Table of Contents

Prerequisites

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"

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:

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