Develop Reference

embedded Neo4j in JVM

I am trying to access a neo4j database from my java program. I tried to create a fresh db and query it, and it ran successfully as per: http://neo4j.com/docs/java-reference/current/#tutorials-java-embedded
Code:
String DB_PATH = "C:/Users/singsand/Documents/Neo4j/newdb";
File f=new File(DB_PATH);
GraphDatabaseService graphDb = new GraphDatabaseFactory().newEmbeddedDatabase(f);
try (Transaction tx=graphDb.beginTx()){
graphDb.execute("CREATE (table1:car {name:'car1'})");
tx.success();
}
But then I started this db as a server through the Neo4j community edition tool and also accessed it through my browser.
After that, when i executed the same java program I used above, it throws the following error:
Exception in thread "main" java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, C:\Users\singsand\Documents\Neo4j\newdb
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:144)
at org.neo4j.kernel.impl.factory.CommunityFacadeFactory.newFacade(CommunityFacadeFactory.java:40)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:108)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:100)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.lambda$createDatabaseCreator$193(GraphDatabaseFactory.java:89)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:183)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:65)
at neo4j.neo4jdemo.App.main(App.java:41)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery#62fca613' failed to initialize. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:416)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:62)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:98)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:508)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:99)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:107)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:140)
... 7 more
Caused by: java.lang.IllegalArgumentException: Unrecognized log entry version -9. At position LogPosition{logVersion=0, byteOffset=16} and entry version null
at org.neo4j.kernel.impl.transaction.log.entry.LogEntryVersion.byVersion(LogEntryVersion.java:147)
at org.neo4j.kernel.impl.transaction.log.entry.VersionAwareLogEntryReader.readLogEntry(VersionAwareLogEntryReader.java:83)
at org.neo4j.kernel.impl.transaction.log.LogEntryCursor.next(LogEntryCursor.java:50)
at org.neo4j.kernel.recovery.LatestCheckPointFinder.find(LatestCheckPointFinder.java:77)
at org.neo4j.kernel.recovery.PositionToRecoverFrom.apply(PositionToRecoverFrom.java:53)
at org.neo4j.kernel.recovery.DefaultRecoverySPI.getPositionToRecoverFrom(DefaultRecoverySPI.java:112)
at org.neo4j.kernel.recovery.Recovery.init(Recovery.java:72)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:406)
... 16 more
I have seen similar errors in other Stack Overflow questions, but wasn't able to solve my issue using their solutions.

If I understand correctly. You are using embedded version of Neo4j in your app and than you are trying to start Neo4j server on your localhost. Is that right?
Neo4j Server vs Embedded mode
The thing is Neo4j embedded is running as part of your Java application. Neo4j server is standalone service which is run separately. And you can't combine those two on the same db.
If you want to use Neo4j browser with your embedded db this should help you - http://graphaware.com/neo4j/2014/11/21/neo4j-browser-with-embedded.html

[ibm][db2][jcc][t4][2055][11259] Execution failed due to a distribution protocol error

I am calling Stored procedure from java based web-application using DB2 as database and WebSphere as server.
Most of the time SP gets executed properly but sometimes it gives following exception:
[ibm][db2][jcc][t4][2055][11259] Execution failed due to a distribution protocol error that caused deallocation of the conversation.
The command requested could not be completed because of a permanent error condition detected at the target system.
Db2jcc Driver version :
IBM DB2 JDBC Universal Driver Architecture 3.1.157 [ v9.1 FP0 (GA) ]
Please help me to sort out this issue.

Not sure if this will match your scenario, but it looks like there is a known fix for an error with the same message as the one you reported
http://www-01.ibm.com/support/docview.wss?uid=swg1IZ07622
which recommends moving up to DB2 V9.5 fixpack 5.

