Changing the GenePattern Database (HSQL to Oracle)
The GenePattern server runs against a database. By default, the GenePattern installation sets up an HSQL database. This section describes how to build and use an Oracle database in place of the HSQL database.
When using Oracle (or another database) you must initialize the database by running the scripts in the <GenePattern_HOME>/resources directory. You or your database administrator must ensure the database is available by JDBC URL from the GenePattern server.
Note: This procedure has been tested using the default Tomcat 5.5 server (Tomcat documentation), which comes with GenePattern.
Edit the genepattern.properties file
# optionally, set a different hibernate.configuration file
The Tomcat/webapps/gp/META-INF/context.xml file has several example configurations for connecting the GP server to a database.
Follow the instructions and examples in the comments. Don't forget to set the username and passwords correctly, as well as entering the server name and sid into the URL property. The resource name you use in the context.xml file must match the one you use in the hibernate configuration file.
Edit the hibernate configuration file
Edit the hibernate.configuration.file that was set in the genepattern.properties file. This file is loaded relative to the classes directory of your web application. For a default installation the file is here:
There are some vendor-specific database settings that must be changed from the default when using Oracle. The specific settings needed are in the comments.
Also be sure to change the hibernate.connection.datasource property near the top of the file to point to the correct Resource in context.xml.
Initialize the database schema
There is a list of files in the installed resources directory for initializing the DB scheme. Run each of the analysis_oracle-3.X.X.sql scripts in order, by version number, up through the installed version of GenePattern.
Start your server
Once the GenePattern Server is running, review the genepattern.log file to verify that the server started correctly and was able to connect to the database.