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This document describes steps to build OpenSpecimen from source code and to set up a development environment. This guide is intended for developers or technical IT staff. Following are high-level steps of building OpenSpecimen code:

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 v4v6.21.4 RC7 # example to checkout source code of OpenSpecimen v4.2.4OpenSpecimen 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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• For database privileges, refer to Database Configuration
• Java 8 JRE and JAVA_HOME is set.
• MySQL on Linux: MySQL Case Sensitivity issues on Linux

Following table lists pre-requisites and their supported versions.

Recommended The recommended memory requirement for OpenSpecimen app is 2GB. To configure Tomcat follow How to fix "out of memory" error ?

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          You'll also need to place appropriate connector jar for MySQL/Oracle under 'lib' directory in tomcat server.

Environment Variables

Following table lists and describes environment variables

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Configuring build.properties

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

Note the path must be made up of forward slashes (/) instead of backward slashes (\)

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app_data_dir

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Create a new folder within 'app_home, say 'os-data' and specify it here.

Note the path must be made up of forward slashes (/) instead of backward slashes (\)

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app_log_conf

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The path of the logging configuration properties file. This property is optional, if kept empty default logging configuration will be used.

Note the path must be made up of forward slashes (/) instead of backward slashes (\)

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Name of JDNI datasource configured in Tomcat/JBoss for connecting to database

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java:comp/env/jdbc/openspecimen

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Specifies type of deployment - whether the database was setup for pre-OS v2.0 or was setup for OS v2.0 onwards.

fresh: Database was created starting with OS v2.0

upgrade: Database was created using pre-OS v2.0 app

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Hostname or IP address of machine running DBMS server software

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Port on which DBMS server software listens for incoming requests

Commonly used port numbers are:

MySQL: 3306

Oracle: 1521

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Database name for storing data. This is same as configured or created in database configuration step above

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Valid DBMS user name for connecting to the database

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Valid DBMS user password for authenticating and connecting to database

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This is optional and needed only if you are using any plugins.

Create a new folder within 'app-dir' and specify there. This is where all the plugin JARs should exist. E.g. 'os-plugins'.

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.

<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" />

Add below XML fragment below  <Resource> tag in $TOMCAT_HOME/conf/context.xml

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

Edit "openspecimen.properties"

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

Attaching openspecimen.properties.

Notes:

• Make sure all the above database and Tomcat configuration are done properly.
• Copy the openspecimen.properties from downloaded location to $TOMCAT_HOME/conf directory.
• Before starting deploy make sure no Tomcat process is running.

Steps to deploy

The OpenSpecimen build system uses Gradle to manage code compilation, building web application archives, and deploying the application. 

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.

1. $TOMCAT_HOME/logs/catalina.out
2. $OS_DATA_DIR/logs/os.log

Setup OpenSpecimen project in Eclipse or Intellij

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1. Open command terminal
2. Change to directory to root directory i.e $OS_HOME.

3. Run below commands for your IDE

   1. For Eclipse : gradle eclipse
This command creates the .project, .classpath files and .settings folder which is essential for project to be recognized as eclipse project.
      
      

   2. For Intellij : gradle idea
This command create openspecimen.iml, openspecimen.ipr, openspecimen.iws files which are essential for project to be recognized as Intellij project.

4. Now import the project into IDE using import from existing sources.

   1. Eclipse: 

      1. Open File -> Import -> Existing Projects into Workspace
      2. Select the root directory of our project (i.e openspecimen). Project will get imported successfully
         
         
   2. Intellij: 
      
      1. Open File -> Open and select the root folder of our project. (i.e openspecimen)
      2. Click on 'ok' on the next dialog. Project The project will get imported successfully.
         

Data Source Configuration in Tomcat Application Server

You will need to setup data source configuration in $TOMCAT_HOME/conf/context.xml file as below.

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Here, driverClassName and URL should be like below:

Driver Class Name:

MySQL:  com.mysql.jdbc.Driver

Oracle:   oracle.jdbc.OracleDriver

Note: The appropriate driver jar file should be added to the Tomcat/lib directory.

DB URL:

MySQL:  jdbc:mysql://<db_host>:<db_port>/<db_name>

Oracle:   jdbc:oracle:thin:@<db_host>:<db_port>:<dbname>

Start and Shut Down the Application Server

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 Operation

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  Windows

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Linux

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 Start

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$TOMCAT_HOME/bin/catalina.bat start


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$TOMCAT_HOME/bin/catalina.sh start


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 Stop

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$TOMCAT_HOME/bin/shutdown.bat

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