# Authenticating and Authorizing Users via Keycloak

⚠️ This documentation is for keycloak <v20, see related ticket ⚠️

# Introduction

The cBioPortal includes support for Keycloak authentication. Keycloak can function as an Identity Provider (IDP) for cBioPortal. This document explains why you might find Keycloak authentication useful for storing your user login information outside the cBioPortal database. It also shows you how to configure Keycloak to communicate with your instance of cBioPortal using SAML (Security Assertion Markup Language).

Please note that configuring your local instance to use Keycloak authentication requires a Keycloak server to be set up. For details on how to set up a Keycloak server, please read online document at https://www.keycloak.org/guides#server.

This document focuses mainly on the steps to configure Keycloak for authenticating cBioPortal users.

To skip to the authorization section see: authorization with Keycloak. Or continue reading to learn how to integrate Keycloak with cBioPortal.

# Why Keycloak?

Keycloak is an open source identity and access management solution. It has a built-in RDBM system to store login information. It can help build a security layer on top of the cBioPortal web application.

Keycloak boils down to three simple terms:

  • realm: A realm secures and manages security metadata for a set of users, application, and registered auth clients.
  • client: Clients are entities that can request authentication of a user within a realm.
  • role: Roles identify a type or category of user. Keycloak often assigns access and permissions to specific roles rather than individual users for a fine-grained access control.

Keycloak offers three types of roles:

  • Realm-level roles are in global namespace shared by all clients.
  • Client roles have basically a namespace dedicated to a client.
  • A composite role is a role that has one or more additional roles associated with it.

# How does Keycloak SAML Authentication work?

Keycloak supports both OpenID-Connect and SAML authentication. When you use SAML authentication, the Keycloak server exchanges XML documents with a web application. XML signatures and encryption are then used to verify requests from the application.

# Configure Keycloak to authenticate your cbioportal instance

  1. Log in to your Keycloak Identity Provider, e.g. http://localhost:8080/auth, as an admin user. ⚠️ when setting this up on something else than localhost (e.g. production), you will need to use/enable https on your Keycloak server. For simplicity, the rest of the documentation below continues on http://localhost.
  2. Hover over the top-left–corner drop down menu (titled ‘Master’) to create a new realm.
    Please note if you are logged in the master realm, this drop-down menu lists all the realms created. The last entry of this drop-down menu is always Add Realm. Click this to add a realm. Then type 'cbioportal' in the name field and click the Create button.
  3. To create a SAML client, go to the Clients item in the left menu. On this page, click the Create button on the right. This will bring you to the Add Client page.
    • Enter a Client ID for the client, e.g. 'cbioportal', this will be the expected issuer value in SAML requests sent by the application.
    • Select saml in the Client Protocol drop down box.
    • Enter http://localhost:8081/saml in the Client SAML Endpoint textbox, this is the URL that the Keycloak server will send SAML requests and responses to. Then click the Save button; this will take you to the client page below.

  1. Choose email as your Name ID Format.
  2. Next, enter a pattern for Valid Redirect URIs that Keycloak can use upon a successful authentication, e.g. http://localhost:8081/*. ℹ️ notice that you can add multiple URLs in this field. You could use this in some cases to support the URLs with and without port (e.g. if tomcat is running on port 80 and you want to allow both http://localhost:80/* and http://localhost/* as redirect URLs).
  3. Set Force POST Binding and Front Channel Logout to OFF and Force Name ID Format to ON.
  4. Expand the subsection Fine Grain SAML Endpoint Configuration and set Logout Service POST Binding URL to http://localhost:8081/saml/logout.
  5. Leave everything else as it is and click Save.

# Map SAML Assertion Attributes

To specify attributes included in the SAML assertion, simply click on the Mappers tab, and add mappers using the Add Builtin and Create buttons. Make sure you add at least:

  • the built-in User Property mapper named X500 email and
  • a Role list-type attribute (keep the default word Role as its Role attribute name).
  • a User Property-type attribute with the name username. Use username for the attributes Property, Name, and SAML Attribute Name.

Edit the email attribute to use the word email as the SAML Attribute Name.

Finally, head to the Scope tab for the client and switch off Full Scope Allowed, to ensure that only those roles relevant to a particular cBioPortal instance are listed in assertions sent to the instance, and not any other roles tracked in Keycloak.

# Export configuration for cBioPortal

There are two known ways to download the keycloak configuration (aka IDP SSO Descriptor) file for cBioPortal.

# I. Download via link

The file can be fetched by the following url:


For example:

curl -o client-tailored-saml-idp-metadata.xml "http://localhost:8081/auth/realms/cbioportal/protocol/saml/descriptor"

Note: if you use https protocol with self-signed protocol you need to add --insecure option to the above curl command.

# II. Export via GUI (legacy)

  1. Next, navigate to the Installation tab for the same client.
  2. Select SAML Metadata IDPSSODescriptor as the Format Option and click the Download button. ⚠️ This GUI option has been removed from the newer versions of Keycloak.