Derby authentication error from Glassfish console but same credentials work from ij

I am trying, for the first time, to run a java EE 7 web app without an IDE and struggling through the learning curve. To keep things simple I have started with Glassfish 4.1 and Derby 10.11.1.2 which is what I used for development.
My current problem is an error configuring the connection pool on the Glassfish web interface. The error is 'Connection authentication failure occurred. Reason: Userid or password invalid'. However I have ij runing in a dos prompt and the Glashfish web console in Chrome.
from ij I can type 'connect 'jdbc:derby:localhost:1527/databasename;user=username;password=password'; and I connect fine and can look at tables, etc. In the Glassfish web console I have name/value pairs with the same 'user' and 'password' values and it fails (exact same letters & case). I've tried changing the 'databaseName' property to make sure the error wasn't misleading and confirmed it has found the database correctly.
At face value, the error message seems wrong as I have proven from the DOS window. I am sure I am doing something wrong but am lost at how to diagnose it. Any suggestions?
More details of the steps taken: (Although I am sure some of these steps superceed others my lack of success has me in the mindset that redundancy is better than omission - all-in-all it seems much more complicated than it needs to be for a basic setup). My target is Wildfly but Glassfish documentation is better so I figured I would start there.
relevant Windows environment variables:
JAVA_HOME=C:\Program Files\Java\jdk1.8.0_40
DERBY_HOME=%JAVA_HOME%\db
DERBY_INSTALL=%DERBY_HOME%
JAVADB_HOME=%DERBY_HOME%
GLASSFISH=C:\Program Files\Java\GlassFish-4.1
Path=%JAVA_HOME%\bin;%DERBY_HOME%\bin;%GLASSFISH%\bin;%GLASSFISH%\glassfish
CLASSPATH=%DERBY_HOME%\lib\derbynet.jar;%DERBY_HOME%\lib\derbytools.jar;%DERBY_HOME%\derbyclient.jar;%DERBY_HOME%\lib\derbyrun.jar
WILDFLY_HOME=C:\program files\java\wildfly\8.2.0.Final
sysinfo shows all the right paths and versions
Copied many of the derby jars from %derby_home%\lib to %glassfish%\glassfish\domains\domain1\lib\ext per a post by BalusC. I think classpath duplicates this it but can't hurt
Started Domain 'asadmin start-domain' defaulting to domain 1
Started DB by changing directories and using java. Wanted to use 'asadmin start-database --dbhome DB path' but this always started the wrong version. Glassfish and JDK both package derby/javadb and I couldn't figure out how to upgrade Glassfish or start the correct version any other way
cd \users\john\.netbeans-derby (root of the DB created by Netbeans)
Java –jar “%derby_home%\lib\derbyrun.jar" server start
connect browser to 'localhost:4848' to create JDBC connection pool and resource
connection pool: pool name=connectionPool, resource type=javax.sql.DataSource, DB driver Vendor=Derby, introspect was not enabled (found very little documentation to explain what it is) - step 2 was left as defaults
editing connectionPool - enabled Ping on General tab to identify errors, Additional Properties tab: changed User to DB username, left other attributes as default, added... password=db password, databaseName=ClubScoring
errors were presented along the way which prompted setting each attribute. No error was presented for lack of URL but tested steps below with and without URL=jdbc:derby://localhost:1527/ClubScoring
jdbc resources. Added jdbc/ClubScoring, pool=connectionPool => selected and enabled
starting db from correct directory using 'asadmin start-database' does let the application find the correct DB but it crashes since the DB was created with version 10.11.1.2 and this command starts the Glassfish version of 10.10.2.0
Sorry for making this so long but I haven't found anywhere that lays out all of the steps in a simple fashion and figured the details would save time in the long run.

I was dealing with this issue today and found a solution:
https://db.apache.org/derby/docs/10.14/ref/rrefattribsecmech.html
Basically the only security options allowable (as far as 10.14 is concerned) is 3, 4 and 9.
4 is the default and means "Just UserID". You would think this means that as long as a UserID is given, you could connect. But having both set appears to be an issue.
In order to use a (clear text) password and userID, you have to specify 3. It works also if the attribute is deleted or 0 as well but I don't think you get any security that way.

