Table of Contents

Download OpenSpecimen

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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.

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	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

language	xml

<Environment
  name="config/openspecimen"
  value="$TOMCAT_DIR/conf/openspecimen.properties"
  type="java.lang.String"/>

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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"

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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

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Ubuntu	sudo apt install openjdk-17-jdk openjdk-17-jre
RedHat	sudo dnf install java-17-openjdk-devel java-17-openjdk

2. Change the existing JAVA_HOME directory path in .bashrc file and point to the Java 17 directory.

3. Check the Java version using the below command.

# java -version

4. Edit the $Tomcat_Dir/bin/setenv.sh file and remove the below lines.

"-XX:PermSize=64m -XX:MaxPermSize=512m"

5. Add the below-mentioned Java specific startup parameters required by Tomcat in $Tomcat_Dir/bin/catalina.sh file.

JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-opens=java.base/java.net=ALL-UNNAMED

6. Deploy the OpenSpecimen build.