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A simplified, all-inclusive installation option with both an embedded database and web server.
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README.md

OpenMRS Standalone provides a simplified, all-inclusive installation option with both an embedded database and web server. Read more at: https://wiki.openmrs.org/display/docs/OpenMRS+Standalone

The master branch of the standalone repo is built by our CI as part of the Platform build at https://ci.openmrs.org/browse/OP and the openmrs-emr2 branch as part of the Reference Application build at https://ci.openmrs.org/browse/REFAPP-OMODDISTRO

Overview

The following guide describes how to build and run an OpenMRS standalone jar file for its different artifacts. You can create the standalone jar in two ways i.e. from command line by following "QUICK SUMMARY FOR BUILDING THE STANDALONE" or using eclipse by following "HOW TO RUN FROM ECLIPSE". Compare your jar build size with the build sizes specified in "SOME ROUGH STATISTICS SO FAR" to verify there is no significant difference.

Make sure your file structure reflects the file structure specified in "DISTRIBUTION FOLDER STRUCTURE (This is a MUST)" before running the jar file. Run your standalone jar either by double clicking the jar to follow "APPLICATION USER INTERFACE" or by following "HOW TO RUN FROM COMMAND LINE". Follow "HOW TO RESPOND TO THE OPENMRS SETUP WIZARD" for the OpenMRS setup in the browser. If you would also like to package a database with the standalone to make it more customized for a usecase please read "HOW TO GENERATE A DATABASE TO INCLUDE WITH A DISTIBUTION" section.

Which Branch to use?

Depending on what OpenMRS software artifact you are releasing, you may need to check out a different branch of this code:

  • If you are building OpenMRS Platform => use the master branch
  • If you are building OpenMRS Reference Application => use the openmrs-emr2 branch

QUICK SUMMARY FOR BUILDING THE STANDALONE

  • Increase the maven memory: e.g. export MAVEN_OPTS="-Xms1012m -Xmx2024m -XX:PermSize=556m -XX:MaxPermSize=1012m"
  • mvn clean package -Dopenmrs.version=1.9.0
  • If you are building standalone for OpenMRS 1.8.x you need to append the above command with -P1.8.x and put in the main directory the Demo-1.8.0.sql file from https://wiki.openmrs.org/x/GwRN, be sure to download the appropriate demo data file for the release line. If you do not see the one for your release, you can create it by loading the latest existing demo data file in its version of openmrs and then upgrade this version of openmrs to the one you are releasing. After the upgrade, you can then dump a sql file to serve as the demo data file for the new release. Then, update the value of the path attribute of the sqlPath tag in liquibase-demo-data.xml file to match the name of the demo data you just downloaded
  • Download the latest CIEL for OpenMRS 1.9.x (use 1.9.x regardless of the maintenance release version) as described here.
  • Upload it to mavenrepo by running (adjust the version and the file parameters to match the downloaded version of CIEL): mvn deploy:deploy-file -DgroupId=org.openmrs.contrib -DartifactId=ciel-dictionary -Dversion=1.9.9-20170409 -Dpackaging=zip -Dfile=openmrs_concepts_1.9.9_20170409.sql.zip -DrepositoryId=openmrs-repo-contrib -Durl=https://mavenrepo.openmrs.org/nexus/content/repositories/contrib
  • Update the CIEL version in pom.xml.
  • If running "mvn clean package" second time, ALWAYS check to make sure mysql processes on port 3326 and/or 3328 and/or 33326 are stopped. If you DON'T do that, then the "mvn clean" will not really clean. A good command to use is: "pkill -f standalone" (kills anything with "standalone" in the path)
  • If compiling the standalone on a linux running machine like on ubuntu 12.04 LTS, move your clone of this standalone project into an ext file system for-example under your home directory; running it on for-example an NTFS file system will result into permission failures since by default linux may fail to modify privileges on non ext file systems.

-> output is in the target folder, as openmrs-standalone-(openmrs.version).zip -> the contents of that zip are in the similarly-named folder under /target, if you want to test in-place

HOW TO RUN FROM ECLIPSE

  • Copy your war file into the "tomcat/webapps" folder. Where the tomcat folder is at the root of the project.

