4.2.7 Building Oscar from Source

If you ever need to reinitialize the database, you can use the same script.

You will need to move the oscar_*.properties files to $CATALINA_HOME as described below.

sudo cp $HOME/src/oscar_source/oscar/web/WEB-INF/classes/oscar_mcmaster.properties $CATALINA_HOME
sudo ln -s $CATALINA_HOME/oscar_mcmaster.properties $CATALINA_HOME/oscar.properties 

The oscar.properties file needs to be localized for your specific configuration.

sudo vi $CATALINA_HOME/oscar.properties

Most users will want turn on the new casemanagement interface Ontario users will probably want to adjust the following (Warning do not put any blank spaces at the end of any line!)
TIP: The phone prefix prepopulates new demographics and is not limited to the area code (although that may be all that can be predicted in an urban area) We will now configure Tomcat. First, adjust the configuration file to allocate more resources to OSCAR otherwise Drugref 2/3 will not run or will not run properly.

sudo vi /etc/default/tomcat6

Find the following sections and configure the variables to match what is below.  Use cat /proc/meminfo to determine your system memory.  I am assuming below that you have at least 1Gb RAM.

# You may pass JVM startup parameters to Java here. If unset, the default
# options (-Djava.awt.headless=true -Xmx128m) will be used.
JAVA_OPTS="-Djava.awt.headless=true -Xmx1024m -Xms1024m -XX:MaxPermSize=512m -server"

Now we’ll enable access to the new echart interface with a utility that adjusts the database assigning patients and providers to the Oscar program.

cd $HOME/src/oscar_source/oscar/database/mysql
java -cp .:$CATALINA_BASE/webapps/oscar/WEB-INF/lib/mysql-connector-java-3.0.11-stable-bin.jar importCasemgmt $CATALINA_HOME/oscar.properties

and adjust some tables (replace ****** with the MySQL password you set earlier.

mysql -uroot -p****** oscar_mcmaster ### will bring you to the mysql database prompt
mysql> insert into issue (code,description,role,update_date) select icd9.icd9, icd9.description, "doctor", now() from icd9;
mysql> quit; ### gets you out of mysql

And finally make a directory for Demographic export and allow read and write privileges for anyone.

Drugref2/3

Download the binary and copy the WAR file to $CATALINA_BASE

wget http://drugref2.googlecode.com/files/drugref.war
sudo mv drugref.war $CATALINA_BASE/webapps/drugref.war

Either MySQL or Postgres can be used for database. Launch your text editor to form drugref.properties

sudo vi $CATALINA_HOME/drugref.properties

Enter the following lines into drugref.properties (replace ****** with the MySQL password you set earlier.) and save.

db_user=root
db_password=******
db_url=jdbc:mysql://127.0.0.1:3306/drugref
db_driver=com.mysql.jdbc.Driver

For simplicity MySQL will be used here. Create an empty drugref database with the following (replace ****** with the MySQL password you set earlier.):

mysql -uroot -p*******
mysql> create database drugref;
mysql> quit;

Edit oscar.properties

sudo vi $CATALINA_HOME/oscar.properties

if you are installing drugref on the same host as Oscar then the url should be as such

Restart tomcat

sudo /etc/init.d/tomcat6 restart

To populate the database with drug data open your browser and navigate to the server.  If you installed on a local desktop version of Ubuntu it is as shown below.

 http://localhost:8080/drugref/Update.jsp (If you installed via a SSH tunnel open firewall access for port 8080 on the server and change localhost to its URL)

****NOTHING**** will seem to happen (except for the page loading symbol) for  between a quarter and half an hour so get a coffee.

When you get back to the screen you will get a page like.

Update Drugref Database!

Table Name	Number of Rows
CdVeterinarySpecies	5583
Interactions	3872
CdDrugProduct	39328
CdDrugSearch	86252
CdDrugStatus	124244
CdActiveIngredients	109956
CdInactiveProducts	59060
CdTherapeuticClass	42694
CdCompanies	43628
CdForm	50971
CdPharmaceuticalStd	23836
CdPackaging	43971
CdRoute	47135
LinkGenericBrand	39298
CdSchedule	44069

Time spent on importing data: 13 minutes

Time spent on new generic import: 8 minutes

The program will then clean up the Health Canada data and will display something like the following (it may take 4 minutes)

Added Descriptor and Strength
Number of drug names being added descriptor: 45
Number of drug names being added strength: 21297

 

Trying It Out

At this point you can test the fairly plain install. To test the connection, open your web browser and go to your the web address of your server.  If you installed on a local desktop version of Ubuntu it is as shown below. You should see the OSCAR login page.

http://localhost:8080/oscar

 The default login parameters for OSCAR is as follows:

User Name: oscardoc
Password: mac2002
2nd Level Passcode: 1117

Activate Rx3 when logged into Oscar navigate Pref > Set To Use Rx3 and click the check box