Glassfish - Application name is already in use

I’ve come to an hold with my programing because I’m getting an error from glassfish. I’m using NetBeans IDE 7.3 for this project. And I’ve built a simple program which runs over the web(jsp file etc). But I keep on getting the weirdest error display from glassfish. I’ve searched the internet for my solution and found people posting similar things, but I never seem actually manage to fix it because I don’t really understand the post which I’ve read.
So what is the error that I get at startup? First time I run it I get this from the Output
Starting GlassFish Server 3.1.2
GlassFish Server 3.1.2 is running.
In-place deployment at C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\build\web
Initializing...
deploy?
DEFAULT=C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\build\web&name=ÄrendeWebApplication&contextroot=/_rendeWebApplication&force=true failed on GlassFish Server 3.1.2
Error occurred during deployment: null. Please see server.log for more details.
C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\nbproject\build-impl.xml:1038: The module has not been deployed.
See the server log for details.
The actually name of the project is ÄrendeWebApplication and sure it’s a weird name for some people.
Well anyhow I tried to run the application again just to make sure it’s not something spooky going on, and I got a totally different error message.
In-place deployment at
C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\build\web
Initializing...
deploy?
DEFAULT=C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\build\web&name=Ärende
WebApplication&contextroot=/_rendeWebApplication&force=true failed on GlassFish Server 3.1.2
Error occurred during deployment: Application name ÄrendeWebApplication is already in use.
Please pick a different name.. Please see server.log for more details.
C:\Users\Vedo\Documents\NetBeansProjects\ÄrendeWebApplication\nbproject\build-impl.xml:1038: The module has not been deployed.
See the server log for details.
Alright so this is the weirdest part since it’s complaining that the name of my application is already in use? So I thought first it could perhaps be something with the database, but went to see the “Java DB Database Process” and it seemed fine, will post it too just in case
Fri Jun 07 11:01:10 CEST 2013 : Security manager installed using the Basic server security policy.
Fri Jun 07 11:01:11 CEST 2013 : Apache Derby Network Server - 10.8.2.2 - (1181258) started and ready to accept connections on port 1527
So the database is not the problem “I Believe” so I went later to check on the Glassfish server 3.1.2 and I found some warning messages which read
WARNING: Multiple [2] JMX MBeanServer instances exist, we will use the server at index [0] : [com.sun.enterprise.v3.admin.DynamicInterceptor#297b0d9d].
WARNING: JMX MBeanServer in use: [com.sun.enterprise.v3.admin.DynamicInterceptor#297b0d9d] from index [0]
WARNING: JMX MBeanServer in use: [com.sun.jmx.mbeanserver.JmxMBeanServer#572b43d] from index [1]
INFO: EJB5181:Portable JNDI names for EJB ÄrendeDao: [java:global/ÄrendeWebApplication/ÄrendeDao!com.Ärende.dao.ÄrendeDaoLocal, java:global/ÄrendeWebApplication/ÄrendeDao]
INFO: WEB0671: Loading application [ÄrendeWebApplication] at [/_rendeWebApplication]
SEVERE: The log message is empty or null. Please log an issue against the component in the logger field.
And here is where I’ve tried different things, well I thought it first complained about the name, it’s alredy in use right…. So I deleted the application and moved it to another place on my hard drive and well, I wouldn’t be posting this if it worked. Then I started considering that perhaps the database was something wrong with, I went to the console admin in glassfish to check the connection and the Ping and showed me that it worked as it should. Also perhaps important information is that I’ve connected glassfish through MySQL, but I hardly believe that this is the problem. I then stumbled across someone saying that you could force “redeploy via Eclipse” well first problem here is that I’m not using Esclipse and second problem is I’ve searched A LOT to find if there is a “Force redeploy in NetBeans” and that is not the easiest task in life. So I believe this is perhaps my last stop hopefully and maybe someone here could help me out.

here are some steps you can try:
Fix your projects name :3
If your problem is the one the question title suggests, undeploy your application first, then redeploy. You can easily undeploy and force redeploy in the Glassfish Admin Gui (http://localhost:4848).
If your application still does not work, update your question with proper formatted log messages of the actual problem.