If you already have openmrs installed and do not want to interfere with it, just rename your war file to something different from openmrs.war. Examples are openmrs-1.6.1.war, openmrs-1.9.0.war, etc

  • Right click on the project and select Run As -> Run Configurations

  • Then create a new launch configuration, with any name you want e.g OpenMRS Standalone, under Java Application

The main class should be org.openmrs.standalone.Bootstrap

If you try to run it now, you will get: "Exception in thread "main" java.lang.NoClassDefFoundError: org/openmrs/standalone/ApplicationController"

This is because we have to build the executable jar file that the Bootstrap class supplies to the new java process it spawns in another JVM instance in order to be able to pass tomcat options for increasing memory as advised at http://wiki.openmrs.org/display/docs/Out+Of+Memory+Errors

You can build this right from eclipse by:

  • Right clicking on the project and then select Export -> Java -> Runnable JAR file. The name of this jar file needs to be standalone-0.0.1-SNAPSHOT.jar because it is hard coded in the Bootstrap class as so.
  • In the "Runnable Jar File Specification" window that shows up, select the launch configuration that you created above. (e.g OpenMRS Standalone)
  • In the "Export Destination" field you can supply the root folder of your project. e.g openmrs/standalone/standalone-0.0.1-SNAPSHOT.jar
  • For "Library handling", select "Extract required libraries into generated JAR".
  • Click "Finish" and just select OK/Yes for any screens that may popup.
  • Now you should be able to run the launch configuration that you created above, which will open the OpenMRS Standalone main window and will eventually open your default browser taking you to the openmrs setup wizard. Ensure that the contextname_runtime.properties file does not exist, else you will not be taken to the setup screen. After successfully running setup, subsequent runs will always take you to the openmrs login screen.

NOTE: Using Maven Package will generate the executable jar file in the target folder. How to run directly from eclipse using maven is not yet done.

APPLICATION USER INTERFACE

Tomcat Port This is the port at which to run tomcat. MySQL Port This is the port at which to run mysql

File -> Quit This menu item stops tomcat and mysql and then closes the application. File -> Launch Browser This menu item opens the openmrs login page for the current web application context. File -> Clear Output This clears the output log in the user interface text area. But does not clear the log file written on the file system.

Start This button runs tomcat, which will automatically start the mysql database engine if it was not already running. For the embedded mysql, the first connection automatically starts the mysql engine.

Stop This button stops tomcat and then also stops the mysql database engine, without closing the application.

NOTE: Minimizing or Maximizing the application window does not have any effect on the server. The window close icon will stop the server (behaves as File -> Quit) but will first ask if you really want to, and will only do so when you select the Yes option.

HOW TO RUN FROM COMMAND LINE

Running from command line requires the -commandline switch. e.g. java -jar standalone-0.0.1-SNAPSHOT.jar -commandline

-mysqlport: Use to override the mysql port in the runtime properties file. -tomcatport: Use to override the tomcat port in the runtime properties file. start Use to start the server. stop Use to stop the server. browser Use to launch a new browser instance.

HOW TO RESPOND TO THE OPENMRS SETUP WIZARD

  1. Copy the "connection.url" value from the default-runtime.properties file, located at the project root folder, and paste it into the "Database Connection:" text field of the openmrs setup wizard.

  2. For the section: "Do you currently have an OpenMRS database installed that you would like to connect to?", select No. And for the database, enter the default as openmrs. Enter "openmrs" and "test" as the username and password

  3. Click "Continue" to go to the next wizard screen.

  4. For the section: "Do you need OpenMRS to automatically create the tables for your current database - openmrs?", select Yes.

  5. For the section: "Do you want to also add demo data to your database - openmrs? (This option only available if creating new tables.)", just choose what you want.

  6. For the section: "Do you currently have a database user other than root that has read/write access to the openmrs database?", Choose Yes, and then enter a "openmrs" and "test" as the user name and password. This account will be created by the embedded database engine. The reason to use 'test' is that when the application starts, it checks for the mysql password and if it is test, it is replaced with a randomly generated 12 character password which is written back to the runtime properties file.

  7. Click "Continue" to go to the next wizard screen, and feel free to fill what you want on this screen.

  8. Click "Continue" to got to the next wizard screen where you will fill the openmrs admin account.

  9. Click "Continue" to go to the next wizard screen where you will fill whatever you want.

  10. Click "Continue" to go to the next wizard screen and click "Finish".

HOW TO GENERATE A DATABASE TO INCLUDE WITH A DISTRIBUTION

1- Make sure you have no runtime properties file that the web application will find. 2- Make sure you have no extra moduls that the web application will find 3- Run the standalone-0.0.1-SNAPSHOT.jar. You can just double click it, or run from command line as above. 4- This will take you through the openmrs setup wizard (because the runtime properties file was not found) and respond to it as per the instructions above under "HOW TO RESPOND TO THE OPENMRS SETUP WIZARD" 5- After the wizard completes, copy the generated runtime properties file and put it in the root folder of the distribution as per the above instructions under "DISTRIBUTION FOLDER STRUCTURE" 6- Run packagezip.sh to create the distributable zip file NOTE: The default location of the "database" folder is that where the standalone-0.0.1-SNAPSHOT.jar file is. Also remember to include the runtime properties file in the root folder of the distribution if you want this database to be used. You should also add the application_data_directory key to the runtime properties file. Something like this: application_data_directory=appdata

DISTRIBUTION FOLDER STRUCTURE (This is a MUST)

The release/distribution (end user) folder structure should look like this: NOTE: Without this folder structure, you will get errors while trying to run the standalone application.

