Oscar EMR Installation with Caisi Integrator from Source

Preface

This document is an A-Z installation guide on installing the Oscar EMR with the Caisi Integrator. The OscarSetup.zip file will be available on Google Drive. In most cases in this document, the process will be described, followed by the bolded instructional steps. All paths are absolute.

* See bottom of document for list of commonly used commands *

Prerequisites

• Install Ubuntu 12.04 LTS (host or vm). Run all updates.

• Java

  • See instructions on how to get sun-java below.

• MySQL 5.1 or 5.5+

  Terminal Commands

  sudo apt-get install mysql-server libmysql-java

• Tomcat

  Terminal Commands

  sudo apt-get install tomcat6

  The tomcat service will run automatically. Enter the following command to stop the service.

  Terminal Commands

  sudo /etc/init.d/tomcat6 stop

• Git

  Terminal Commands

  sudo apt-get install git

• Maven2

  • Download the apache-maven-2.2.1.zip file. It must be 2.2.1.

  • Create a directory called bin in the home folder.

  • Extract the zip file to the bin folder.

• Configure your environment variables:

  • Enter these lines at the bottom of the file:source

    Terminal Commands

    JAVA_HOME="/usr/lib/jvm/java-6-sun"
    CATALINA_HOME="/usr/share/tomcat6"
    CATALINA_BASE="/var/lib/tomcat6"
    M2_HOME=”/home/username/bin/apache-maven-2.2.1”
    M2=”$M2_HOME/bin”PATH=”$M2:$PATH”
    export JAVA_HOME CATALINA_HOME CATALINA_BASE M2_HOME M2\

    Logout and in to see changes

• Check your versions to confirm it’s all working

  Terminal Commands

  java -version (if this says Ice Tea, you have the wrong Java)
  mvn –version
  mysql –V (capital)

• MySQL Workbench

  Terminal Commands

  sudo apt-get install mysql-workbench

• Eclipse (install java first, instruction below)

  Terminal Commands

  sudo apt-get install eclipse

Your working directory should be named "workspace" and is located at /home/username/

How to get sun-java

To install the official Sun JDK, enter the following commands:

wget https://github.com/flexiondotorg/oab-java6/raw/0.2.7/oab-java.sh -O oab-java.sh
chmod +x oab-java.sh
sudo ./oab-java.sh
sudo apt-get update
sudo apt-get install sun-java6-jdk
sudo update-java-alternatives -s java-6-sun #If you install this Jdk only and not Iced Tea, you don't need this last command.

Running  java -version in command line should now read

java version "1.6.0_38"
Java(TM) SE Runtime Environment (build 1.6.0_38-b05)
Java HotSpot(TM) 64-Bit Server VM (build 20.13-b02, mixed mode)

Lastly the new Java environment needs to be pointed to a different SWT library. Execute:

ln -s /usr/lib/jni/libswt-* ~/.swt/lib/linux/x86_64/ 

on a 64-bit installation and

ln -s /usr/lib/jni/libswt-* ~/.swt/lib/linux/x86/

on a 32-bit. I have not confirmed the 32-bit one.

*If using eclipse, you will want to install egit and m2e (Help > Install New Software > All Available Sites > search for ‘egit’ and ‘m2e’ and install each).

MySQL Setup

You will want to create a mysql user named 'oscar' with the password 'oscar' and grant this user all permissions to your databases. The easiest way to perform these mysql operations is to use mysql workbench.

Setup a new Server Instance:

1. Click New Server Instance (Under Server Administration)

2. Select localhost

3. Click Next

4. Make sure Connection Name is localhost

5. Host Name is localhost

6. Username is root

7. click Next, Select your Install Variant and continue until Finish appears.

When the Server Instance has been created, click Finish.

1. Open (Double Click) your new server instance from the list box on the right (mysqld@localhost)
2. Select Users and Privileges under Security on the left menu.
3. Click the Add Account button and enter the following credentials:
4. Login name: oscar
5. Limit connectivity: localhost
6. Password: oscar
7. Confirm password: oscar
8. Select Administrative Roles tab and select the DBA Role. This way the oscar user has all permissions.

The user oscar@localhost will be used for all mysql operations from this point on, rather than root@localhost.

Getting the Latest Version of Oscar

To clone Oscar from gerrit, you will have create an account on gerrit - the code review system of choice for Oscar – generate an ssh key, and link it to your account. In terminal, follow the steps below:

This will display the ssh-key that you will be copying into gerrit.

1. Log into gerrit (https://source.oscartools.org:8080)

2. Click Settings (top-right)

3. Click SSH Public Keys

4. Click the Add Key button

Now copy the ssh key from the text editor, and paste it into the ssh-key field in Gerrit and click "Add".

In order to get the latest version of the Oscar project, we will have to clone the oscar project from Gerrit. Enter these commands to setup a new project directory in your workspace folder:

cd /home/username/workspace/ (mkdir workspace first if this directory does not exist)
git clone ssh://<your username>@source.oscartools.org:29418/oscar

Setting Up a Custom Tomcat Installation

Download the OscarSetup.zip file from the google docs and unzip it into the user directory.

Next you will have to copy the tomcat-local folder into your local workspace

Setting Up the Oscar Database

Don’t do this unless you have to. Instead ask for the latest MySQL dump from someone who cares. If you can’t find anyone, do it this way.

Run the initialization script to setup your databases. This script accepts 3 parameters:

i. mysql username (oscar)

ii. mysql password (oscar)

iii. the name of the database that you are running creating

cd /home/username/workspace/oscar/database/mysql/
chmod 755 createdatabase_on.sh
./createdatabase_on.sh oscar oscar oscar_spec4
cd /home/username/OscarSetup/

Next you will need to fill the oscar database with sample data:

If you get a fresh mysql dump, login to mysql as oscar and run

mysql> create database oscar_spec4;

Then run

mysql> use oscar_spec4;
mysql> source thesqlfile.sql;

Now we will want to create the test database. 

create database oscar_test # if this database already exists, it’s ok

Now run

mysql> create database drugref;
mysql> use drugref;
mysql> source drugref.sql;

Building and Running Oscar

Copy the files into your home folder

• Oscar.properties

• Deploy-oscar.sh

• Drugref.properties

Now to build the project, in terminal, you’ll want to run the following:

cd /home/workspace/oscar/
mvn clean package

Go to home folder and run

chmod +x workspace/tomcat-local/bin/catalina.sh
chmod +x deploy-oscar.sh
./deploy-oscar.sh

Now open up a web browser, and navigate to http://localhost:8080/oscar

You’re done! You should now have a "working" copy of the Oscar EMR. Lucky You!!!

-------------------------------------------------------

Command: Description:

sudo /etc/init.d/tomcat6 

start/restart/stop

sudo nano /etc/profile/

mv /home/mohawk/workspace/oscar_source/oscar/target/oscar-SNAPSHOT.war $CATALINA_BASE/webapps/oscar.war

mvn clean package 
from ~/workspace/oscar_source/oscar

sudo /etc/init.d/tomcat6 stop