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Table of Contents

Introduction

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  1. Install/Setup pre-requisite software. These pre-requisites can be downloaded from http://www.openspecimen.org/prerequisites/
  2. Use the below command to download the source code:
    $ git clone --depth 10 https://github.com/krishagni/openspecimen.git
  3. Above command will checkout the master branch or unreleased version of code. If you wish to build source code of a specific release then use below command before proceeding to build. The list of available release version tags can be view here: https://github.com/krishagni/openspecimen/releases
    $ git checkout <release-version-tag>
    $ git checkout v6.1.RC7 # example to checkout source code of OpenSpecimen v6.1.RC7

  4. Do all the pre-requisites setup before deploying WAR file.

  5. Use gradle to build and deploy the application.

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Following table lists pre-requisites and their supported versions.

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DatabaseCommand
MySQL

create database <database-name>

<database-name>: name of the database to be used for storing OS data

Oracle

create user <username> identified by <password>

Note: <username>, <password> has to be replaced with database username and password

Configure Tomcat context.xml

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.

Code Block
<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 namecom.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

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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"/>

Note: The word "openspecimen" above could be different based on your configuration. E.g. "os-test", "os-prod" etc.

Edit "openspecimen.properties"

Note: Please make sure data & plugin directory are present at the specified path.

Attaching openspecimen.properties.


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.dirThe 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

The folder where the OpenSpecimen logs should be created

If left empty logs are created in "app.data_dir/logs"

datasource.jndiName 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.typeMySQL 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"

Configure build.properties

Property NameDescriptionDefault ValueAllowed Values
app_home

The absolute path of the directory where Tomcat server is extracted and installed.

NoneExample: /usr/local/openspecimen/tomcat-as

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  1. Open command terminal
  2. Change to the directory where OpenSpecimen source code is checked-out
    • cd $OS_HOME
  3. Setup npm & bower dependencies.
    • cd www/
    • npm install
    • bower install

      Note: Above commands needs to be executed successfully.

  4. Change directory to root directory of source code.
    • cd ..
  5. Use the following command to build and deploy OpenSpecimen into app_home directory (Tomcat or JBoss server).
    • gradle deploy
  6. To only compile Java source files use the following command
    • gradle compileJava
  7. To build OpenSpecimen web app archive without deploying use following command
    • gradle build

Once "gradle deploy" is ran successfully, start the Tomcat process and monitor the log files.

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