable informations in the log file debug.log are as below:
2022-07-19 23:11:53.896+0000 ERROR [c.n.d.DbmsReconciler] Encountered error when attempting to reconcile database graph.db (request by SystemGraph:1) to state 'online', database remains in state 'offline'
org.neo4j.dbms.api.DatabaseManagementException: Unable to start database DatabaseId{7a8c6b65[graph.db]}
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.database.Database#3da82075' was successfully initialized, but failed to start. Please see the attached cause exception "Unknown store version 'v0.A.7'".
The version of the dump you are trying to import is pretty old. From the readme
The database has been migrated to the Neo4j 3.0.1 Community Edition.
If you use a current 4.4 version of the database, the only thing you can do is to cascade through multiple versions and upgrade the store.
I am not yet sure if you really need each minor version to work properly.
Maybe it's already enough to go from 3.0 to 3.5 and follow this guide https://neo4j.com/docs/upgrade-migration-guide/current/migration/migrate-to-4.0/migrate-single-instance/
Otherwise starting 3.1-3.5 with allow_upgrade=true on the stores is the only option I see. There are Docker images available at
https://hub.docker.com/_/neo4j/ also for those older, unsupported versions.
Edit: You should be able to start/upgrade it with 3.3 and then again with 3.5 and then run a 4.4 neo4j-admin copy

Simple JNDI lookup from JDK 11 client to Weblogic 10.3.6 (JDK 7) server not working

