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/biotestmine/blob/master/data/biotestmine.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 | biotestmine | 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 | biotestmine | 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 | biotestmine | 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 | biotestmine | 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 | biotestmine | 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 biotestmine | “subject” for email send when account created |
| mail.text | You have successfully created an account on BioTestMine | “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:
add a suffix to the name of your property file:
- biotestmine.properties.dev - points to the development database and a webapp
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