Everyone have ideas, dreams, aspirations. But only very few achieve those. Well some call it fortune, some say hard work, some say fate, some say god's will. But I believe that is a mixture of all of those said above.

Over the past few days, I have been focusing on modifying some XSLT used by OpenMRS to transform InfoPath-rendered XML to HL7 messages.  OpenMRS uses HAPI, the HL7 open source Java API, to parse and process HL7 messages.  InfoPath generates XML based on schemata that the FormEntry module renders.  Being a complete novice to HL7, I had to gather a few tools to validate formats and examine the message contents.  Specifically, I needed reliable, open source tools for evaluating and processing XML, XSLT and HL7.

For evaluating HL7 messages, I first happened upon HL7Spy (not free, except for a trial period).  It is really good at not only evaluating HL7 messages, but explaining what each section of each field should be.  Apparently, HL7Spy is good for manipulating files with large amounts of messages in them.  I only need to look at one message, for now.  Looking for an open source solution, I tried to implement the HAPI HL7 Conformance Tools, but ran into issues getting the Message Validator to work in my environment.  I then found HL7 Inspector, which is perfectly fine for examining HL7 messages.  It leaves me wanting for more information, but there are numerous random HL7 documents and the HAPI docs to help with that.

I had much better luck finding XML/XSLT tools.  I really liked using the free trial of Stylus Studio, but the free version of EditiX is perfect.  The pay version does some fancy footwork, like XSLT debugging and profiling, but for validation of both XML and XSLT, browsing the DOM and applying transforms, EditiX works.

OpenMRS developers: if you start running into HL7 issues, definitely pick up one or more of these tools.  It will certainly help you understand the message better than counting the number of pipes on each line in a text editor.

I have become an OpenMRS developer.  


The process began when I first heard about OpenMRS, a "community-developed, open-source, enterprise electronic medical record system platform," while perusing job postings in Indianapolis.  The Regenstrief Institute site was driven by Plone, so naturally, I was intrigued.  Several phone calls and one trip to this illustrious city later, I was given the opportunity to come on as a Systems Engineer, dedicated to OpenMRS development.


What I did not know at the time is how extensive OpenMRS's installation base is (click to see a map, courtesy of RI's Michael Downey).  My role at Regenstrief Institute also incorporates support for the AMRS / AMPATH installation in Eldoret, Kenya.  In just a few very short weeks, I have enjoyed conversations with several developers and implementers from around the world.  This is exactly what I have been waiting for.


Open source development requires a developer to change perspectives.  One has to be open to new ideas, from other cultures as well as other paradigms.  A developer has to stay informed and be ready to contribute advice, especially if another developer begins work down a similar path.  The grammar and language used to document, within code or on a wiki, has to be internationally understandable and accessible.  Finally, if a developer really wants to affect the direction of development, participation in the online community is mandatory.  This includes frequent discussions and meetings, and contributing effective, well-formed and useful code on a regular basis.


To be fair, my experience in the client-driven software development realm allowed me some opportunities for exciting innovation.  I was involved in implementing an early WSGI framework on top of Zope (and Plone) to deliver highly targeted content in unique ways.  We brought a static site with literally millions of daily hits into a multi-server Wordpress installation with a custom ajax rating plugin, and saw it bought up by NBC Sports.  I also became integrated with voice technology used in distribution centers and long term care, and got to travel quite a bit.


I appreciate everything I have learned over the last several years, working for both open source and for-profit efforts.  That said, I am very excited to be on board at Regenstrief Institute, and cannot wait to meet the people I work with daily in Kenya.  For now, I believe I am in the right place at the right time.

Update: February 18, 2010

I just fixed the last two configuration issues and can now hotswap most classes, jsps, and other resources for both OpenMRS core and OpenMRS modules! See the instructions below.

Update: February 17, 2010

This is AWESOME! With the JRebel configuration (see below), I am now able to hotswap the following resources:

• web classes (e.g. modify existing controllers)
  
• api classes (e.g. create a new api class called Regimen)
  
• JSPs under WEB-INF (e.g. add or modify
  
• Controllers (e.g. create annotated controllers and JSPs)
• messages.properties (e.g. change i18n properties on the fly)
• Spring-managed objects get reloaded on the fly when you change any classes referenced in spring configuration files
• module classes
  
• module web resources like JSPs
  

I'm still in the process of configuring/testing whether changes to the following resources:

• openmrs-servlet.xml (does not seem to hotswap these changes?)
  