  • contextname-runtime.properties
  • e.g openmrs-runtime.properties, openmrs-1.6.1-runtime.properties, openmrs-1.9.0-runtime.properties, etc
  • If you want to use this runtime properties file, make sure that the web application context name does not match with any existing runtime properties file in say the user's home folder. This is because of the openmrs runtime properties file search order which will only look in the current application folder as the last resort if no runtime properties file has been found in any of the other possible locations.
  • standalone-0.0.1-SNAPSHOT.jar
  • This is the output executable jar for this standalone project.
  • You can build this right from eclipse by right clicking on the project and then select Export -> Java -> Runnable JAR file.
  • The name of this jar file needs to be standalone-0.0.1-SNAPSHOT.jar because it is hard coded in the Bootstrap class as so.
  • tomcat/conf/web.xml
  • This has the jsp servlet mapping, mime mappings, and other parameters shared by all web applications in this tomcat instance. You can copy this from "tomcat/conf" folder of your tomcat installation.
  • tomcat/webapps/openmrs.war
  • This is the application war file. You could as well use the expanded folder.
  • The name of this war file, or expanded web app folder is used to determine the context name. Therefore this tomcat/webapps/ folder should not contain any other file or folder apart from the war file or expanded app folder. If you ever want to run multiple versions of openmrs, then make sure that the name of the war file is different for each. e.g openmrs.war, openmrs-1.6.1.war, openmrs-1.7.0.war, etc
  • database/data
  • If you do not want the user to be taken through the openmrs web database setup wizard, just copy all the contents of the mysql data folder into this. This folder is the default one but you can change the location using the database connection string.
  • tomcat/logs
  • This is where the log files are created with names having a convention of day-month-year.log That means each day has a separate log file.
  • You do not need to create this folder because it can be automatically created by the application. The logs displayed in the textarea of the UI are just a convenient way of showing what is going on without having to first open the log file. Not to run out of memory, the text area displayed logs are trimmed, starting with the oldest, in order not to exceeed 1,000 characters.
  • splashscreen-loading.png
  • This is the splash screen displayed on startup. It can be any .png as long as the name remains the same because it is hardcoded in the application.

DATABASE CONNECTION STRING

jdbc:mysql:mxj://localhost:3316/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8&server.initialize-user=true&createDatabaseIfNotExist=true&server.basedir=database&server.datadir=database/data&server.collation-server=utf8_general_ci&server.character-set-server=utf8

The above default database connection string has all in the openmrs mysql default database connection string plus a few additional parameters as explained below:

mxj This is required for the MySQL Connector/MXJ utility which we use for embedding mysql More information about it can be found at: http://dev.mysql.com/doc/refman/5.1/en/connector-mxj.html

server.initialize-user The value of true tells the database engine to create the user account that will be specified in the openmrs web database setup. This is the account referred to as connection.username & connection.password in the runtime properties file.

createDatabaseIfNotExist The value of true tells the database engine to create the database if it does not exist.

server.basedir This is the directory where the mysql database server will be installed. The default value is a database folder in the current directory where the executable jar file is located.

server.datadir This is the dirrectory where mysql stores the database. The default value is the data folder under the database folder in the current directory where the executable jar file is located.

server.collation-server This sets the collation of the database server. If you do not set it to this value, you will get problems running the openmrs liquibase files. This is because the default value is swedish collation yet openmrs uses utf8

server.character-set-server This is the character set used by the database server.

NOTE: When creating a new database using the openmrs database setup wizard, remember to replace the default connection string with the one above in the "Database Connection:" text field.

  The embedded mysql database engine is a fully functional database engine that you can connect too using any database 
  GUI query tools like Navicat, EMS MySQL Manager, etc

SOME ROUGH STATISTICS SO FAR

The following are the various compressed standalone distribution sizes:

For all operating systems with a database that has demo data: 142 MB For all operating systems with a database that has no demo data: 139 MB For all operating systems without a database: 136 MB

Mac-OS-X-i386 without a database 59 MB Linux-i386 without a database 54 MB FreeBSD-x86 without a database 53 MB Windows-x86 without a database 44 MB

NOTE: With database (either with or without demo data) means the user will not run through the openmrs setup wizard. Where database does not mean mysql, it is rather the database files.

SUMMARY: Using a single package for all (most) platforms approximately tripples the download size. Including an empty database without demo data increases the size by only around 3 MB Including a database with demo data increases the size by only around 6 MB

MySQL MXJ documentation can be found at: http://dev.mysql.com/doc/refman/5.1/en/connector-mxj.html

Details on how to add or remove platform specific databases can be found at: http://dev.mysql.com/doc/refman/5.1/en/connector-mxj-usagenotes-packaging.html http://blog.teamlazerbeez.com/2011/10/03/embedded-mysql-on-java-with-connectormxj-and-64-bit-linux/

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