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Posted: Apr 05, 2010 17:45 by ctoth
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About my system:
Windows 7 64 bit
JDK 1.6.0_18
Maven version 2.2.1
Ant 1.8.0

Environment variables are properly set up AFAIK.

I'll include three logs. First is the very first build:
http://atoth.sote.hu/~tocsa/download/buildlog1.txt
Then I gave another install command to summarize the errors only:
http://atoth.sote.hu/~tocsa/download/buildlog1_5.txt
Finally I added the sysnetint repository to the pom, it didn't help too much:
http://atoth.sote.hu/~tocsa/download/buildlog2.txt

Interesting parts from the first log: I get authorization failed from the openxds.projects.openhealthtools.org openxds repo, and there are some checksum failed messages also.

Is there anyone here to help? I really would like to contribute.


Posted: Apr 15, 2010 18:38 by ctoth
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!!!For anyone who wants to build OpenEMPI. I analyzed my build logs again, and realized that Maven cannot connect to https://openhie.projects.openhealthtools.org/ (unathorized access). This led me to the following discovery:

Instead of some repository tweaks I describe in this topic, I advise you to do the following:
1. Register a user for https://openhie.projects.openhealthtools.org/
2. create a user settings.xml for your Maven where you specify credentials for your user, which will be used to access the repository for maven. From this repository Maven will be able to find the simmetrics jar and the hapi jar also mentioned in this topic.

In Windows, the place of your user settings.xml is ${USERHOME}\.m2, specifically in my system it is C:\Users\ctoth\.m2
And my settings.xml is:
<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
http://maven.apache.org/xsd/settings-1.0.0.xsd">
<localRepository>CHmmmUsers/ctoth/.m2/repository</localRepository>
<interactiveMode>true</interactiveMode>
<usePluginRegistry>false</usePluginRegistry>
<offline>false</offline>
<servers>
<server>
<id>openxds</id>
<username>your username</username>
<password>your password</password>
</server>
</servers>
<!-- <profiles>
<profile>
<properties>
<release.version>2.0.4</release.version>
</properties>
</profile>
</profiles> -->
</settings>

This still won't solve some jar problems, namely:
1. You'll have to replace the broken jmxri-1.2.1.jar
2. You'll have to replace the broken jmxtools-1.2.1.jar
3. You'll have to replace the gxt-2.1.1.jar with the one available it's own website, beware to download the proper version

Basically with this you should be good to go.


Posted: Apr 05, 2010 18:37 by ctoth
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Ok, now I address the missing simmetrics-1.6.2.jar issue.
I've found a repo on the inet, which contains it:
http://maven.mse.jhu.edu/m2repository/uk/ac/shef/wit/simmetrics/
So I thought I won't download and hack it into my local repo, but instead I try to add this repo to my pom:
<repository>
<id>jhumaven</id>
<url>http://maven.mse.jhu.edu/m2repository</url>
</repository>

But for some reason maven searches in the wrong path in this repository, it adds another extra simmetrics into the path, which turns down my effort (notice the extra directory):
Downloading: http://maven.mse.jhu.edu/m2repository/uk/ac/shef/wit/simmetrics/simmetrics/1.6.2/simmetrics-1.6.2.jar

http://atoth.sote.hu/~tocsa/download/buildlog3.txt

So I gave up and downloaded the jar by hand, and installed it:
http://atoth.sote.hu/~tocsa/download/buildlog3_5.txt

After that the build looks like that: hapi jar is missing
http://atoth.sote.hu/~tocsa/download/buildlog3_51.txt



Posted: Apr 06, 2010 14:28 by ctoth
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Note: just as in my next post, finally I managed to tune the pom files so the repository works. You have to modify to pom files. One is the pom file which lists a jar file as a dependency target. In this pom file you can tune the <groupId> tag until maven searches in the proper folder. The other pom file is the main pom file where you have to add the repository root folder's URL.

Note also, that the "repositories" I've found on the internet with web searches sometimes are not Maven repositories, but only svn or cvs repos. This means that maven won't be able to download hash file. Also, some of them can be very slow, so I think that it might be better to just download these problematic jar files locally and install them by hand.