• web.xml (does not seem to hotswap these changes by default?)
• applicationContext-*.xml (?)
  
• dwr.xml (?)
  
• hibernate mapping files (supposed to be available in JRebel 3.0)

---

Update: February 15, 2010

This is still a work in progress, but I've managed to configure JRebel, Tomcat, and Eclipse to hotswap classes within the core openmrs webapp as well as the reporting module. This took a bit of work because of our custom classloaders and module framework as well as the fact that we've adopted some pretty unconventional mechanisms within our current Ant build process and project structure.

---

Overview
Here's a brief summary of how JRebel works taken from the Zero Turnaround website:

How does JRebel work?
JRebel maps your project workspace directly to your running application. When you change any class or resource in your IDE, you can immediately see the change in your application, skipping the build and redeploy phases and reducing the 3-7 weeks your team wastes each year.

You can simply follow the instructions on the JRebel blog or the Reference Manaul included in the JRebel installation zipfile. Here are a few of the resources that were used throughout the process:

• HOWTO Install and use JRebel with Tomcat and Eclipse
  
• Reference Manual
  
• Installation Guide
  
• Configuration Guide
  

Here's the basic procedure that we need to follow:

1. Install JRebel
   
2. Install the JRebel Eclipse plugin (optional)
3. Configure Eclipse
   
4. Configure Tomcat
   
5. Configure your application
   

Step 1 - Install JRebel
Follow the instructions from the HOWTO guide above. I installed JRebel to /var/lib/jrebel.

Step 2 - Install the JRebel Eclipse
Again, just follow the instructions in the HOWTO Guide.

Step 3 - Configure Eclipse
Simply set the path to the JRebel JAR under Window > Preferences > JRebel to /var/lib/jrebel/jrebel.jar.

Step 4 - Configure Tomcat
If you're running Tomcat on Windows/Mac you need to figure out how to add command-line options to the Tomcat start script or Tomcat Manager utility that eventually calls java to start the Tomcat threads. For Ubuntu users, locate the tomcat startup script (e.g. /etc/init.d/tomcat5.5) and add the following -noverify and -javaagent options to the script's JAVA_OPTS value.

I actually added the following three options to JAVA_OPTS:

-Xverify:none
I still don't have a very clear idea of what this option does, but it seems to disable class verification and might have something to do with modification to constructors (see the Troubleshooting section below).

-javaagent:/var/lib/jrebel/jrebel.jar=org.openmrs.util.OpenmrsClassLoader,org.openmrs.module.ModuleClassLoader
The java agent option is required to configure the JRebel JAR that is responsible for monitoring/reloading files when they are modified. Note that we had to add the OpenmrsClassLoader and ModuleClassLoader classes to let JRebel know where to locate/reload classes.

-Drebel.log=true
Included for debugging purposes only.

Your JAVA_OPTS variable should/might look similar to mine (displayed below):

JAVA_OPTS="-noverify -javaagent:/var/lib/jrebel/jrebel.jar=org.openmrs.util.OpenmrsClassLoader,org.openmrs.module.ModuleClassLoader -Drebel.log=true $JAVA_OPTS -Xmx512m -Xms512m -XX:PermSize=256m -XX:MaxPermSize=256m -XX:NewSize=128m -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5000"

More options can be found in the JRebel Configuration Guide.