Server Environment: Weblogic 10.3.6, JDK 1.7
I have a simple working Java SE client application runing with JDK 7. In client I am doing very simple JNDI look of a resource hosted server mentioned above.
Jars in ClassPath: wlthint3client.jar
public static void main(String[] args) throws Exception {
Hashtable t = new Hashtable();
t.put(InitialContext.INITIAL_CONTEXT_FACTORY, "weblogic.jndi.WLInitialContextFactory");
t.put(InitialContext.PROVIDER_URL, "t3://localhost:7003/");
InitialContext ic = new InitialContext(t);
String jndiName = "weblogic.jdbc.DataSource.Workflow";
Object obj = ic.lookup(jndiName);
System.out.println("Found it");
}
I have to upgrade my working Java SE client application from JDK 7 to JDK 11. The server environment remains same.
As soon as I upgrade client to JDK 11, I hit following error. Which is expected because corba jars have been moved out from JDK 11.
Exception in thread "main" java.lang.NoClassDefFoundError: org/omg/CORBA/SystemException
at weblogic.jndi.WLInitialContextFactoryDelegate.<clinit>(WLInitialContextFactoryDelegate.java:202)
at weblogic.jndi.spi.EnvironmentManager$DefaultFactoryMaker.<clinit>(EnvironmentManager.java:27)
at weblogic.jndi.spi.EnvironmentManager.getInstance(EnvironmentManager.java:49)
at weblogic.jndi.Environment.getContext(Environment.java:315)
at weblogic.jndi.Environment.getContext(Environment.java:285)
at weblogic.jndi.WLInitialContextFactory.getInitialContext(WLInitialContextFactory.java:117)
at java.naming/javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:730)
at java.naming/javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:305)
at java.naming/javax.naming.InitialContext.init(InitialContext.java:236)
at java.naming/javax.naming.InitialContext.<init>(InitialContext.java:208)
at com.test.JndiLookupTestJdk11.main(JndiLookupTestJdk11.java:16)
Added jacorb-omgapi-3.8.jar to client classpath to fix above exception.
After this I am hitting following timeout exception and not giving any clue. Server is up and running because my old client is working.
Error is at this line
InitialContext ic = new InitialContext(t);
Stacktrace
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weblogic.rjvm.MsgAbbrevInputStream (file:/C:/Users/ke64/OneDrive%20-%20Sun%20Life%20Financial/work_eclipse-jee-2018-12-R/jndi-lookup-test-jdk11/lib/wlthint3client.jar) to method java.io.ObjectInputStream.clear()
WARNING: Please consider reporting this to the maintainers of weblogic.rjvm.MsgAbbrevInputStream
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Exception in thread "main" javax.naming.CommunicationException [Root exception is java.net.ConnectException: t3://localhost:7003: Bootstrap to: localhost/0:0:0:0:0:0:0:1:7003' over: 't3' got an error or timed out]
at weblogic.jndi.internal.ExceptionTranslator.toNamingException(ExceptionTranslator.java:40)
at weblogic.jndi.WLInitialContextFactoryDelegate.toNamingException(WLInitialContextFactoryDelegate.java:792)
at weblogic.jndi.WLInitialContextFactoryDelegate.getInitialContext(WLInitialContextFactoryDelegate.java:368)
at weblogic.jndi.Environment.getContext(Environment.java:315)
at weblogic.jndi.Environment.getContext(Environment.java:285)
at weblogic.jndi.WLInitialContextFactory.getInitialContext(WLInitialContextFactory.java:117)
at java.naming/javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:730)
at java.naming/javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:305)
at java.naming/javax.naming.InitialContext.init(InitialContext.java:236)
at java.naming/javax.naming.InitialContext.<init>(InitialContext.java:208)
