Version: 4.0.0


The file configures several attributes for the InterMine web application.


Used to configure hyperlinks, generally to external dbs. See External Links below


Text present in the list upload form. See List upload examples below


Redirects links in query results. See Link redirects


See Galaxy


See Region Search


Links at upper right corner


Will populate meta tag for keywords


Will populate meta tag for description. Google uses this in their search results, I think


Populates the "Cite" text in the footer.


The message to show when a user arrives at the webapp via the portal action (eg. <something>/


Text displayed in search box


Colour scheme for the webapp. Available options are blue, bright_blue, gold, green, grey, brown, ecoli_blue, metabolic, modmine, ratmine and purple


Used to configure hyperlinks for CrossReferences. See below


Used to enable structured data in JSON-LD format in InterMine web pages. Available options are true or false


These parameters are returned by the branding API end point, and are used by external applications, e.g. the InterMine iOS app, the InterMine registry and the InterMine R client.

branding.images.logoThis image should be 45px by 45px
branding.colors.header.mainMain colour for your mine, defaults to grey, #595455
branding.colors.header.textText colour for your mine, defaults to white, #fff

Home page#

Search box (first box on the left)

begin.searchBox.titletitle of box on left
begin.searchBox.descriptiontext in the box on the left
begin.searchBox.exampletext in the form field

List upload box (middle box)

begin.listBox.titleTitle of box
begin.listBox.descriptionText in box
bag.example.identifiersText in form field

Third box

begin.thirdBox.titleTitle of box if user is new
begin.thirdBox.visitedTitleTitle of box if user has visited before
begin.thirdBox.descriptionText in box
begin.thirdBox.linkTitleText for large button
begin.thirdBox.linkURL for large button


Templates tagged with each category will appear under the appropriate tab.

begin.tabs.1.idName of category, eg. Genes
begin.tabs.1.descriptionText for that tab

List upload examples#

Using the bag.example.identifiers key, one can provide a list of keyword examples on the list create/upload page. This could lead to a mixed list of items being updated and only, say Protein or Gene, identifiers being uploaded.

External links#

You can add links to other websites by adding entries to the file.

The format for this property is:

# on the report page - a single identifier
'attributelink' + unique_name + class + taxonId + attributeName + (url|imageName|text)
# on the list analysis page - a list of identifiers
'attributelink' + unique_name + class + taxonId + attributeName + 'list' + (url|imageName|text)


Used to distinguish between multiple configurations for the same attribute/organism/class combination


Class of object to link, eg. Protein


Either a proper id or '*' when no assumption is made regarding the organism


Which identifier field to pass to the URL, e.g. if attributeName is primaryIdentifier, the value of primary identifier field will be used as the attribute value


Indicates the link will have a list of identifiers


URL to link to


Name of logo (optional), must be in /model directory


Text that will appear next to the logo

The value of the attribute (for the current object) is substituted anywhere the string "<<attributeValue>>" occurs in the text or the URL

For example:

attributelink.flybase.Gene.7227.primaryIdentifier.text=FlyBase: <<attributeValue>>

In this case Gene pages for Drosophila melanogaster will have a link that uses the organismDbId field.

A list example:


Only if a taxonId is specified, the code will check if the link to the external db is relevant.

Settings for the xrefLink property#

You can configure the URLs for querying CrossReference from external sources by adding entries to the file.

The format for this property is:

# on the report page
'xreflink' + dataSource_name + (url|imageName)


The name of the external database


URL to link to


Name of logo (optional), must be in /model directory

For example:


Cross references represent identifiers used in external databases, eg. FlyBase, UniProt. An object in InterMine which has CrossReference will have an identifier and data source for that cross reference. In order to find the cross reference in that data source, a URL is required to link to, and the full path should look like url+identifier, e.g. ''''. In, the first part of the full path could be configured as in "url", and identifier will be added programmatically to the rear of it. The dataSource_name should be consistent with the source name of the CrossReferences in the InterMine database.

OpenAuth2 Settings (aka. OpenID Connect)#

You can configure your mine to accept delegated authentication from one or more identity resources which are protected by OAuth2 authentication. This involves sending the user to another site, having them sign in there, and being sent back to your InterMine with their credentials.

We are using the Apache OLTU library to help manage the authentication flow. This means that configuring some of the more common providers, such as Google, Facebook, Github and Microsoft is very simple. It also allows us to add any identity provider that meets certain minimum sanity requirements.

Warning Google has closed down their OpenID-2 based authentication solution in favour of OpenID Connect (OAuth2). If you want to use Google as an authentication provider you must use OAuth2.

Configuration is managed through adding values to the web-properties.

Registering your Application.#

You must register your application with the provider, giving them details of your application such as its name, and where it will be located. This varies from provider to provider - see this tutorial for a good guide to the registration process for a number of popular providers. For example, for Google, you will need a Google+ account and to visit the Google developer's console to create an application.

