Hi All,

After a longer-than-expected delay, and a few bugfixes, the OpenMRS 1.6 Release Candidate is ready, and available on the prereleases page.

Have at it!

Assuming no bugs, this should become the official release by March 19th.

-Darius

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

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

It's been a while since I last updated on the progress of the Facility Data Module. So without farther adieu here we go:

• The relation between the FacilityDataFormSchema and FacilityDataFormSection is now Many to Many meaning that sections can now be re-used between several form schemas (or reports).
• It now runs without errors on OpenMRS 1.5.x
  

The first item was a big problem that was a sore spot for this project since it wasn't too intuitive, ideally a user should be able to re-use a section. The second item was a freebie since the errors were likely all due to the incorrect modeling.

What's next on my list is the following:

1. Allow for sections to be re-ordered within the schema (this is currently not possible and is a show-stopper.
   
2. Fix up the calendar management pages -- those are horribly ugly, but this is after all a first pass, so that is to be expected right?
3. Currently, it does not validate inputs for Numeric data types -- It need to.
   
4. There still needs to be the ability to analyze the data that exists in the system to submit to funding sources; those pages need to be implemented but that is phase two of the project.
   
5. There are likely other sore spots that exist that I do not see at this point and time that will be fixed at a later date.

That is all for now.

Hi OpenMRS Community,

Our first alpha preview release of OpenMRS 1.6 is ready!

First off, I’d like to thank the 35 developers who contributed code to this release: Agnor, arthurs, ayeung, ball, bmckown, bwolfe, cliff.mcintosh, dfuterman, djazayeri, dthomas, emendez, ewolodzko, hkwathome, jamesm, jmiranda, Keelhaul, Knoll_Frank, luzhuangwei, madanmohan, mkopinsky, mogoodrich, mseaton, msheley, n.nehete, nribeka, Pascal, r0bby, rarcos, rcrichton, samrajni, sunbiz, suneeth, tmdugan, upul, yatitandon

You can read the release notes here or, if you’re impatient, you can go straight to the prerelease downloads page.

Note that this is a PRE-release, intended for testing, and not for production deployment. The changes made in 1.6 are much less invasive than those we made in 1.5, so I expect there to be far fewer bugs, and I expect us to be able to get to beta, or even to a release candidate, within a couple weeks. But to do that we need your help. We need people to install 1.6 alpha, play around with it and look for bugs.

There are three specific things I’d really like to ask for help testing:

• Everyone, even if you don’t have time for thorough testing, should try making a copy of their database, upgrading it by running this 1.6 alpha war, and reporting any failures
• People who use logic should test their code and make sure it still works now that most logic code has been pulled out into a module
• If you want to have Patients-who-are-Users then that is now possible. Please test it!
• Module owners should re-test their modules, because of a small number of unavoidable non-backwards-compatible changes. HTML Form Entry is broken, for instance.

A week from today I would like to release an alpha-2 or a beta release, so do your testing sooner rather than later.

Thanks,
Darius

In order to improve the performance of mysql when dealing with large databases, there's a couple of settings that can be tweaked in your my.cnf file (or through a MySQL administration tool). The following line has proven to be the most useful.

innodb_buffer_pool_size = 1G

I've been meaning to write about this improvement for the last few weeks, but I wanted to test it myself first. So far I'm very pleased with the performance improvement (database restore time is down from about 3 hours to about 45 minutes on a ~1.2G database). I haven't tested how this setting affects MySQL during normal execution, but it certainly helps improve performance during backups and restores. So if you find yourself backing up and restoring large MySQL databases, you should test this out. You should (obviously) not set innodb_buffer_pool_size to a value greater than the available memory on your machine.

Thanks to Marc Harrison for the tip.

If you want to read some more about this configuration, I found a couple of blog entries from a few years ago Enjoy!

http://www.mysqlperformanceblog.com/2007/11/01/innodb-performance-optimization-basics/
http://www.mysqlperformanceblog.com/2007/11/03/choosing-innodb_buffer_pool_size/

More to come ...

OpenMRS is planning a Meet-and-Greet at AMIA 2009 in San Francisco on Tuesday, 17-November, at 7:30 pm.  We will meet for drinks at the Urban Tavern next to the Hilton.