After you've downloaded the XML file with one of the above ways, move it to portal/src/main/resources/ if you're compiling cBioPortal yourself or if you're using the Docker container, mount the file in the /cbioportal-webapp folder with -v /path/to/client-tailored-saml-idp-metadata.xml:/cbioportal-webapp/WEB-INF/classes/client-tailored-saml-idp-metadata.xml.

# Create a signing key for cBioPortal

Use the Java 'keytool' command to generate keystore, as described here on the page about SAML in cBioPortal:

keytool -genkey -alias secure-key -keyalg RSA -keystore samlKeystore.jks

Important: The validity of this keystore is 90 days. You can change the default value by adding the -validity parameter and the number of days (e.g. -validity 200 for 200 days). If the keystore expires, then 'invalid requester' errors are thrown.

Install the generated JKS file to portal/src/main/resources/ if you're compiling cBioPortal yourself or if you're using the Docker container, mount the file in the /cbioportal-webapp folder with -v /path/to/samlKeystore.jks:/cbioportal-webapp/WEB-INF/classes/samlKeystore.jks.

Import the key's certificate into Keycloak, so that Keycloak knows that it can trust the holder of this key. To do that, head to the SAML Keys tab in the keycloak admin screen about the cbioportal client and:

  1. Click the Import button.
  2. Select the JKS archive format.
  3. Specify the key alias secure-key.
  4. Type the store password apollo1 (not the private key password, as Keycloak only needs to know the certificate)
  5. Select the file you just installed.

Important: Keycloak may not give an indication of successful completion, but when navigating to the SAML Keys tab again you should now see the certificate and no private key.

# Modifying configuration

  1. Within the application.properties file , make sure that this line is present:
  1. Then, modify the properties under the comment # authentication. In particular, see the options listed in the example below:
    # global logout (as opposed to local logout):

# Obtain user identities

# Optional: create users in Keycloak

To create a user, click on Users in the left menu bar. This menu option brings you to the user list page. On the right side of the empty user list, you should see an Add User button. Click that to start creating your new user.

# Optional: integrate company-wide authentication services

Keycloak can read credentials from existing user databases, for instance over LDAP. This is referred to as user federation. Keycloak can also allow authentication by an external login form altogether using a protocol such as SAML, it calls this identity brokering. In either case, Keycloak acts as a proxy between your user directory and cBioPortal, deciding which authorities to grant when telling cBioPortal that the user has authenticated.

Please refer to the Keycloak documentation on user federation and identity brokering for more information on how to integrate Keycloak with your local LDAP or SAML service.

# Federate LDAP/AD user directories

Some notes on user federation using LDAP/Active Directory:

By specifying the Vendor of your LDAP server, Keycloak will choose sensible defaults for the required objectClasses and attributes of your user entries. Apart from the Dedicated Name of the tree in which to search for users and the DN and password that Keycloak should use to bind to the server, make sure to specify the following Custom User LDAP Filter to ensure that only user entries that have an email address are considered:


When using LDAP to load users from your institute's user directory, you will most likely want Keycloak to refrain from trying to synchronise changes in user details back to the central directory. You should set Edit Mode to READ_ONLY, as the alternative UNSYNCED would mean that users can be changed in the Keycloak database once imported from LDAP, and start diverging. Also disable Sync Registrations unless you want Keycloak to add new users to the LDAP store.

Do turn on Import Users to make Keycloak remember users after the first login, if you want to be able to assign non-default roles. If the LDAP tree holding your users is large and you do not want to import all users into Keycloak, make sure to disable Periodic Full Sync and Periodic Changed Users Sync.

# Authorization with Keycloak

# Create roles to authorize cBioPortal users

The roles you assign to users will be used to tell cBioPortal which studies a user is allowed to see.

To create a role, head to the Roles tab that is displayed along the top while configuring the cbioportal client – this tab is not the link of the same name in the left sidebar. Click the Add Role button. Enter a name (e.g. brca_tcga_pub) and description for the role and hit the Save button.

Note: if filter_groups_by_appname is set to false as specified above, the Role Name has to match with an id of the study you would give access to by assigning this role. Otherwise, if filter_groups_by_appname is set to true (DEFAULT), you have to add the application name (app.name) followed by the colon as a prefix to the study id. e.g. cbioportal:brca_tcga_pub

# Groups

Keycloak allows you to create Groups for easy mapping of multiple studies to multiple users. One can, for example, make a Keycloak group with name PUBLIC_STUDIES and add all the individual Keycloak roles corresponding to public studies to this group. It is also possible to configure a group to be "default" in Keycloak, meaning new users are automatically added to this group when logging in for the first time.

Alternatively, the Keycloak roles can correspond to the groups specified in the metadata files of studies instead of corresponding to individual study identifiers. Although this will result in less roles that need to be added and maintained in Keycloak, it does result in group configuration being spread over both Keycloak and meta study files.

# Assign roles to users

Next, assign roles to users. Head to Users in the left sidebar, find a user (users from external providers should be known to Keycloak after they have logged in for the first time), click the ID and open the Role Mappings tab for that user. Select the cbioportal client in the dropdown under Client Roles, and use the Available Roles selection and its Add selected button to assign client roles to this user.

