Quick Links


Support Email:bioms@alliancenctn.org

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

Looking for help? Email bioms@alliancenctn.org
Or Phone 1(855)-55-BIOMS or 1(855)-552-4667

Skip to end of metadata
Go to start of metadata

Updating BioMS Adaptor for caTissue2.0A v1.0 to v1.1

1. Introduction

This document describes the steps for updating an existing BioMS Adaptor for caTissue2.0A version 1.0 deployment to BioMS Adaptor for caTissue2.0A version 1.1.

2. Update Instructions

  1. Shutdown caTissue JBOSS server
  2. Take a backup of the caTissue DB (for recovery if any error occurs during update)
  3. Take a backup of the caTissue Jboss folder (for recovery if any error occurs during update)
  4. 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.
  5. 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 were the 1.0 adaptor is deployed)

  6. Set environment variable BIOMS_HOME to point to the current .bioms folder, e.g BIOMS_HOME=/home/bms/.bioms. In the adaptor 1.0 setup the folder will be at the users home folder. With BioMS adaptor 1.1, the adaptor configuration folder need NOT be at the user home, the folder can be moved to any where else with BIOMS_HOME set to point to the new location. Set the BIOMS_HOME  environment variable in .bashrc (in linux) or in system environment for windows. If you choose to move the .bioms folder to some other location from its current location, update the log4j.appender.R.File property in .bioms/log4j.properties to point to the new location.

  7. Edit $BIOMS_HOME/bioms-adaptor.properties and add the following line to the end of the file 

    catissue.events.startDelay=60000

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

  8. For WASHU Deployments ONLY :Configure syslog logging in catissue jboss server, Edit <jboss>/server/default/conf//jboss-log4j.xml add or uncomment and edit the existing SYSLOG appender to make it look like the following

    <appender name="SYSLOG" class="org.apache.log4j.net.SyslogAppender">
    
    <errorHandler class="org.jboss.logging.util.OnlyOnceErrorHandler"/>
    
    <param name="Facility" value="LOCAL7"/>
    
    <param name="FacilityPrinting" value="true"/>
    
    <param name="SyslogHost" value="10.39.197.123"/>
    
    <layout class="org.apache.log4j.PatternLayout">
    
    <param name="ConversionPattern" value="[%d{ABSOLUTE},%c{1}] %m%n"/>
    
    </layout>
    
    </appender>

    Add the following to the <root> element at the end of the file

    <appender-ref ref="SYSLOG"/>



  9. Run the following SQL update command on the caTissue database

    delete from catissue_user where email_address is null;
    delete from catissue_site_users where user_id in (select identifier from catissue_user where identifier not in (select min(identifier) from catissue_user group by email_address));
    delete from catissue_user where identifier not in (select min(identifier) from catissue_user group by email_address);
    update catissue_user set login_name = email_address;
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5019,'CPT Na Citrate (blue/black)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5020,'CPT Na Heparin (red/green)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5021,'Na Heparin (dark blue)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5022,'EDTA (dark blue)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5023,'Na Heparin (dark green)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5024,'No Additive (gold)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5025,'Na Fluoride/DiNa EDTA (grey)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5026,'Na Heparin (light blue)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) 
    values (5027,'Na Fluoride/K oxalate (light grey)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) 
    values (5028,'Na poly ethanol sulfonate (orange)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5029,'Thrombin (orange)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5030,'K EDTA (pink)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5031,'Na Heparin (royal blue)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5032,'Clot Activator SST (red/grey)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5033,'K2 EDTA (tan)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5034,'Na Heparin (tan)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5035,'K EDTA (white)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5036,'Broth mixture (yellow/black)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5037,'Cell Save','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5038,'Li/Heparin (green/grey)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5040,'Thrombin 2u (grey/yellow)','2003997');
    
    insert into catissue_permissible_value (identifier,VALUE, PUBLIC_ID ) values (5018,'Na Citrate (black)','2003997');
  10. Start caTissue Jboss server.
  11. Check the jboss server.log and make sure both catissuecore application and bioms-adaptor application are started successfully.
  12. Check the syslog server for the server and console log and configure daily rotation of the log file
  13. 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
 

  • No labels