Posted: Apr 05, 2010 20:13 by ctoth
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I managed to modify pixpdq-adapter\pom.xml's hapi reference:
<dependency>
<groupId>ca.uhn.hl7v2</groupId>
<artifactId>hapi</artifactId>
<version>${hapi.version}</version>
</dependency>

Modifying the openempi main pom file:
<repository>
<id>hl7repo1</id>
<url>http://repo.openehealth.org/maven2/releases</url>
</repository>

It looks like that originally they wanted to use that repository, but in the
http://repo.openehealth.org/maven2/releases/ca/uhn/hapi/hapi/ path there's a 0.6-p1 version hapi jar.
And the hapi-0.5.1 was moved to the hl7v2 folder:
http://repo.openehealth.org/maven2/releases/ca/uhn/hl7v2/hapi/0.5.1/

So now the build went on, and the org.openempi.webapp.Application cannot compile:
http://atoth.sote.hu/~tocsa/download/buildlog4.txt

[INFO] Compiling module org.openempi.webapp.Application
[INFO] Refreshing module from source
[INFO] Validating newly compiled units
[INFO] Removing units with errors
[INFO] [ERROR] Errors in 'jar:file: /C: /Users/ctoth/.m2/repository/com/extjs/gxt/2.1.1/gxt-2.1.1.jar!/com/extjs/gxt/ui/client/event/Events.java'
[INFO] [ERROR] Line 548: Event.ONPASTE cannot be resolved
[INFO] [ERROR] Line 766: Event.ONPASTE cannot be resolved
[INFO] Removing invalidated units

My server (atoth.sote.hu) is a little slow also, maintenance going on... sorry about that


Posted: Apr 05, 2010 22:51 by ctoth
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I don't use the repository I mention in this post, I use two other for hapi

Posted: Apr 05, 2010 22:50 by ctoth
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Ok, so I dig deep down into the problem. gxt-2.1.1.jar indeed has references (in com/extjs/gxt/ui/client/event/Events.java, just as the error message says) to ONPASTE Events into GWT 1.7.1. Which is not good, because I dig into that jar, and there's no such event. Google didn't give any answer to such error message. Finally I went to
http://www.extjs.com/products/gwt/download.php (note: jar is not available there any more, read further) and I downloaded the same version, 2.1.1 gxt jar, and it turned out to be different than the one I had in my maven repository. And interestingly, it doesn't have this bogus ONPASTE reference, so I simply overwrote the file in my repository, and now my OpenEMPI source builds!
http://atoth.sote.hu/~tocsa/download/buildlog5.txt

Build successful!

The question is now: will it deploy?
I'll be back with this.

Addition:
It seems that 2.1.1 GXT jar is not available on the Sencha site any more. Until OpenEMPI dependencies will be changed, download this:
http://atoth.sote.hu/~tocsa/download/extjs.tar.gz
And unpack it into the ~/.m2/repository/com, or replace the existing files.
It'll provide: extjs/gxt/2.1.1/* files.


Posted: Apr 06, 2010 11:49 by odysseas
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It looks like you worked through most of the issues. Let me know if you have any other issues.

Odysseas

Posted: Apr 06, 2010 14:21 by ctoth
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Thanks. I may need help later.
Can you make the sysnetint repository work? Normally this repository should contain the simmetrics and the hapi jar?

I documented my way, because hopefully it'll help others.

Now the war deploys but the ear doesn't. I try to fix that right now


Posted: Apr 06, 2010 20:14 by odysseas
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What problem are you having with the repository at sysnetint.com? From the log file I saw that you were having problems with the one at Open Health Tools.


Posted: Apr 07, 2010 05:25 by ctoth
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I'm not sure. Probably you are right. Some repository should be down though, which would supply hapi and the simmetrics jar file.

