OpenSpecimen HowTo Install

Tags: OpenSpecimen HowTo

See ​https://openspecimen.atlassian.net/wiki/display/CAT/Deployment+steps

• Have to make install.sh and catalina.sh executable.
• Have to amend apache config:
  • Amend loadmodule.conf to:

    ...
    # Tomcat - used for JBoss
    #LoadModule jk_module /usr/lib64/apache2/mod_jk.so
    
    # Proxy to divert to the JBoss Application Server
    LoadModule proxy_module                   /usr/lib64/apache2-prefork/mod_proxy.so
    LoadModule proxy_http_module               /usr/lib64/apache2-prefork/mod_proxy_http.so
    
    

  • Amend httpd.cong to

    ...
    # Proxy to provide access to the JBoss Application Server
     ProxyPass / http://localhost:8280/ timeout=180
     ProxyPassReverse / http://localhost:8280/
     ProxyTimeout 180
    
    # Use mod_jk to forward to JBoss - not used now, cos it broke
    # Include /local/apache2/etc/mod.d/mod_jk.conf
    ...
    

Process

1. Download the latest release from ​LCBRU OpenSpecimen Repository
2. cd /local
3. Unzip the release unzip openSpecimen_v2_4.zip
4. cd openSpecimen_v2_4
5. Run install.sh
6. sudo -u wwwrun ./first_run_open_specimen.sh
7. Check for process still running ps -ef|grep cat
8. If the process is still running, kill it using sudo -u wwwrun kill {process id}
9. sudo -u wwwrun ./run_open_specimen.sh
10. Check it starts by running tail -f app/logs/catalina.out

UPDATE WORKFLOW table to correct format

Run the command:

update os_cp_workflows set workflows = '[{"name":"registerParticipant","view":"plugin-ui-resources/le/collect-specimens.html","ctrl":"leRegAndCollectSpecimensCtrl","data":{"boxOpts":{"dimension":{"rows":8,"columns":12},"compact":false}}}]';

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