1. Purpose

This document is meant for the administrators of the BioMS application. This document describes the process of deploying the BioMS application and regular administration activities to be performed on the BioMS application.

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1. One Oracle 10g/11g Schema with permissions for creating table and sequences
2. 3 4 Server machine with the following minimum configuration
   
   1. Dual core, 4GB RAM, 50 GB HDD x 2 – for BioMS cluster nodes and caTissue2
   2. Dual core, 4GB RAM, 50 GB HDDx1 -for caTissue 2.0A on BioMS. One of these machines , this machine should have oracle client installed on it. This is required for installing caTissue.
   3. Dual Core, 1GB RAM, 50 GB HDD x 1 – for the apache load balancer
3. OS : RHEL 5.0+
4. JBoss 5.1

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Get the caTissue 2.0A installer from files.cbmi.wucon.wustl.edu:/files/bioms/1.0/RC1/caTISSUE_Suite_v2.0_Installable.zip and unpack in BioMS Node 1 it on caTissue2.0A on BioMS server. Follow the caTissue 2.0 installation instruction to install caTissue to the BioMS Oracle DB.

Change the following properties in the install.properties

application.base.path.linux=/usr/local/bms/catissueBMS-webapp

# Required for local installs
database.re-create=false
database. This caTissue should be installed with all caTissue external system integrations like GSID, CTRP and C3PR disabled in install.properties. Also choose a different set of JBOSS port numbers to avoid conflict with the BioMS JBoss node running on the same server.-- Add specific install.properties that needs to be changed.system.user=    (this property should be left empy)
database.system.password=(this property should be left empy)
database.system.url=<db connection url> (e.g. jdbc:oracle:thin:@orad1m1.cbmi.wucon.wustl.edu:1521:clindbd1)

# Require for all installs
database.drop-schema=true
database.type=oracle
database.server=orad1m1.cbmi.wucon.wustl.edu
database.port=1521
database.name=clindbd1
database.user=ALLIANCEMBMS
database.password=<DB PASSWORD>
database.url=jdbc:oracle:thin:@orad1m1.cbmi.wucon.wustl.edu:1521:clindbd1
oracle.tns.name=clindbd1

#CSM DATABASE CREDENTIALS

csm.database.type=oracle

csm.database.host=orad1m1.cbmi.wucon.wustl.edu

csm.database.port=1521

csm.database.name=clindbd1

csm.database.username=ALLIANCEMBMS

csm.database.password=<DB_PASSWORD>

gsid.isEnabled=false

ccts.integration.isEnabled=false

ctrp.isEnabled=false

gridgrouper.isEnabled=false

 To install run ant install from the installer unpack folder


To upgrade an existing installation to a newer build , update the install.properties as detailed above and run ant upgrade:jboss from the installer unpack folder. Make sure the database properties in the install.properties is pointing to the database where the current catissue is running.

6. Setup BioMS on Bioms-node1

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1. Get the BioMS 1.0 distribution from files.cbmi.wucon.wustl.edu:/files/bioms/1.0/RC1/bioms-1.0.zip and unpack into a folder (lets call this folder BIOMS_INSTALL_HOME)
2. Get JBoss 5.1 from here and unpack into a folder (lets call this JBOSS_HOME).
3. Copy the folder JBOSS_HOME/server/all/ to JBOSS_HOME/server/bioms-node1
4. Copy the contents of BIOMS_INSTALL_HOME/jboss-overlay onto JBOSS_HOME/server/bioms-node1/
5. Copy BIOMS_INSTALL_HOME/war/bioms.war to JBOSS_HOME/server/bioms-node1/deploy
6. Edit JBOSS_HOME/bin/run.conf and replace the JAVA_OPTS variable with the following

JAVA_OPTS="-Xms128m -Xmx2048m -XX:MaxPermSize=1024m -Dorg.jboss.resolver.warning=true -Dsun.rmi.dgc.client.gcInterval=3600000 -Dsun.rmi.dgc.server.gcInterval=3600000 -Dgov.nih.nci.security.configFile=$HOME/.bioms/conf/ApplicationSecurityConfig.xml"

7. Edit JBOSS_HOME/server/bioms-node1/conf/login-config.xml and update the database connection details under the application-policy element with name 'bms' to point to the BioMS database schema.

