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| Field | Description | Values |
|---|---|---|
| app.name | 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.dir | The absolute path to the Tomcat directory | |
| app.data_dir | Absolute path to OpenSpecimen data directory. | Best practice: Create a folder in parallel to 'tomcat.dir' with the name "openspecimen/data" |
| app.log_conf | Folder where the OpenSpecimen logs should be created | If left empty logs are created in "app.data_dir/logs" |
| datasource.jndi | Name of datasource configured in "context.xml" | Usually, it is "jdbc/openspecimen". |
| datasource.type | "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.type | MySQL or Oracle | "mysql" or "oracle" |
| plugin.dir | 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 system | Command |
|---|---|
| Linux | ./install.sh <absolute_path_to_openspecimen.properties> |
| Windows | ./install.bat <absolute_path_to_openspecimen.properties> |
Example : ./install.sh /usr/local/openspecimen/tomcat-as/conf/openspecimen.properties
NoteNotes for upgrade:
- The installer scripts automatically copies the new WAR and plugin and
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- take the backup of existing WAR and plugins into $os_data/old_builds directory.
- Stop the Tomcat if running
- Take the backup of the custom plugins if any
- Take the backup of the database before upgrade
Starting/Stopping OpenSpecimen
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