Step 5 - Configure your application
Now here's the part that needs to be Create a rebel.xml file and place this under TOMCAT_HOME/webapps/openmrs/WEB-INF/classes. Eventually, this file could be included within the OpenMRS source and deployed within the WAR file on it's initial deployment, but unfortunately our WEB-INF source directory is a little "crazy" at the moment and getting the file into WEB-INF/classes would require some changes to the Ant build.xml file. For now, it would be better if we required developers to configure JRebel on their own.

rebel.xml

<?xml version="1.0" encoding="UTF-8"?>
<application
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://www.zeroturnaround.com"
xsi:schemaLocation="http://www.zeroturnaround.com http://www.zeroturnaround.com/alderaan/rebel-2_0.xsd">
<classpath>
<dir name="/home/jmiranda/Workspace/openmrs-1.6.x-trunk/build"></dir>
<dir name="/home/jmiranda/Workspace/module-reporting-trunk/build"></dir>
<dir name="/home/jmiranda/Workspace/module-serialization.xstream/build"></dir>
<dir name="/home/jmiranda/Workspace/module-htmlwidgets/build"></dir>
</classpath>
<web>
<link target="WEB-INF/">
  <dir name="/home/jmiranda/Workspace/openmrs-1.6.x-trunk/web/WEB-INF">
     <exclude name="**/*.xml"/>
  </dir>
</link>
</web>
<web>
<link target="WEB-INF/view/module/reporting/">
  <dir name="/home/jmiranda/Workspace/module-reporting-trunk/web/module">
      <exclude name="**/*.xml"/>
  </dir>
</link>
</web>
</application>

Step 6 - Restart Tomcat
Any time you make a change to the rebel.xml file, you should restart Tomcat. For me, after playing around with JRebel and the rebel.xml file for a little while, hotswapping of web classes started working. Now I need to test whether the service layer is

Next Steps

• Configure with Eclipse IDE using WTP Server Integration with Tomcat, Glassfish
  

Troubleshooting
I ran into a couple of issues while working on this little project. These are all sort of fixed at this point, but I'm not entirely thrilled with the solutions so suggestions would be much appreciated.

• [SOLVED] Invalid option -noverify
  
• [SOLVED] JspRemovedException
• [WORKAROUND] I/O failure during classpath scanning
• [SOLVED] Unable to refresh JSPs on save
• [SOLVED] BeanCurrentlyInCreationException: Error creating bean with name 'sessionFactory'

[SOLVED] Invalid option -noverify
Problem
Unfortunately, when I include the -noverify option within the JAVA_OPTS variable, I get an error (see below) during Tomcat 5.5 startup. I
need to do a little more research on this one, but for now I just
remove the -noverify option.

Invalid option -noverify
Cannot parse command line arguments

Workaround
Remove the -noverify option. However, when starting Tomcat 5.5 with the "-noverify" option removed, I get the following warning in the JRebel log. I can live with not being able to hotswap classes that have changes to their constructor, but if anyone can figure this out, please let me know. I'm hoping this does not prevent hotswapping of newly defined classes.

JRebel: '-noverify' missing, changing/adding/removing constructors will not be enabled!

Solution
Thanks to Jevgeni (from ZeroTurnaround - it's even true with blog comments) we resolved this issue by using the alternative syntax (Xverify:none).

[SOLVED] JspRemovedException
Problem

ERROR - ApplicationDispatcher.invoke(711) |2010-02-13 12:33:48,206| Servlet.service() for servlet jsp threw exception
org.zeroturnaround.javarebel.integration.jasper.JspRemovedException: /WEB-INF/view/module/reporting/reports/manageReportDesigns.jsp
at org.apache.jasper.compiler.Compiler.isOutDated(Compiler.java)
at org.apache.jasper.compiler.Compiler.isOutDated(Compiler.java:333)
at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:561)
...

Solution
I believe this was before I added support for the /openmrs/module/reporting "web" resources to the JRebel configuration. This exception was probably caused by the fact that JRebel was resolving all JSP/class files to the /openmrs "web". Therefore, by adding in another "web" element for the reporting module, JRebel is able to resolve the module's files correctly. However, this means that we need to manually add a "web" element for each new module that we deploy. Not a big deal, but it would be nice to find a way to include a rebel.xml within each module and allow that file to be picked up by JRebel at deployment time.

[WORKAROUND] FileNotFoundException: I/O failure during classpath scanning

Problem

ERROR - ContextLoader.initWebApplicationContext(215) |2010-02-13 02:40:39,394| Context initialization failed
org.springframework.beans.factory.BeanDefinitionStoreException: I/O failure during classpath scanning; nested exception is java.io.FileNotFoundException: class path resource [org/springframework/test/context
/support/AbstractTestExecutionListener.class] cannot be opened because it does not exist
at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:222)
at org.springframework.context.annotation.ClassPathBeanDefinitionScanner.doScan(ClassPathBeanDefinitionScanner.java:201)
...