Posted: Apr 06, 2010 16:20 by ctoth
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The cause of the exceptions I get during the ear deploy might be lack of configuration files.
I cannot find any ICS.properties and IcsSql.xml (these are mentioned at the last part of the installation instructions) in the source tree, I cannot see dist/conf directory also (where those files supposed to be).
At the same time, in the precompiled release of OpenEMPI 2.0.4 contains a conf directory with sample data and two configuration files: mpi-config.xml and mpi-config.xsd. How should I use these?
Do I need any other project, like PIXPDQ?

With the war I managed to load data into the DB even on Friday, using some test data shipped with OpenEMPI.


Posted: Apr 06, 2010 17:15 by ctoth
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I've found these files in the older (version 1.0) OpenEMPI source. So I gonna try to use these.
But before that, I realized that I only issued a build _without_ tests ("mvn -Dmaven.test.skip=true install").
The tests don't run unfortunately, the reason is partly lack of some openempi2 database.
http://atoth.sote.hu/~tocsa/download/buildlog6.txt
The tests should create this database, or I also supposed to use some SQL script to set it up? I gonna search for that.

One more important addition, which came to my mind: I could only try out the OpenEMPI war, if the "openempi" user created according to the installation instructions (the handler of the openempi database) has _exatly_ the password "openempi". Is this user's password is not openempi, the deployment was not successful, the DB connection couldn't be established. I haven't taken a closer look into that also - lack of time. Is there any hardcoded password in the source, more probably I misse dto tune some configuration files?


Posted: Apr 06, 2010 20:27 by odysseas
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You don't need the files ICS.properties and IcsSql.xml in the 2.0 version of OpenEMPI.

Since you are building the ear file from source, make sure the jdbc.properties file in webapp-web/src/main/resources has the correct values for your database, username and password. Then build everything and redeploy the ear file based on the instructions. I just noticed that the openempi-webapp-web war file in the ear is not the latest one so we need to fix this in our assembly process for the next release.

Let me know if you are now able to deploy the ear file or not.

Odysseas

Posted: Apr 06, 2010 22:53 by ctoth
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Hmmm. There shouldn't be a problem with jdbc.properties, because I set up the same system, username and pwd is openempi. I'll look.

Posted: Apr 06, 2010 22:23 by ctoth
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I want to track down why the tests don't pass during the build.
In http://atoth.sote.hu/~tocsa/download/buildlog6.txt (Tests run: 92, Failures: 1, Errors: 58, Skipped: 0)
We can see that there's a missing openempi2 database. Or something should create it?
Anyway, I created an empty openempi2 database:
http://atoth.sote.hu/~tocsa/download/buildlog7.txt (Tests run: 92, Failures: 1, Errors: 46, Skipped: 0)
Still not good enough. So I ran the database schema creation sql script on openempi2:
http://atoth.sote.hu/~tocsa/download/buildlog8.txt (Tests run: 92, Failures: 2, Errors: 10, Skipped: 0)
I tried even to load the dataset_A_1000 into it and run the tests, but still I'm at 8-10 errors (WARNING: this logfile is 20 megs!):
http://atoth.sote.hu/~tocsa/download/buildlog9.txt


Posted: Apr 06, 2010 22:56 by ctoth
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One obvious error: one test searches for a file FellegiSunterConfiguration.ser. The path is invalid in my system, but I cannot find this configuration file anywhere.

"DEBUG - org.openhie.openempi.matching.fellegisunter.ProbabilisticMatchingService.loadParameters(249) | Attempting to load the configuration
file for the migration log from: DHmmmtmp/FellegiSunterConfiguration.ser
ERROR - org.openhie.openempi.matching.fellegisunter.ProbabilisticMatchingService.loadParameters(257) | Failed while loading the Fellegi-Sunt
er configuration file: D:\tmp\FellegiSunterConfiguration.ser (The system cannot find the path specified)
java.io.FileNotFoundException: D:\tmp\FellegiSunterConfiguration.ser (The system cannot find the path specified)"

Some errors might induce more. If some test cannot load data (one insert fails with scheme violation, it wants to insert a NULL value into a not nullable field), later test can also fail which would query that data.