at com.test.JndiLookupTestJdk11.main(JndiLookupTestJdk11.java:16)
Caused by: java.net.ConnectException: t3://localhost:7003: Bootstrap to: localhost/0:0:0:0:0:0:0:1:7003' over: 't3' got an error or timed out
at weblogic.rjvm.RJVMFinder.findOrCreateInternal(RJVMFinder.java:216)
at weblogic.rjvm.RJVMFinder.findOrCreate(RJVMFinder.java:170)
at weblogic.rjvm.ServerURL.findOrCreateRJVM(ServerURL.java:165)
at weblogic.jndi.WLInitialContextFactoryDelegate.getInitialContext(WLInitialContextFactoryDelegate.java:353)
... 8 more
Caused by: java.rmi.ConnectException: Bootstrap to: localhost/0:0:0:0:0:0:0:1:7003' over: 't3' got an error or timed out
at weblogic.rjvm.ConnectionManager.bootstrap(ConnectionManager.java:365)
at weblogic.rjvm.RJVMManager.findOrCreateRemoteInternal(RJVMManager.java:260)
at weblogic.rjvm.RJVMManager.findOrCreate(RJVMManager.java:197)
at weblogic.rjvm.RJVMFinder.findOrCreateRemoteServer(RJVMFinder.java:238)
at weblogic.rjvm.RJVMFinder.findOrCreateRemoteCluster(RJVMFinder.java:316)
at weblogic.rjvm.RJVMFinder.findOrCreateInternal(RJVMFinder.java:205)
... 11 more
Questions
Has anyone got it working with configuration? Any idea
how to fix this? Do I need to add any specific version of corba jars?
I am thinking that standard J2EE feature of JNDI lookup should work. Is Weblogic 10.3.6 not compatible with JDK 11 client?
Any help is greatly appreciated.
There is no shipping version of WebLogic Server that works on JDK 11.
WLS 10.3.6 isn't even close (it doesn't even work on JDK 8).
The closest shipping version is WLS 12.2.1.3.0, which was pretty much working on JDK9 but has been broken with subsequent changes in JDK 10 and JDK 11.
A version of WebLogic Server that is certified on JDK 11 is planned for the second half of 2019.
Responding to an old question .. I had to look into a similar scenario recently. Just adding my findings here. Real credit should go to stephen-felts as his reply gave me the idea to try this out.
Looked at a Spring Boot client on OpenJDK 11 attempting to talk to JMS queues on WebLogic 10.3.6.0 on Oracle JDK 6.
Trying to use the wlthint3client.jar from 10.3.6 wasn't of much help because of the CORBA dependencies. Following this SAS post for dependencies to add for JDK 11. Could make the ClassNotFound errors go away by adding dependencies org.glassfish.corba:glassfish-corba-org:4.2.4 org.glassfish.pfl: pfl-tf:4.1.2 but still kept seeing the 't3' got an error or timed out exception message as the OP.
Seeing WLS 14.1.1 is certified for JDK 11, installed that and copied out the bundled wlthint3client.jar from the <WLS_SERVER>/lib folder and configured the SpringBoot client to use it. Could successfully post messages to the queue.
I couldn't find any official confirmation on the Oracle website though, so I don't know if this approach is good enough to use in a production environment.
Got the same Problem whilst using jdk11 and wlthint3client 10.3.6.0.181016 and trying to connect to weblogic with t3.
Solution was to use the glassfish-dependencies mentioned above (but there is a typo, must be -orb in artId; see below for the correct ones) and using Version 12.2.1.3.180717 of wlthint3client. Here's the Set:
<dependency>
<groupId>com.oracle.weblogic</groupId>
<artifactId>wlthint3client</artifactId>
<version>12.2.1.3.180717</version>
</dependency>
<dependency>
<groupId>org.glassfish.corba</groupId>
<artifactId>glassfish-corba-orb</artifactId>
<version>4.2.4</version>
</dependency>
<dependency>
<groupId>org.glassfish.pfl</groupId>
<artifactId>pfl-tf</artifactId>
<version>4.1.2</version>
</dependency>