Solution (temporary)
I temporarily fixed this by adding the spring-test.jar to TOMCAT_HOME/webapps/openmrs/WEB-INF/lib.

[SOLVED] Unable to refresh JSPs on save
Problem
This would appear to be the easiest thing to get working, but I've only spent a few minutes trying to configure it to work. We can still use the deploy-web target within our Ant build.xml for the time being, but it would awesome to get all classes/web resources being hotswapped when they are modified within Eclipse.

Solution
This was solved by making sure to specify the correct web > link target in the rebel.xml configuration. I was incorrectly using the webapp context (e.g. /openmrs) instead of the webapp root config directory (e.g. WEB-INF). I still need to make sure to incorporate all resources above WEB-INF including openmrs.css, openmrs.js, and others.

[SOLVED] BeanCurrentlyInCreationException: Error creating bean with name 'sessionFactory'
Problem

Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hL7ServiceTarget' defined in class path resource [applicationContext-service.xml]: Cannot resolve reference to bean 'hL7DAO' while setting bean property 'HL7DAO'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hL7DAO' defined in class path resource [applicationContext-service.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCurrentlyInCreationException: Error creating bean with name 'sessionFactory': FactoryBean which is currently in creation returned null from getObject

Solution
This was solved by adding in an exclude element into the web > link > dir compoment. This prevents the Spring configuration files from being read multiple times (JRebel already appears to be handling it through its Spring plugin).

 <web>
   <link target="WEB-INF/">
     <dir name="/home/jmiranda/Workspace/openmrs-1.6.x-trunk/web/WEB-INF">
        <exclude name="**/*.xml"/>
     </dir>
   </link>
 </web>

Hi All,

OpenMRS 1.6 Beta 2 is now ready for testing. You can get it here.

Assuming no major bugs, we should have the release candidate out in a week. We’re looking for one implementation (in addition to AMPATH, who has generously offered) to test out the release candidate in production, so we can be totally sure it’s stable. Let me know if you’re interested in that being you.

-Darius

First of all, JRebel is amazing. In an effort to reduce development time, I ran across JRebel (thanks Christian), a tool that allows you to reload a webapp (jsps, classes, jars) without the need to redeploy the entire application.

So far, I've been able to configure Eclipse/Tomcat to hotswap classes from OpenMRS core and modules without the need for redeploying the entire webapp. I'm currently working on getting the JSPs to be reloaded on save from within Eclipse, rather than requiring us to run deploy-web.

Download JRebel from the ZeroTurnaround site
http://www.zeroturnaround.com/

Very exciting. More details about how to configure JRebel coming soon ...

Hi All,

Thanks to everyone who tested our alpha release of 1.6, we’re releasing 1.6 Beta. You can get it on the downloads page.

We’ve made only two significant changes since the alpha:

• We’ve implemented “core modules” properly, meaning that we may now have modules that are required by core, and OpenMRS will not start up if they are not present. (The purpose is to make it easier for feature development to happen independently. Logic is the only one of these at the moment.)
• We had switched the role name from “System Developer” to “Administrator” but we’ve switched that back. It will change to Administrator again in the future, but not until we have added an integer primary key to the table so that we may correctly rename the role, instead of deleting and re-adding it. (Thanks Mark Goodrich for testing with the Patient Flags module and catching this.)

You can see the additional trivial changes in the release notes.

We still need to see some further testing of Beta release before we’re ready to move onto a release candidate. And I’m actually going on vacation for a week. So…go ahead and test away so that when I get back we’ll be all set to release.

-Darius

Soon I'll be putting here a post about Open source development and its benefits, please visit again soon to read it.

After the above posting i will then tailor it to openMRS, its objectives and tell you more about this great application that is focused at solving one of the fundamental problems in developing countries which encapsulates data collection, storage, maintenance, retrieval and being able to use this data to make reports and critical health decisions based on a person's medical record maintained over a given period of time span. Make sure you don't miss this one. If you feel you can't wait for the posting, you visit can openmrs.org to read more about it and download it if you want give it a try.

Cheers