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This field is useful for deploying multiple OpenSpecimen instances on the same Tomcat server. E.g. You can use "os-test" and "os-prod".

Typically this is "openspecimen".
tomcat.dirThe absolute path to the Tomcat directory

Absolute path to OpenSpecimen data directory.

Best practice:

Create a folder in parallel to 'tomcat.dir' with the name "openspecimen/data"


Folder where the OpenSpecimen logs should be created

If left empty logs are created in "app.data_dir/logs"

datasource.jndiName of datasource configured in "context.xml"Usually, it is "jdbc/openspecimen".

"fresh": If your database schema is created by OpenSpecimen from scratch.

"Upgrade": if your database schema is upgraded from a caTissue database.

Note: The name is a bit misleading, we will fix this in v5.2.

"fresh" or "upgrade"
database.typeMySQL or Oracle

"mysql" or "oracle"


Absolute path to the plugin directory.

Best practice:

Create a folder in parallel to 'tomcat.dir' with the name "openspecimen/plugins"

Install / Upgrade

For Upgrading installing new or upgrading OpenSpecimen from versions after v5.0 or installing OpenSpecimen for the first time. Use the below command.

Before running the installer.

  • Stop the tomcat if running.
  • Take the backup of the specific plugins if any.
  • Take the backup of the database.

previous versions use the below command:

Operating systemCommand
Linux./ <>
Windows./install.bat <>

Example : ./ /usr/local/openspecimen/tomcat-as/conf/

NoteNotes for upgrade:

  1. The installer scripts automatically copies the new WAR and plugin and


  1. take the backup of existing WAR and plugins into $os_data/old_builds directory.
  2. Stop the Tomcat if running
  3. Take the backup of the custom plugins if any
  4. Take the backup of the database before upgrade

Starting/Stopping OpenSpecimen