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Download OpenSpecimen
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- Database: MySQL 5.7 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
- Apache for Linux
- Apache for Windows
Note: Make sure MySQL prerequisites are configured correctly before moving on to the next steps.
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MySQL | Oracle | |
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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 $TOMCAT_HOME/conf/context.xml
Code Block | ||
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<Environment name="config/openspecimen" value="$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.
Deployment
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- Unzip the installer file. Let's call the new folder OSPM_HOME
- Change directory to OSPM_HOME
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Field | Description | Values |
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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 OpenSpecimen from older versions before 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 |
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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
Starting/Stopping OpenSpecimen
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