Open Enterprise Master Patient Index: Developer Forum: Attempt to build

Csaba Toth

Posted: April 05, 2010 17:45 by Csaba Toth

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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.

Csaba Toth

Posted: April 15, 2010 18:38 by Csaba Toth

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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>C Hmmm

Users/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>

</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.

Csaba Toth

Posted: April 05, 2010 18:37 by Csaba Toth

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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

Csaba Toth

Posted: April 06, 2010 14:28 by Csaba Toth

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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.

Csaba Toth

Posted: April 05, 2010 20:13 by Csaba Toth

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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

Csaba Toth	Posted: April 05, 2010 22:51 by Csaba Toth » Permalink
	I don't use the repository I mention in this post, I use two other for hapi

Csaba Toth

Posted: April 05, 2010 22:50 by Csaba Toth

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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.

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

Csaba Toth	Posted: April 06, 2010 14:21 by Csaba Toth » Permalink
	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

odysseas	Posted: April 06, 2010 20:14 by odysseas » Permalink
	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.

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

Csaba Toth

Posted: April 06, 2010 16:20 by Csaba Toth

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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.

Csaba Toth

Posted: April 06, 2010 17:15 by Csaba Toth

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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?

odysseas

Posted: April 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

Csaba Toth	Posted: April 06, 2010 22:53 by Csaba Toth » Permalink
	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.

Csaba Toth

Posted: April 06, 2010 22:23 by Csaba Toth

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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

Csaba Toth

Posted: April 06, 2010 22:56 by Csaba Toth

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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: D Hmmm

tmp/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.

Csaba Toth

Posted: April 06, 2010 23:27 by Csaba Toth

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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?

odysseas

Posted: April 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

Csaba Toth	Posted: April 07, 2010 05:38 by Csaba Toth » Permalink
	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.