Issue with C# sonarqube plugin

I have a SonarQube 5.6 installed since a year now, It's integrated with TFS. Installed with few additional plugins, C#, dependency-check, fxcop, java, Checkmarx, scm-cvs, scm-git, scm-svn and scm-tfvc.
everything was working fine. Today it's started failing build with error
2017-06-26T17:54:22.7387533Z Downloading SonarQube.MSBuild.Runner.Implementation.zip from http://xxxxxxx:9000/static/csharp/SonarQube.MSBuild.Runner.Implementation.zip to E:\agnt\_work\41\.sonarqube\bin\SonarQube.MSBuild.Runner.Implementation.zip
2017-06-26T17:54:22.7397520Z ##[error]Could not find a file on the SonarQube server. Url: http://xxxxxxxxxx:9000/static/csharp/SonarQube.MSBuild.Runner.Implementation.zip
2017-06-26T17:54:22.7407523Z ##[error]Failed to update the SonarQube Scanner for MSBuild binaries. Check the server url, verify that the C# plugin is correctly installed on the SonarQube server and that the SonarQube server has been restarted.
2017-06-26T17:54:22.7417526Z ##[error]Pre-processing failed. Exit code: 1
2017-06-26T17:54:22.8678238Z ##[error]System.Exception: Unexpected exit code received from batch file: 1
2017-06-26T17:54:22.8698250Z ##[error] at Microsoft.TeamFoundation.DistributedTask.Task.Internal.PowerShell.InvokeBatchScriptCmdlet.ProcessRecord()
2017-06-26T17:54:22.8708248Z ##[error] at System.Management.Automation.CommandProcessor.ProcessRecord()
From the error, I can it's something related to C# plugin. I checked that plugin under /extensions/plugins and it's there. I thought it can be something compatibility issue, I tried to upgrade it to latest one 6.0
After installing 6.0 tried again and got the same error.
I also tried with old version of same plugins. tried 5.3, 5.0. After manually copied jar file under /plugins. Tried to restart the sonar server and it didn't started successfully. I got the error as below,
2017.06.26 18:31:11 ERROR web[o.s.s.p.Platform] Fail to stop server - ignored
java.lang.IllegalStateException: Cannot stop. Current container state was: CONSTRUCTED at org.picocontainer.lifecycle.DefaultLifecycleState.stopping(DefaultLifecycleState.java:72) ~[picocontainer-2.15.jar:na] at org.picocontainer.DefaultPicoContainer.stop(DefaultPicoContainer.java:794) ~[picocontainer-2.15.jar:na]
2017.06.26 18:31:11 ERROR web[o.a.c.c.C.[.[.[/]] Exception sending context initialized event to listener instance of class org.sonar.server.platform.PlatformServletContextListener
java.lang.IllegalStateException: Fail to load plugin FxCop [fxcop] at org.sonar.server.plugins.ServerExtensionInstaller.installExtensions(ServerExtensionInstaller.java:74) ~[sonar-server-5.6.jar:na] at org.sonar.server.platform.platformlevel.PlatformLevel4.start(PlatformLevel4.java:691) ~[sonar-server-5.6.jar:na] at org.sonar.server.platform.Platform.start(Platform.java:216) ~[sonar-server-5.6.jar:na]
Caused by: java.lang.IllegalStateException: Unable to register extension org.sonar.api.config.PropertyDefinition at org.sonar.core.platform.ComponentContainer.addExtension(ComponentContainer.java:248) ~[sonar-core-5.6.jar:na] at org.sonar.server.plugins.ServerExtensionInstaller.installExtension(ServerExtensionInstaller.java:111) ~[sonar-server-5.6.jar:na] at org.sonar.server.plugins.ServerExtensionInstaller.installExtensions(ServerExtensionInstaller.java:66) ~[sonar-server-5.6.jar:na]
Caused by: org.picocontainer.PicoCompositionException: Duplicate Keys not allowed. Duplicate for 'org.sonar.api.config.PropertyDefinition-sonar.cs.fxcop.timeoutMinutes'at org.picocontainer.DefaultPicoContainer.addAdapterInternal(DefaultPicoContainer.java:438) ~[picocontainer-2.15.jar:na]
2017.06.26 18:31:11 ERROR web[o.a.c.c.StandardContext] One or more listeners failed to start. Full details will be found in the appropriate container log file 2017.06.26 18:31:11 ERROR web[o.a.c.c.StandardContext] Context [] startup failed due to previous errors
2017.06.26 18:31:11 WARN web[o.a.c.l.WebappClassLoaderBase] The web application [ROOT] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread
2017.06.26 18:31:11 WARN web[o.s.p.ProcessEntryPoint] Fail to start web
java.lang.IllegalStateException: Webapp did not start at org.sonar.server.app.EmbeddedTomcat.isUp(EmbeddedTomcat.java:84) ~[sonar-server-5.6.jar:na]at org.sonar.server.app.WebServer.isUp(WebServer.java:47) [sonar-server-5.6.jar:na]at org.sonar.process.ProcessEntryPoint.launch(ProcessEntryPoint.java:105) ~[sonar-process-5.6.jar:na]at org.sonar.server.app.WebServer.main(WebServer.java:68) [sonar-server5.6.jar:na]
can someone please help to fix this issue?
You need to update the Scanner for MsBuild as well. The old versions are not compatible with SonarC# 6+.
I fixed this issue by removing FxCop plugin. Somehow that plugin stopped working. can be the version what i was using that was not compatible with C# plugin. I installed C# plugin version 5.0 (latest is 6.0)
as mentioned above, if i want to use C# latest version, i need to update sonar scanner for MSBuild.

Starting Neo4j failed: unmanaged extensions

I'm trying to create an unmanaged extension using this. I'm currently using a Windows environment
Now, I followed everything and here is what my pom file looks now:
POM
and here is my java class containing the unmanaged extension
HelloWorldResource
Now, I tried to run "**mvn clean package**", and it produced a jar file around 10MB which I then put into the plugins folder of my database.
When I start the server, the following error always appears:
Starting Neo4j failed:
org.neo4j.server.web.NeoServletContainer-49fd135#9bfd861c==org.neo4j.server.web.NeoServletContainer,-1,false
The log file is not useful as it doesn't show any exception that cause the it. Other people also reported the issue in stack overflow and appears to be a jar issue. What else could I have missed?
Neo4j fails to start
Neo4j fails in startup
PS: I'm using 3.0.3 Neo4j Community Edition.

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