I need some help with Sakai 2.7.1 and Tomcat 5.5.33, in regards to SQL issues

Today I managed to recreate the farms with Scalr.net and apparently after a few times restarting tomcat and fixing issues, I get this error once again. The thing is I was using MySQL with a clean install on the entire server, that includes Java 6.1_24, Tomcat 5.5.33, Sakai 2.7.1. The issue I keep running into is user denied when the fact that I have this user in the MySQL Instance, as well giving it complete remote access with sakai#% and even this is not working when it was working about an hour ago since this post was made.
... Continued from above log, everything before logs just fine
2011-03-31 18:31:14,120 WARN main org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy - Could not retrieve default auto-commit and transaction isolation settings
org.apache.commons.dbcp.SQLNestedException: Error preloading the connection pool
... continued over 400+ lines...
Here is another error in regards to the access denied error...
2011-03-31 18:31:16,854 WARN main org.hibernate.cfg.SettingsFactory - Could not obtain connection metadata
java.sql.SQLException: Access denied for user 'sakai'#'ec2-50-17-184-70.compute-1.amazonaws.com' (using password: YES)
.... continued....
I now get this error whenever I startup, this is with a fresh install of tomcat/sakai
SEVERE: Unable to set localhost. This prevents creation of a GUID. Cause was: ec2-72-44-56-167.compute-1.amazonaws.com: ec2-72-44-56-167.compute-1.amazonaws.com
java.net.UnknownHostException: ec2-72-44-56-167.compute-1.amazonaws.com: ec2-72-44-56-167.compute-1.amazonaws.com
(This most recent error (Localhost) was simply fixed by restarting the amazon aws instance. Thankfully) Although I keep getting the same errors even with a fresh install... Almost as if the information is being refreshed from a cache... Or something

As with the last question you posted on this topic, the error message seems very clear: the user 'sakai'#... does not have access to login to the database you have set it up to. I recommend taking a look at the Mysql documentation to understand how to administer the user accounts to find out if you've missed a setting somewhere to allow this account to have access.

I believe I may have figured out how to fix this problem. It has nothing to do with mysql, or the apache server itself. It has to do with the failure of Scalr.net not Initializing the IP or something of that sort. After doing some research I found some issues with the HostInit issues such as....
Cannot deliver message 'HostInit' (message_id: af9dcfdb-a09e-4971-bdb7-7871b3f7e21c) via REST to server '50.17.135.98' (server_id: e49cfec9-5bcb-44d1-bbc5-fde32450fc89). Error: 0 Timeout was reached; connect() timed out! (http://50.17.135.98:8013/control)
Cannot deliver message 'BlockDeviceAttached' (message_id: a153d83f-3d96-4d53-920a-ccb80701675a) via REST to server '50.17.135.98' (server_id: e49cfec9-5bcb-44d1-bbc5-fde32450fc89). Error: 0 Timeout was reached; connect() timed out! (http://50.17.135.98:8013/control)
Cannot deliver message 'HostUp' (message_id: 1adde27c-9982-4551-b266-c3c432d1dd44) via REST to server '50.17.135.98' (server_id: e49cfec9-5bcb-44d1-bbc5-fde32450fc89). Error: 0 Timeout was reached; connect() timed out! (http://50.17.135.98:8013/control)
Cannot deliver message 'HostInit' (message_id: f1aa4b14-ef57-4361-ae56-87702d674b11) via REST to server '50.17.135.98' (server_id: e49cfec9-5bcb-44d1-bbc5-fde32450fc89). Error: 0 Timeout was reached; connect() timed out! (http://50.17.135.98:8013/control)
So what I did was I made a snapshot image of the apache server/mysql etc. and terminated them allowing the recreation of the instance and this managed to solve the problem in one manner.