Posted: Apr 06, 2010 23:27 by ctoth
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I searched for "D:\" in *.* in the source, and there's a reference to the Jboss home in \openempi\ear\pom.xml
D:\server\jboss-4.2.3 or something, I modified that.
Here's the deployment log:
http://atoth.sote.hu/~tocsa/download/deploylog1.txt

There's something with the database access? But the war file deployment works, and I can even access the database and load data in it. In my psotgres-ds.xml config in the JBoss deployment I gave the postgres admin username and password (I fiddled with this on Friday, and I think otherwise it didn't work). Should I give the openempi DB user credentials?


Posted: Apr 07, 2010 02:00 by odysseas
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The FellegiSunterConfiguration.ser file should be generated if it does not exist but the default location may not be appropriate for your system. The location of this configuration file is set in the mpi-config.xml file which resides in the user.home directory.. During startup, the system will load the mpi-config.xml file first from the user.home directory and then from the classpath. You need to copy mpi-config.xml to the directory pointed to by user.home (depending on the OS you are building on this will vary) and the set the location of the probabilistic algorithm configuration file to something appropriate for your system.

Odysseas

Posted: Apr 07, 2010 05:38 by ctoth
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Great, I wanted to ask how to use the mpi-config.xml. I put it now to the C:\Users\ctoth in my system. Thanks for pointing this out, I'll search the source code about this, how this goes.

Posted: Apr 07, 2010 01:56 by odysseas
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Rather than creating a blank openempi2 database, which actually will not help you successfuly deploy the ear file, you can do one of two things:
1. Check the jdbc.properties file that resides in the openempi-webapp-web.war file in ear file to confirm that the instance name in the JDBC URL has openempi2 as the database name. That should be the case. You can fix it by extracting the war file from the ear, extracting the jdbc.properties from the war file, make the change and repackage. The alternative is to regenerate the ear file from source since you are almost there now.

2. run the create_database script against the openempi2 database instance and use that instead of openempi (not recommended since you are working around the problem).

The following problem is caused by a mis-configuration of the DefaultDS JDBC. Check your deploy directory for the configuration file that sets up this data source and correct it accordingly. Another option is to turn off the EJBTimer bean since we don't use it in our ear file. You do that in the ejb-deployer.xml file in the deploy directory.

java.lang.NullPointerException
at org.jboss.ejb.txtimer.DatabasePersistencePolicy.listTimerHandles(DatabasePersistencePolicy.java

Posted: Apr 07, 2010 05:36 by ctoth
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Maybe I confused you because I have two problems.
1. The tests fail during the openempi build.
2. The ear deployment is not successful

I created the openempi2 database only for the test, because it seems they need it. I know that the ear deploy has nothing to do with the openempi2 database. I checked out the jdbc.properties (there are some), and each one which is related to a test referes to openempi2 database (with openempi user) and each "normal" one refers to openempi. I'll dig into the ear and war, but I guess these files are just copied during the packaging process.

Posted: Apr 07, 2010 16:26 by ctoth
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There must be something wrong with my system. I went back to my deploy log http://atoth.sote.hu/~tocsa/download/deploylog1.txt, and looked for any warning or error from the beginning.

The first warning:
"18:16:31,572 WARN [JAXWSDeployerHookPreJSE] Cannot load servlet class: com.google.gwt.junit.server.JUnitHostImpl"

This can go away if I copy all three GWT related jars (gwt-incubator-march-02-2009.jar, gwt-servlet-1.7.1.jar, gxt-2.1.1.jar) into $(JBOSS_HOME)\server\default\lib\ and $(JBOSS_HOME)\lib\endorsed. I don't know if it is enough to copy them to just one directory, or just one file (maybe gwt-servlet one?), but that fixes this warning. This warning doesn't seem to be serious though.

And then there was an error, which was independent from the ear deployment also:
"18:16:40,261 ERROR [URLDeploymentScanner] Incomplete Deployment listing:

--- MBeans waiting for other MBeans ---
ObjectName: jboss.ejb:service=EJBTimerService,persistencePolicy=database
State: CONFIGURED
I Depend On:
jboss.jca:serviceGrinataSourceBinding,nameGrinefaultDS

... (series of configured MBeans, which are dependent and waiting for another) ...

--- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---
ObjectName: jboss.jca:serviceGrinataSourceBinding,nameGrinefaultDS
State: NOTYETINSTALLED
Depends On Me:
jboss.ejb:service=EJBTimerService,persistencePolicy=database
jboss:service=KeyGeneratorFactory,type=HiLo
jboss.mq:service=StateManager
jboss.mq:service=PersistenceManager"

From seeing the Binding name DefaultDS it came to my mind, that I deleted the hsqldb-ds.xml from the JBoss deployment directory. I've read lots of tutorials on how to configure JBoss with PostgreSQL, and some of them suggests deleting several files. The hsqldb-ds.xml defines the DefaultDS binding, while my postgresql-ds.xml is based on the xml which can be found in the JBoss's example directory ($(JBOSS_HOME)\docs\examples\jca). Besides that I copied the postgresql JDBC driver jar file into the deployment's lib directory ($(JBOSS_HOME)\server\default\lib\). I'll open a new topic on how to install PostgreSQL to JBoss, because the Wiki is very detailed except this little thing.

So putting back hsqldb-ds.xml fixed things, and actually I could deploy the ear once! I got the same UI as with the war, and I imported data into the DB using the Febrl dataset.

Interestingly, after stopping JBoss and restarting, it didn't deploy again, I see an exception I saw also before sometimes:
http://atoth.sote.hu/~tocsa/download/deploylog2.txt
So it is not deterministic right now. I cannot deploy it again.
I've found this:
http://www.mail-archive.com/jboss-de...@lists.sourceforge.net/msg40849.html
Should I remove jar files from the ear? Can there be any collisions?

BTW, would ear allow any additional functionality over war?


Posted: Apr 09, 2010 16:42 by ctoth
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Ear deployment successful.
I restarted my attempts with a new, clean install of JBoss 4.2.3.GA-jdk6. As you suggested, I haven't fiddle with any PostgresSQL JDBC driver jar or Postgres-ds.xml file.
I could successfully deploy my compiled EAR.


Posted: May 26, 2011 15:15 by edwin_uestc
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dear sir,I use the command line mvn -Dgpg.skip=true -Dmaven.test.skip=true install.
http://repository.jboss.org/maven2/org/jboss/client/jbossall-client/4.2.3.GA/jbossall-client-4.2.3.GA.jar
I encounter a problem
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] OpenEMPI Application .............................. SUCCESS [8.390s]
[INFO] OpenEMPI - Core ................................... SUCCESS [1:05.935s]
[INFO] OpenEMPI - OpenPIXPDQ Adapter ..................... FAILURE [2:11.886s]
[INFO] OpenEMPI - NHIN Adapter ........................... SKIPPED
[INFO] OpenEMPI - NHIN Proxy ............................. SKIPPED
[INFO] OpenEMPI - EJB Interface .......................... SKIPPED
[INFO] OpenEMPI - Web (Server Side) ...................... SKIPPED
[INFO] OpenEMPI - Web (Client Side) ...................... SKIPPED
[INFO] OpenEMPI - EAR .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE


[ERROR] Failed to execute goal on project openempi-openpixpdq-adapter: Could not resolve dependencies for project org.openhie.openempi:openempi-openpixpdq-adapter:jar:2.1.2: The following artifacts could not be resolved: org.jboss.client:jbossall-client:jar:4.2.3.GA, org.jboss:jnp-client:jar:4.2.2.GA: Could not transfer artifact org.jboss.client:jbossall-client:jar:4.2.3.GA from/to jboss (http://repository.jboss.com/maven2): Access denied to: http://repository.jboss.com/maven2/org/jboss/client/jbossall-client/4.2.3.GA/jbossall-client-4.2.3.GA.jar -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project openempi-openpixpdq-adapter: Could not resolve dependencies for project org.openhie.openempi:openempi-openpixpdq-adapter:jar:2.1.2: The following artifacts could not be resolved: org.jboss.client:jbossall-client:jar:4.2.3.GA, org.jboss:jnp-client:jar:4.2.2.GA: Could not transfer artifact org.jboss.client:jbossall-client:jar:4.2.3.GA from/to jboss (http://repository.jboss.com/maven2): Access denied to: http://repository.jboss.com/maven2/org/jboss/client/jbossall-client/4.2.3.GA/jbossall-client-4.2.3.GA.jar


