OpenSpecimen HowTo Install

Tags: OpenSpecimen HowTo

Process

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

1. Log onto the appropriate LAMP server.
2. cd /local
3. Download this repository using the command svn export https://svn.rcs.le.ac.uk/LCBRU/utilities/OpenSpecimen/trunk/v3.2/
4. cd v3.2
5. Backup the database.
6. Run the command ./doInstall.sh
7. If the process is still running, kill it using sudo -u wwwrun kill {process id}
8. 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
   
   

9. 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
   ...
   

10. sudo -u wwwrun /local/openspecimen/run_open_specimen.sh
11. Check it starts by running tail -f /local/openspecimen/app/logs/catalina.out
12. Check for errors by running tail -f /local/openspecimen/openspecimen.log

Error: Macro BackLinks(None) failed

'Environment' object has no attribute 'get_db_cnx'