Table of Contents |
---|
Download OpenSpecimen
...
Prerequisites
- Database: MySQL 5.7/8.0 or Oracle 11g/12c
- Java 8 JDK and JAVA_HOME is set.
- Tomcat 9 and its service
- MySQL prerequisites
Please visit the respective download centers and download the latest version available for your operating system:
- MySQL (Ignore if you are going to use Oracle)
- Java
- Tomcat (Use the Tomcat zip provided into OpenSpecimen build zip)
- Apache for Linux
- Apache for Windows
Note: Make sure MySQL prerequisites are configured correctly before moving on to the next steps.
...
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 $TOMCAT_HOME/conf/context.xml
Code Block | ||
---|---|---|
| ||
<Environment name="config/openspecimen" value="$TOMCAT_DIR/conf/openspecimen.properties" type="java.lang.String"/> |
...
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, shut down the Tomcat service (Windows user only).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
...
- 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
...