when I go to the website http://repository.jboss.org, I could not find the maven2 repository.I clearly read your buildlog and in the buildlog4 I find you successfully download it message is just like this:
Downloading: http://repository.jboss.org/maven2/org/jboss/client/jbossall-client/4.2.3.GA/jbossall-client-4.2.3.GA.jar
Downloading: http://repository.jboss.org/maven2/org/jboss/jnp-client/4.2.2.GA/jnp-client-4.2.2.GA.jar
31K downloaded (jnp-client-4.2.2.GA.jar)
could you save me??

Posted: May 26, 2011 20:41 by ctoth
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I haven't encountered this error message before. I'm working with 2.1.3-SNAPSHOT, and it compiled fine.

Posted: May 27, 2011 05:43 by edwin_uestc
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yeah I have fixed it ,and you could find the key to it :http://community.jboss.org/wiki/MavenGettingStarted-Users
the reason is that the old repository does not work now :http://community.jboss.org/wiki/MavenRepository-FAQ
you will just change the repository URL of jboss in the root pom.xml to
https://repository.jboss.org/nexus/content/groups/public-jboss/
then everything is OK

Posted: Jun 06, 2011 19:41 by ctoth
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Great!

Posted: Jun 10, 2011 05:43 by edwin_uestc
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I just run mvn -Dgpg.skip=true install without modifying any configuration file.

It seems something is wrong with JDBC URL
Is this the problem of systems,I use windows XP?

-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running CoreTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec
Running org.openhie.openempi.blocking.basicblocking.BlockingServiceTest
INFO - org.springframework.test.AbstractSingleSpringContextTests.loadContextLocations(210) | Loading context for locations: /applicationContext-resources.xml,classpathHmmmapplicationContext-dao.xml,/applicationContext-service.xml,classpath*HmmmapplicationContext-module*.xml,classpath*Hmmm**/applicationContext.xml
WARN - org.hibernate.util.JDBCExceptionReporter.logExceptions(77) | SQL Error: 0, SQLState: 28P01
ERROR - org.hibernate.util.JDBCExceptionReporter.logExceptions(78) | ?????e?`: ???a???C??????"openempi"????
WARN - org.hibernate.cfg.SettingsFactory.buildSettings(117) | Could not obtain connection metadata
org.postgresql.util.PSQLException: ?????e?`: ???a???C??????"openempi"????


[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- dbunit-maven-plugin:1.0-beta-3:operation (delete) @ openempi-core ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] OpenEMPI Application .............................. SUCCESS [2.266s]
[INFO] OpenEMPI - Core ................................... FAILURE [6.767s]
[INFO] OpenEMPI - OpenPIXPDQ Adapter ..................... SKIPPED
[INFO] OpenEMPI - NHIN Adapter ........................... SKIPPED
[INFO] OpenEMPI - NHIN Proxy ............................. SKIPPED
[INFO] OpenEMPI - EJB Interface .......................... SKIPPED
[INFO] OpenEMPI - Web (Server Side) ...................... SKIPPED
[INFO] OpenEMPI - Web (Client Side) ...................... SKIPPED
[INFO] OpenEMPI - EAR .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 9.408s
[INFO] Finished at: Fri Jun 10 13:42:00 CST 2011
[INFO] Final Memory: 10M/247M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:dbunit-maven-plugin:1.0-beta-3:operation (delete) on project openempi-core: Error executing database operation: DELETE: ?????e?`: ???a???C??????"openempi"???? -> [Help 1]
[ERROR]




Posted: Jun 11, 2011 17:27 by ctoth
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Is this happening with 4.2.3GA JBoss? Something is wrong with the ORM layer again.

Posted: Jun 12, 2011 05:47 by edwin_uestc
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I just follow the "Building OpenEMPI from Source" does it need configure JBoss directory?


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