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BioMS Application Link:https://bioms.wustl.edu/bioms/

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Installing BioMS Adaptor 1.3 in caTissue 2.0.5+ (for OSU repo)

1. Introduction

This document describes the steps for installting BioMS Adaptor for caTissue2.0A version 1.1 in caTissue 2.0.5A at OSU repository

2. Install Instructions

  1. Shutdown caTissue JBOSS server
  2. Unpack the BioMS adaptor package, this will create a folder bioms-adaptor and will be referred as BA_HOME in the remaining of this document.
  3. Copy $BA_HOME/war/2.0A/bioms-adaptor.war to CATISSUE_HOME/jboss-5.1.0.GA/server/default/deploy/deploy.last folder (where CATISSUE_HOME is the the home folder of caTissue)
  4. Set environment variable BIOMS_HOME to point to BA_HOME/.bioms folder.
  5. Edit $BIOMS_HOME/bioms-adaptor.properties and update the properties appropriately as specified in the table below or take the bioms.properties from the OSU catissue at WASHU and update the http.proxyHost and http.proxyPort as appropriate for the OSU environment

    Property

    Description

    Example

    bioms.appurl

    The base url of the bioms application to which this bioms adaptor will be linked. Obtain this URL from the BioMS admin. The url should NOT end with a '/'

    https://alliancebmsdemo.wustl.edu/bioms

    repo.name

    A unique name assigned to this caTissue instance assigned by the BioMS admin

    pco-repo

    repo.authkey

    A secret authentication key assigned to this repo by the BioMS admin. 

    The repo.name and repo.authkey combination is used to authenticate repository caTissue when it tries to sync with the BioMS. This combination must match with the value assigned by the BioMS admin

    Jndy383snhs7

    catissue.urlBase url of the repository caTissue application (setup in Section 2. above) the adaptor needs to be linked to.http://loclahost:8080/catissuecore

    catissue.username

    The login name of the BioMS Admin user created in Step 1.a. BioMS Adaptor would use this user credentials to connect to repository caTissue to sync data to caTissue.

    admin@bms.com

    catissue.password

    The password  for the above mentioned super admin user (noted down as catissue.password during step 1.aabove)

     

    http.proxyHost

    The name or Ip of the httpProxy host (if any). The adaptor should be able to reach the bioms.appurl via this proxy host. If there is no value provided then a direct connection is made to the bioms app url.

     

    http.proxyPort

    The http proxy server port

    Default is 80

    catissue.dummyCSMUserIdObsolete . No need to set 


    and change the value of the existing property catissue.events.pollinginterval to 10000 from the current value of 10

  6.  Edit $BIOMS_HOME/log4j.properties and replace ${user.home}/.bioms with the actual value of BIOMS_HOME environment variable (e.g. /home/bioms/.bioms)
  7. Start caTissue Jboss server.
  8. Check the jboss server.log and make sure both catissuecore application and bioms-adaptor application are started successfully.
  9. Check the syslog server for the server and console log and configure daily rotation of the log file
  10. Check $BIOMS_HOME/logs/bioms-adaptor.log and look for messages like the following showing up every 10 secs

18:11:55,852 INFO  [STDOUT] 2012-10-08 18:11:55 SyncMessageReceiver [DEBUG] No mssage received, sleep for 10sec before trying again...

18:11:58,113 INFO  [STDOUT] 2012-10-08 18:11:58 CaTissueChangeListener [DEBUG] Fetching record from Catissue event
 

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