= OpenSpecimen HowTo Build from Source Code

Tags: [[OpenSpecimen Summary]] [[HowTo]]

This guide is based on my experience and the [[https://openspecimen.atlassian.net/wiki/pages/viewpage.action?pageId=1115955|Official Guide on How to Build Open Specimen]]

This is the procedure for building the `war` file.  The [[Gradle]] build script can also be used to deploy OpenSpecimen to a local instance, but that is not covered here.

== Prerequisites

- Java JDK v1.8
- Gradle 2.0
- git
- node.js 10+
- npm
- bower - `npm install -g bower`
- grunt - `npm install -g grunt-cli`
- `$JAVA_HOME` set to the JDK directory

=== Gotchas

1. The first time I build OpenSpecimen using this method I had to upgrade node and npm before installing bower and grunt.
2. Gradle could not find node because on Ubuntu it is called nodejs so I had to create a symbolic link `sudo ln -s nodejs node` in the directory `/usr/local/bin/`.

== Procedure

See: [[https://openspecimen.atlassian.net/wiki/pages/viewpage.action?pageId=1115955]]

1. Download the source code from the **releases** tab of the [[https://github.com/krishagni/openspecimen.git|Open Specimen Github Repository]] - **Make sure to get the correct branch for the required version**
2. Edit the `build.properties` file with the correct values.  Here are the values for the university LAMP servers.  The other values not in this list can be deleted:
{{{
#!ini
app_home = /local/openspecimen_{version_number}/app
app_data_dir = /local/openspecimen_{version_number}/app/osdata
datasource_jndi = java:/comp/env/jdbc/openspecimen
deployment_type = upgrade
database_type = mysql
show_sql = false
plugin_dir = /local/openspecimen_{version_number}/app/plugins
}}}
3. `cd` into the `www` directory
4. Run the command `npm install`
5. Run the command `bower install`
6. `cd ..`
7. Run the command `gradle build`

== Deploying to [[Tomcat]]

1. Copy the `war` file to the [[Tomcat]] `webapps` directory.
2. Amend the file in the Tomcat directory `conf/context.xml` to set up the resource:
{{{
#!xml
<Resource name="jdbc/openspecimen" auth="Container" type="javax.sql.DataSource"
     maxActive="100" maxIdle="30" maxWait="10000"
     username="{database_username}" password="{database_password}" driverClassName="com.mysql.jdbc.Driver"
     url="jdbc:mysql://localhost:3306/openspecimen"
     validationInterval="3600"
     testOnBorrow="true"
     validationQuery="Select 1 from dual"
/>
}}}

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