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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 # 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

9. CTEP Authentication Setup

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BioMS application run integrated with tissue repository caTissue application. When the BioMS application is integrated with repository caTissue application it automatically synchronizes specimen data and shipment data between BioMS and caTissue to keep the data in sync across the two application. BioMS application can be configured to sync with multiple repository caTissue instances.The sections below lists out all the data that gets synced between BioMS and caTissue

More details on the repository sync can be found here.

13. Administration

This section describes various ongoing administrative tasks to be performed on the BioMS application.

13.1. Setup sync with a repository caTissue 2.0A

Given below are steps for linking a new repository caTissue instance to BioMS for data synchronization.

1. Assign a unique name for the repository (<repo-name>)caTissue instance. E.g pco-repo.
2. Assign a secret authorization key (<authkey>) for the repository

Add new row to the BMS_REMOTE_REPOSITORY table in the BioMS database with the following data.

Securely share the <repo-name> and <authkey> 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...

13.2. Setup a new Repository Site

Once the repository caTissue instance is linked with BioMS as described above the follow the steps below to setup a new Repository Site for sync. A single caTissue instance can host multiple independent repository sites and BioMS can handle that.

1. Request the caTissue Admin to create Repository Site and the repository coordinator user with the same details like name and address and note the ids of the Site and User created.
2. Get the details of the Repository Site and the Coordinator user details from the repository caTissue admin.
3. Create a Site of type Repository in BioMS via the 'caTissue2.0A on BioMS' and select the coordinator user created by the caTissue admin as the coordinator (this user would have been synced to BioMS automatically). Note the id of the site as <bms_repo_site_id> just created from caTissue2.0A on BioMS.

4. Link the repository site created above with the caTissue remote repository created in step 5.1. For this insert a new row into the BMS_REMOTE_REPOSITORY_SITE table as shown below.

   REMOTE_REPOSITORY_ID	SITE_ID
   <id of the remote repo entry for the remote repo>	<site_id>

5. Map the new Site created in BioMS with the Repository with the same name in caTissue. For this request the repository caTissue admin to insert the following row into BMS_CATISSUE_ENTITY table in the repository caTissue data base

   ID	ENTITY_TYPE	BMS_ID	CATISSUE_ID
   1 (or the next available id)	edu.wustl.catissuecore.domain.Site	<bms_repo_site_id>	<id_of_repo_site_in_catissue >

   
   
   We should now be able to create studies with the new repository as the ship to site for specimen and sync the studies. When the study is synced study should show up in the caTissue.

   13.3. Building and rolling out new Study

Note: This section needs to be revised based on the business process
This section describes the steps for building and rolling out a new Study in BioMS.

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The current version of BioMS has some restrictions on form fields and constraints and doesn't support all the capabilities of forms that could be created in caTissue. Given below is the summary of what is supported in the BioMS specimen forms.
Textfield (string ,numeric,URL datatypes and width, max length, min and max constraints are supported)

TextArea ( width, max length and rows constraints are supported)CheckboxRadion ButtonListBox ComboBoxDate

Checkbox

Radio Button

ListBox

ComboBox

Date picker (Date only)

File picker is not supported at this time.Also form inheritance and forms associations are not supported.

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 . This page lists all the erros occurred during the sync with the sync message and the error details including any stack trace.

BioMS admin should review this list of error at least once in a day to make sure sync functions are working properly.