Enterprise Edition | Email contact@openspecimen.org |
Community Edition | Download the code from Github and follow steps on How to build from code?) |
Please visit the respective download centers and download the latest version available for your operating system:
Note: Make sure MySQL prerequisites are configured correctly before moving on to the next steps.
Note: Applicable only for a fresh install
Database | Command |
---|---|
MySQL |
|
Oracle |
Note: |
Refer to Database Configuration to set the proper privileges. |
Note: This section is applicable for the fresh install and upgrading OpenSpecimen from older versions before v5.0.
For Linux, configure the PID.txt path using the instructions here: How to run Tomcat using PID on Linux?
Refer to the attached context.xml for reference.
Configure the data source name in $TOMCAT_HOME/conf/context.xml using the snippet below.
<Resource name="jdbc/openspecimen" auth="Container" type="javax.sql.DataSource" maxActive="100" maxIdle="30" maxWait="10000" username="<db_user_name>" password="<db_password>" driverClassName="<DRIVER_CLASS_NAME>" url="<DB_URL>" testOnBorrow="true" validationQuery="select 1 from dual" /> |
MySQL | Oracle | |
---|---|---|
Driver class name | com.mysql.jdbc.Driver | oracle.jdbc.OracleDriver |
DB URL | jdbc:mysql://<db_host>:<db_port>/<db_name> | jdbc:oracle:thin:@<db_host>:<db_port>:<dbname> |
Add below XML fragment below <Resource>
tag in $TOMCAT_HOME/conf/context.xml
<Environment name="config/openspecimen" value="$TOMCAT_DIR/conf/openspecimen.properties" type="java.lang.String"/> |
Notes: The word "openspecimen" above could be different based on your configuration. E.g. "os-test", "os-prod" etc.
Note: If the data & plugin directory is not present at the specified path, installer script will create data & plugin directory at the specified path provided in the openspecimen.properties file.
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" |
For Upgrading OpenSpecimen from versions after v5.0 or installing OpenSpecimen for the first time. Use the below command.
Before running the installer, shut down the Tomcat service (Windows user only).
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
Note: The installer scripts automatically copies new WAR and plugin and took the backup of existing WAR and plugins into $os_data/old_builds directory.
Windows | Start: Go to Task manager => Services tab => Click on Apache Tomcat 9 service => Click on Start link. (In left panel) Stop: Go to Task manager => Services tab => Click on Apache Tomcat 9 service => Click on Stop link. (In left panel) |
Linux | The installer starts OpenSpecimen automatically. If not started, run the following command: Start: $TOMCAT_HOME/bin/startup.sh Stop: $TOMCAT_HOME/bin/shutdown.sh -force |