OPENSPECIMEN DEPLOYMENT
root password: openspecimen_test
mysql root password: Openspecimen_test1
Users: dak3004 (cwid and password, no LDAP auth)

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

Software installed:
	JDK 1.8
	Tomcat/Apache
	MySQL 5.7
	Gradle
	git
	node.js
	npm
	bower
	grunt
	vim

How to install:
THIS ASSUMES THAT sudo dnf update && sudo dnf upgrade WERE PERFORMED PRIOR
	Java: sudo dnf install java javaws
	Javac: rpm -ivh jdk-<version>-linux-x64.rpm
	Tomcat: sudo dnf install tomcat
	MySQL: http://www.if-not-true-then-false.com/2010/install-mysql-on-fedora-centos-red-hat-rhel/
	Gradle: sudo dnf install gradle
	git: already installed, otherwise sudo dnf install git
	Node.js: sudo dnf install nodejs
	npm: sudo dnf install npm
	bower: sudo npm install -g bower
	grunt: sudo npm install -g grunt
	vim: sudo dnf install vim

NEXT: Set JAVA_HOME environment variable
	vim $HOME/.bash_profile
	add export JAVA_HOME="/usr/bin/java/latest" to the end of the file
	add :/usr/bin/java to $PATH
	unknown how to edit /etc/profile to add this path
NEXT: Set TOMCAT_HOME environment variable
	vim $HOME/.bash_profile
	add export TOMCAT_HOME="/usr/share/tomcat/"
	add :/usr/share/tomcat to $PATH

NEXT: set up mysql database
	mysql -u root -p
		enter password
	create database openspecimen_test_db;
	create user 'os_admin'@'localhost' identified by 'OS_admint1'
	GRANT ALTER, ALTER ROUTINE, CREATE, CREATE ROUTINE, CREATE VIEW, DELETE, DROP, EXECUTE, INDEX, INSERT, LOCK TABLES, SELECT, TRIGGER, UPDATE ON openspecimen_test_db.* TO 'os_admin'@'localhost'
		This can be found by following the link in the confluence article
			https://openspecimen.atlassian.net/wiki/display/CAT/Database+Configuration
	FLUSH PRIVILEGES;
	Make sure that INNODB is the default storage engine
		sudo vim /etc/my.cnf
		add line "default-storage-engine=INNODB"
		systemctl restart mysqld
	make DB backup
		mysqldump -u root -p --routines db_name > db_backup.sql
			enter password
		This saves it into the pwd, move it where necessary for backups

NEXT: clone the git repo
	clone git repo
		git clone https://github.com/krishagni/openspecimen.git
		place this in some directory
		Set this as $OS_HOME in .bash_profile (e.g. $HOME/openspecimen)

NEXT: Prepare to deploy OpenSpecimen
	Edit build.properties with the proper information
		app_home = /usr/share/tomcat/
		app_data_dir = <app_data_dir>
		app_log_conf =
		datasource_jndi = java:/comp/env/jdbc/openspecimen
		deployment_type = fresh

		database_type = mysql
		database_host = localhost
		database_port = 3306
		database_name = openspecimen_test_db
		database_username = os_admin
		database_password = OS_admin1

		show_sql = false

		plugin_dir = <path-to-directory-containing-plugin-jars>

	navigate into www/ directory in $OS_HOME
		sudo npm uninstall grunt-contrib-imagemin
		sudo npm cache clean
		sudo npm i --save-dev grunt-contrib-imagemin
		sudo npm install gifsicle@1.0.3
		npm install
		bower install
		grunt build
	change directory to parent (cd ..)
	sudo gradle deploy

NEXT: Edit TOMCAT Conf
	<Resource name="jdbc/openspecimen" auth="Container" type="javax.sql.DataSource"
      maxActive="100" maxIdle="30" maxWait="10000"
      username="os_admin" password="OS_admin1" driverClassName="com.mysql.jdbc.Driver"
      url="jdbc:mysql://localhost:3306>/openspecimen_test_db" />