For ELIXIR, you will need:

  1. an ELIXIR identity. Please register the ELIXIR ID here , if you don't already

    have it

  2. register the new client here, using the Self-service client registration page.

  3. send an email to in order to receive a form that you have to complete with additional information

For each application you will need to register the callback URI, which looks like:


Where webapp.baseurl and webapp.path are the corresponding values from your configuration, and PROVIDER is the name of the provider in all uppercase letters (as configured below). Google requires the provider parameter as part of the URI, but other providers do not - you should check with each of them.

You will probably be asked to register a JavaScript domain. This is not used by us, but you can enter the webapp.baseurl.

Enabling Supported Providers#

You will need to inform the InterMine system of the names of the providers which have been configured to work with your application. This should be a comma separated list of provider names. The values are case insensitive, and will be processed as upper-case values. E.g.:

# in ~/.intermine/
# You can list just a single provider:
oauth2.providers = GOOGLE
# or multiple providers, combining standard and custom providers:

Configuring OLTU Supported Providers#

To configure an OLTU supported provider (such as Github or Facebook), you simply need to define the client-id and client-secret you registered your application with, eg:

Warning All secrets, including these ones (especially the client-secret) MUST not be committed to version control or made publicly accessible. DO NOT add them to your file, but instead, add them to your file (eg. ~/.intermine/

# ~/.intermine/
oauth2.GITHUB.client-id = $GH-CLIENT-ID
oauth2.GITHUB.client-secret = $GH-CLIENT-SECRET

Configuring a Custom Provider#

To configure a custom provider, some other properties need to be provided. Taking AIP's araport system as an example, this can be configured thusly:

# All OAuth2 clients need this configution. Do not commit to version control!
oauth2.AIP.client-id = YOUR_CLIENT_ID
oauth2.AIP.client-secret = YOUR_CLIENT_SECRET

The URLs needed by the flow - contact your provider to find these out:

oauth2.AIP.url.auth =
oauth2.AIP.url.token =

The scopes need to access the identity resource. This should include sufficient levels of permission to access the name and email of the authenticating user.

oauth2.AIP.scopes = PRODUCTION

Information about the way the token endpoint functions. If the token endpoint expects parameters to be passed in the query-string use the value "QUERY", and if the endpoint expects the parameters to be passed in the message body provide the value "BODY":

oauth2.AIP.messageformat = BODY

Information about the way the token endpoint responds. If the token endpoint responds with JSON, then provide the value "JSON", and if the endpoint responds with url-encoded form-data, then provide the value "FORM"

oauth2.AIP.responsetype = JSON

Information about the way the identity resource operates. If the resource expects the bearer token to be in the query parameters, provide the value "query", and if the bearer token is expected to be in the Authorization header, pass the value "header".

oauth2.AIP.resource-auth-mechanism = header

The location of the identity resource. This must be a resource that can respond with JSON. If query parameters are needed they should be included in the URL. An Accept header will be provided with the value application/json.

oauth2.AIP.identity-resource =

Guides to interpreting the response from the identity resource. These are all optional.

# Provide a value if the identity is within a message envelope. The value is the
# key of the envelope.
oauth2.AIP.identity-envelope = result
# Provide a key to access a unique identifier for the user. Default = id = uid
# Provide a key to access the user's email. Default = email = email
# Provide a key to access the user's name. May be a composite value (comma separated). Default = name = first_name,last_name

Delegated Authentication with JWTs#

InterMine supports completely automated delegated authentication, whereby a mediator may add a token that authenticates the user according to a chain of trust. This uses public-key cryptography to establish trust, and JWTs to transmit assertions.

Note All the configuration in this section can (and should) go in your ~/.intermine/ file.

To enable this feature you need to do a couple of things:

Create a Key Store [optional]#

InterMine needs access to public keys - this can mean creating a JKS key store ( with the certificate used to sign the JWTs - you should store the certificate against the alias with the same name as used in the iss claim in the JWT. The keystore file should be saved as keystore.jks.$release in the ~/.intermine directory, or moved as part of your release cycle to MINE/resources/webapp/WEB-INF/ immediately prior to building your webapp.

If you do this, then you need to provide the following configuration:

security.keystore.passwordThe password for this keystore.

If your keystore has no password, then you do not need to set that property. See below for a quick guide to creating a valid keystore.

Provide Public Keys in your properties files [optional]#

Instead of (or in addition to) creating a keystore, you can also provide keys in property files. Even though these are public keys, they are best included in your ~/.intermine/ file, since they will be specific to a particular instance. Internally if you do not provide a keystore, an empty one will be created.

