Database and Web application

InterMine is governed by a properties file located in the $HOME/.intermine named $MINE_NAME.properties. This page describes which values are set in that file.

Example: https://github.com/intermine/intermine/blob/dev/bio/tutorial/malariamine.properties

Database names and locations

The following properties determine the settings for the production database. This database is used by the build system and the webapp.

Property name	Example	Determines
db.production.datasource.serverName	server_name	server name
db.production.datasource.databaseName	malariamine	database name
db.production.datasource.user	postgres_user	database username
db.production.datasource.password	SECRET	database password

The following properties determine the settings for the items database. This database is used during builds only.

Property name	Example	Determines
db.common-tgt-items.datasource.serverName	server_name	server name
db.common-tgt-items.datasource.databaseName	malariamine	database name
db.common-tgt-items.datasource.user	postgres_user	database username
db.common-tgt-items.datasource.password	SECRET	database password

The following properties determine the settings for the user profile database. This database is used by the webapp only. It holds all user related information, including lists, queries and tags.

Property name	Example	Determines
db.userprofile-production.datasource.serverName	server_name	server name
db.userprofile-production.datasource.databaseName	malariamine	database name
db.userprofile-production.datasource.user	postgres_user	database username
db.userprofile-production.datasource.password	SECRET	database password

Web application name and location

Property name	Example	Determines
os.production.verboseQueryLog	true	if true, all queries are logged. Defaults to false
webapp.deploy.url	http://localhost:8080	location of tomcat server
webapp.path	malariamine	location of path of webapp
webapp.manager	TOMCAT_USER	tomcat username, needed to deploy webapp
webapp.password	TOMCAT_PWD	tomcat password, needed to deploy webapp
webapp.baseurl	http://www.flymine.org	home link; used by client side JavaScript AJAX requests
superuser.account	test_user@mail_account	account name for superuser
superuser.initialPassword	secret	password used when account is created
project.standalone	true	run with associated web site. Defaults to false
project.title	MalariaMine	name of mine
project.subTitle	An example of InterMine.bio with data from <i>Plasmodium falciparum</i>	text that appears in the header at the top of the page
project.releaseVersion	tutorial	text that appears at the top of the page next to the mine name
project.sitePrefix	http://www.flymine.org	various URLs use this as the prefix
project.helpLocation	http://www.flymine.org/help	various URLs use this as the prefix

Warning

webapp.baseurl and webapp.path must be correct or else your queries will not run

Email

Emails are sent to users when they create an account, forget their password, or use the contact form.

Property name	Example	Determines
mail.host	localhost	mail host to use
mail.from	account@my_mail_host	“from” email address
mail.subject	Welcome to MalariaMine	“subject” for email send when account created
mail.text	You have successfully created an account on MalariaMine	“body” for email send when account created
feedback.destination	test_user@mail_address	recipient of feedback form located on bottom of every page

This is the normal mailer. There is a different configuration for SMTP.

Multiple versions of a mine

It’s possible to use several properties files by adding a suffix. Here’s an example scenario:

1. add a suffix to the name of your property file:

   • malariamine.properties.dev - points to the development database and a webapp

2. use the -Drelease ant target

# dev is the suffix on the properties filename

# malariamine/integrate
ant build-db -Drelease=dev

# malariamine/webapp
ant default remove-webapp release-webapp -Drelease=dev

Default Intermine properties

In addition to the user properties above, each mine needs two global properties file. These should be in the root directory of the mine - e.g. in the malariamine directory. You should not edit these files.

default.intermine.integrate.properties

used by the loading/integration stage

default.intermine.webapp.properties

used by the intermine webapp code when running inside Tomcat.