GNUmed and OpenClinica

OpenClinca is a enterprise grade clinical study management solution. It runs on the Apache tomcat webserver version 5.5. OpenSuse 10.2 provides all packages once you add JAVA:addon/openSUSE_10.2 to the channel list for smart. Install tomcat5.5. Dependencies will be pulled automatically. In my setting a lot of symlinks were not created so follow the Openclinics install instructions for the basics. Once done make sure you have the following setup (took me hours)

ls -l /srv/www/tomcat55/base/common/lib/
insgesamt 396
lrwxrwxrwx 1 root root 24 16. Aug 16:41 bcel.jar -> /usr/share/java/bcel.jar
lrwxrwxrwx 1 root root 34 16. Aug 16:41 catalina-ant55.jar -> /usr/share/java/catalina-ant55.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 jakarta-commons-beanutils.jar -> /usr/share/java/jakarta-commons-beanutils.jar
lrwxrwxrwx 1 root root 40 16. Aug 16:19 jakarta-commons-dbcp.jar -> /usr/share/java/jakarta-commons-dbcp.jar
lrwxrwxrwx 1 root root 44 16. Aug 15:58 jakarta-commons-digester.jar -> /usr/share/java/jakarta-commons-digester.jar
lrwxrwxrwx 1 root root 38 16. Aug 15:58 jakarta-commons-el.jar -> /usr/share/java/jakarta-commons-el.jar
lrwxrwxrwx 1 root root 43 16. Aug 15:58 jakarta-commons-modeler.jar -> /usr/share/java/jakarta-commons-modeler.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 jakarta-commons-validator.jar -> /usr/share/java/jakarta-commons-validator.jar
lrwxrwxrwx 1 root root 40 19. Aug 17:47 jakarta-taglibs-core.jar -> /usr/share/java/jakarta-taglibs-core.jar
lrwxrwxrwx 1 root root 44 19. Aug 17:35 jakarta-taglibs-standard.jar -> /usr/share/java/jakarta-taglibs-standard.jar
lrwxrwxrwx 1 root root 37 19. Aug 17:24 jasper55-compiler.jar -> /usr/share/java/jasper55-compiler.jar
lrwxrwxrwx 1 root root 36 19. Aug 17:24 jasper55-runtime.jar -> /usr/share/java/jasper55-runtime.jar
lrwxrwxrwx 1 root root 37 19. Aug 17:44 jasper-compiler -> /usr/share/java/jasper55-compiler.jar
lrwxrwxrwx 1 root root 26 19. Aug 17:52 javacc.jar -> /usr/share/java/javacc.jar
lrwxrwxrwx 1 root root 27 19. Aug 17:55 jdtcore.jar -> /usr/share/java/jdtcore.jar
lrwxrwxrwx 1 root root 41 19. Aug 17:43 jsp-api.jar -> /usr/share/tomcat55/common/lib/jspapi.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 jspapi.jar -> /usr/share/java/jspapi.jar
lrwxrwxrwx 1 root root 23 19. Aug 17:40 jsp.jar -> /usr/share/java/jsp.jar
lrwxrwxrwx 1 root root 43 19. Aug 14:58 naming-factory.jar -> /usr/share/java/tomcat55/naming-factory.jar
lrwxrwxrwx 1 root root 45 19. Aug 14:58 naming-resources.jar -> /usr/share/java/tomcat55/naming-resources.jar
-rw-r--r-- 1 tomcat tomcat 402505 3. Mär 00:13 postgresql-8.1-405.jdbc3.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 postgresql-8.2-506.jdbc3.jar -> /usr/share/pgsql/postgresql-8.2-506.jdbc3.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 regexp.jar -> /usr/share/java/regexp.jar
lrwxrwxrwx 1 root root 32 16. Aug 16:32 servletapi55.jar -> /usr/share/java/servletapi55.jar
lrwxrwxrwx 1 root root 31 16. Aug 15:58 servletapi5.jar -> /usr/share/java/servletapi5.jar
lrwxrwxrwx 1 root root 16 19. Aug 17:43 servlet-api.jar -> servletapi55.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 struts.jar -> /usr/share/java/struts.jar


start with 'rctomcat55 start' and watch /var/log/tomcat55/catalina.out for messages.

go to http://localhost:8080 in a webbrowser and test the jsp and servlet examples. If that works fine go to http://localhost:8080/OpenClinica and you will be greeted by the login screen

With respect to GNUmed one can think of a feature to submit patients to studies in OpenClinica or import follow-up visits as encounters in GNUmed.

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