Version: 5.0.0

InterMine Properties

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


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 nameExampleDetermines
db.production.datasource.serverNameserver_nameserver name
db.production.datasource.databaseNamebiotestminedatabase name
db.production.datasource.userpostgres_userdatabase username
db.production.datasource.passwordSECRETdatabase password

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

Property nameExampleDetermines
db.common-tgt-items.datasource.serverNameserver_nameserver name
db.common-tgt-items.datasource.databaseNamebiotestminedatabase name
db.common-tgt-items.datasource.userpostgres_userdatabase username
db.common-tgt-items.datasource.passwordSECRETdatabase 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 nameExampleDetermines
db.userprofile-production.datasource.serverNameserver_nameserver name
db.userprofile-production.datasource.databaseNamebiotestminedatabase name
db.userprofile-production.datasource.userpostgres_userdatabase username
db.userprofile-production.datasource.passwordSECRETdatabase password

Web application name and location#

Property nameExampleDetermines
os.production.verboseQueryLogtrueif true, all queries are logged. Defaults to false
webapp.deploy.urlhttp://localhost:8080location of tomcat server
webapp.hostnamelocalhostname of host
webapp.pathbiotestminelocation of path of webapp
webapp.managerTOMCAT_USERtomcat username, needed to deploy webapp
webapp.passwordTOMCAT_PWDtomcat password, needed to deploy webapp
webapp.baseurlhttp://www.flymine.orghome link; used by client side JavaScript AJAX requests
superuser.accounttest_user@mail_accountaccount name for superuser
superuser.initialPasswordsecretpassword used when account is created
project.standalonetruerun with associated web site. Defaults to false
project.titlebiotestminename of mine
project.subTitleAn example of with data from <i>Plasmodium falciparum</i>text that appears in the header at the top of the page
project.releaseVersiontutorialtext that appears at the top of the page next to the mine name
project.sitePrefixhttp://www.flymine.orgvarious URLs use this as the prefix
project.helpLocation URLs use this as the prefix

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


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

Property nameExampleDetermines
mail.hostlocalhostmail host to use
mail.fromaccount@my_mail_host“from” email address
mail.subjectWelcome to biotestmine“subject” for email sent when account is created
mail.textYou have successfully created an account on BioTestMine“body” for email sent when account is created
feedback.destinationtest_user@mail_addressrecipient of feedback form located at the 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: - points to the development database and a webapp

  2. Use -Dorg.gradle.project.release=dev

    # dev is the suffix on the properties filename

    # build the database specified in dev properties file
    ./gradlew builddb -Dorg.gradle.project.release=dev
    # deploy the webapp specified in dev properties file
    ./gradlew cargoReDeployRemote -Dorg.gradle.project.release=dev