This is done by listing them as follows:


You can provide multiple keys and they will all be stored in the applications key-store under the given alias. Every key must have an alias, even if there is only one. If there is a problem with the key (it cannot be decoded, it is not valid, etc) it will be skipped by default, unless the following property is set to true (in which case it will throw an error and prevent your web-application from starting):

keystore.strictpublickeydecodingtrue or false

The value BASE64_ENCODED_PUBLIC_KEY is the base64 encoding of the bytes of public key. Below is a sample program to illustrate how to do this in Java and python respectively:

import org.apache.commons.codec.binary.Base64;
public class EncodeKey {
public static void main(String... args) throws Exception {
PublicKey key = getKey();
Base64 encoder = new Base64();
KeyPairGenerator keyGen = KeyPairGenerator.getInstance("RSA");
private static PublicKey getKey() {
// Generating a random key - provide your own of course.
return keyGen.generateKeyPair().getPublic();


# using pycrypto
from Crypto.PublicKey import RSA
from Crypto import Random
# Generate a new random public key.
random =
pair = RSA.generate(1024,
public_key = pair.publickey()
print(base64.encodestring(public_key.exportKey(format = 'DER')))

Selecting keys at runtime.#

Since this feature relies on public key cryptography, you need to tell the InterMine application which keys to use to verify which JWT tokens. This can be done with the following properties:

jwt.verification.strategyNAMED_ALIAS (default), ANY, or WHITELIST - optional

This property defaults to the most secure option, NAMED_ALIAS, where only keys associated with the issuer of the token will be used to verify it. This means you will need to link the two. Each token must identify its issuer (with the iss claim), you can map from that value to a key available to InterMine by providing the alias it is available as in the keystore. If you plan on accepting your own tokens, then you can provide the alias of your private key.

security.keystore.alias.$issThe alias for the key certificate used to sign the JWT.

If you use the WHITELIST strategy, then you must provide the list of aliases that can be used to verify JWTs. All of them will be tried until one verifies successfully.

jwt.alias.whitelistThe comma separated list of aliases to use.

If you select the ANY strategy, no further configuration is needed.

Multiple issuers can be supported by providing a key for each alias.

Managing non-standard claims#

InterMine reads to claims about the end user from the JWT - who it identifies, and their email address. The email claim is non-standard, and needs to be configured. The subject claim can be overridden if the JWT tokens you are receiving have their subject identified in a different claim. To do so provide the following properties (in the following table, $iss is the value of the iss claim of the token):$issThe name of the claim that provides the email of the subject. Defaults to
jwt.key.sub.$issThe name of the claim that provides the identity of the subject. This should be unique for each issuer. Not needed if the token provides the sub claim

Other properties#

The following properties may also be important

jwt.publicidentityUsed as the iss claim on any tokens the application issues itself. Also, if the tokens received include an aud claim (see aud definition) then this value must match that value for verification to complete. Defaults to your project title.
jwt.verifyaudiencetrue or false (default = true). Whether to verify the aud claim.
security.privatekey.passwordUsed to gain access to the private key used by the application for signing its own tokens.
security.privatekey.aliasUsed to retrieve the private key used by the application for signing its own tokens. To provide a private key you must configure a key store.

Checking your configuration#

An ant task is provided to make checking this (admittedly rather complex) set-up easier. To make use of it you should configure your keys as for production, acquire a valid JWT representative of one of the ones you expect to encounter in production, enter you webapp directory ($MINE/webapp) and then call the following ant task:

ant verify-jwt \
-Drelease=$RELEASE \ # Needed to read the correct properties file

If correctly set up, you should get a message printed to the console telling you who the token identifies.

Setting up the Key-Store#

You will need a Java Key Store to use public-key cryptography for security. To get started, you can use the following command to generate a keystore.jks file with a new public/private key-pair:

keytool -genkey -alias ALIAS_A -keyalg RSA -keystore keystore.jks -keysize 2048

The following command will allow you to add a certificate to your key-store:

keytool -import -trustcacerts -alias ALIAS_B -file B.crt -keystore keystore.jks

This set-up would allow you to start accepting JWT tokens signed by the owner of B.crt, which could be configured by making sure they are associated in your property files. So if the owner of B.crt identified themselves with the iss (issuer) claim, then you could link the certificate to the claim with the following property:

security.keystore.alias. = ALIAS_B

Overriding properties#

  • intermine/webapp/main/resources/webapp/WEB-INF/ -

    used by all mines. Properties set here will be available to everyone, even the test model mine.

  • bio/webapp/resources/webapp/WEB-INF/ -

    used by all bio-mines. Properties set here will be available to all mines that use the bio layer. So, not the test model. Can overwrite properties in the file.

  • flymine/webapp/resources/ - used by a mine. Properties set here will be available to only that specific mine. Can create mine-specific properties or overwrite properties in the above two files.

  • $HOME/.intermine/ - used by a mine. Properties set here will be available only to that specific mine, and will override all other properties. Put sensitive values here that should not be committed to version control.