8. Edit JBOSS_HOME/server/bioms-node1/deploy/bioms-ds.xml and update the database connection details

9. Copy BIOMS_INSTALL_HOME/.bioms to users home folder ($HOME)

10. Edit $HOME/.bioms/ApplicationSecurityConfig.xml and replace ${user.home} with the home directory path of the user.

11. Edit $HOME/.bioms/bioms-config.groovy, and update the datasource section with the database connection details for the BioMS database schema.

12. Start the JBoss Server bioms-bioms-node1

run.sh –b0.0.0.0 –cbioms-node1 -u 239.255.100.100 –gBioMSPartition -Djboss.messaging.ServerPeerID=1

This will start the server and the BioMS application deployed. Try accessing the BioMS application at url http://<bioms-node1-server>:8080/bioms. Login to the application using credentials admin@bms.com/Passw0rd and we should see a page similar to the following snapshot.

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Follow the same steps give in Section 3.3 substituting all bioms-node1 with bioms-node2 to setup second node of the BioMS cluster . on server BioMS node2

Start the BioMS Node with the command

run.sh –b0.0.0.0 –cbioms-node2 -u 239.255.100.100 –gBioMSPartition -Djboss.messaging.ServerPeerID=2

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 # Define list of workers that will be used
 # for mapping requests
 worker.list=loadbalancer,status
 
 # Define Bioms-node1
 # modify the host as your host IP or DNS name.
 worker.bioms-bioms-node1.port=8009
 worker.bioms-node1.host=<bioms-node1-host> 
 worker.bioms-node1.type=ajp13
 worker.bioms-node1.lbfactor=1
 worker.bioms-node1.cachesize=10
 
 # Define Bioms-node2
 # modify the host as your host IP or DNS name.
 worker.bioms-node2.port=8009
 worker.bioms-node2.host=<bioms-node2-host> 
 worker.bioms-node2.type=ajp13
 worker.bioms-node2.lbfactor=1
 worker.bioms-node2.cachesize=10
 
 # Load-balancing behaviour
 worker.loadbalancer.type=lb
 worker.loadbalancer.balance_workers=bioms-node1,bioms-node2
 worker.loadbalancer.sticky_session=1
 #worker.list=loadbalancer
 
 # Status worker for managing load balancer
 worker.status.type=status

  - add laodbalancer worker urls

9. CTEP Authentication Setup

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Securely share the <repo-name> and <authkey> and the bioms application url (the loadbalancer url) with the repository caTissue admin. They would need to update the bioms-adaptor.properties with these details.
Once the bioms-adaptor is setup properly at the repository caTissue and started you should see message like

controller.RepoSyncMessageController 2012-10-08 09:59:11,996 Sending 204 (no message available) to repo <repo-name>
in the bioms log.
Also messages like the following would be there on the BioMS adaptor log file.
5:01:14,745 INFO [STDOUT] 2012-10-08 15:01:14 SyncMessageReceiver [DEBUG] No mssage received, sleep for 10sec before trying again...

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Participant registrations usually comes from Mayo Rando Node applications. But until the Mayo Rando Node integration is enables, BioMS admin can register participants to study via teh the participant registration page provided in BioMS. The participant registration page can be accessed at <bioms-base-url>/patientRegistrationfrom the ADMIN TASKS menu group when logged in as BioMS Admin.

13.4. Watching for Sync issues

BioMS admin can see if there are any happening during syncing of data between BioMS and repository caTissue at <bioms-base-url>/syncError from the Sync Errors menu in the ADMIN TASKS menu group accessible only for BioMS admins. This page lists all the errors occurred during the sync with the sync message and the error details including any stack trace.

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