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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.hostname localhost name of host
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.