To automatically assign roles to all users when Keycloak first sees them, the Roles pane accessed from the left sidebar has a Default Roles tab. The interface for assigning roles here is much the same as the one for assigning roles to individual users.

# Doing a Test Run

Rebuild the WAR file and follow the Deployment with authentication steps using authenticate=saml.

Then, go to: http://localhost:8081/.

If all goes well, the following should happen:

  • You will be redirected to the Keycloak Login Page.
  • After authenticating, you will be redirected back to your local instance of cBioPortal.

If this does not happen, see the Troubleshooting Tips below.

# Add client for OAuth2 token-based data access

With cBioPortal instances that require user authentication the API can be queried when including a data access token in the request header (see Authenticating Users via Tokens). KeyCloak can be configured as an OAuth2 authentication provider that distributes data access tokens to users and validates these tokens when used while querying the API. This feature is enabled by creating a cbioportal_api OpenID Connect client that has access to the user roles defined in the cbioportal SAML client.

The step below were verified to work with Keycloak versions 4.8.3.Final and 8.0.2.

  1. Create a client with name cbioportal_api. Set Client Protocol to openid-connect.

  1. On the configuration page of cbioportal_api client apply the following settings:

# Settings tab

parameter value comment
Access Type confidential
Standard Flow Enabled ON (default value)
Enabled ON (default value)
Consent Required OFF (default value)
Client Protocol openid-connect (default value)
Access Type confidential (default value)
Standard Flow Enabled ON (default value)
Implicit Flow Enabled OFF (default value)
Direct Access Grants Enabled OFF
Service Accounts Enabled OFF (default value)
Authorization Enabled OFF (default value)
Valid Redirect URIs url/api/data-access-token/oauth2 url refers to base url of cBioPortal instance

# Credentials tab

Select Client Id and Secret. Take notice of the value of Secret the secret field. This secret should be added to application.properties file of the cBioPortal backend.

parameter value comment
Client Authenticator Client Id and Secret (default value)

# Client Scopes tab

Keep only scopes roles and offline_access (remove all others).

# Mapper tab

Create a new Audience mapper with name cbioportal_api_audience. This value will be used by the cBioPortal backend during validation of access tokens.

parameter value comment
Name cbioportal_api_audience
Mapper Type Audience
Included Client Audience cbioportal_api
Add to ID token OFF (default value)
Add to access token ON (default value)

# Scope tab

Enable Full Scope. This setting will include the user roles defined in the cbioportal SAML client in access tokens distributed by the cbioportal_api client.

parameter value comment
Full Scope Allowed ON (default value)

  1. Add these parameters to application.properties of the cBioPortal backend.
parameter value comment
dat.method oauth2
dat.oauth2.clientId cbioportal_api
dat.oauth2.clientSecret ? see Secret field in the Credentials tab
dat.oauth2.accessTokenUri keycloak_url/auth/realms/cbioportal/protocol/openid-connect/token keycloak_url refers to URL of the KeyCloak server from perspective of the cBioPortal instance
dat.oauth2.jwkUrl keycloak_url/auth/realms/cbioportal/protocol/openid-connect/certs keycloak_url refers to URL of the KeyCloak server from perspective of the cBioPortal instance
dat.oauth2.issuer keycloak_url/auth/realms/cbioportal keycloak_url refers to URL of the KeyCloak server from perspective of the browser
dat.oauth2.userAuthorizationUri keycloak_url/auth/realms/cbioportal/protocol/openid-connect/auth keycloak_url refers to URL of the KeyCloak server from perspective of the browser
dat.oauth2.redirectUri cbioportal_url/api/data-access-token/oauth2 cbioportal_url is url up to /api path
dat.oauth2.jwtRolesPath '::'-separated path to array with user roles in JWT token returned by Keycloak example: resource_access::cbioportal::roles

More information on configuration of the cBioPortal backend can be found in Authenticating Users via Tokens.

# Troubleshooting

# Logging

Getting this to work requires many steps, and can be a bit tricky. If you get stuck or get an obscure error message, your best bet is to turn on all DEBUG logging. This can be done via src/main/resources/logback.xml. See logback.DEBUG.EXAMPLE.xml file for an example of how to configure debug levels for cbioportal.

Then, rebuild the WAR, redeploy, and try to authenticate again. Your log file will then include hundreds of SAML-specific messages, even the full XML of each SAML message, and this should help you debug the error.

If you're using the Docker container, mount the file instead with -v ./logback.xml:/cbioportal-webapp/WEB-INF/classes/logback.xml.

# Determining jwtRolesPath for OAuth2 Token

By default user-roles are extracted from path resource_access::cbioportal::roles in the JWT json. Changes to the configuration of roles at the realm and client level in Keycloak instance can alter this path and must be set acordingly with the dat.oauth2.jwtRolesPath property in the application.properties file.

To check the the roles path, go into the Client Scopes tab inside KeyCloak. Enter the Evaluate section, select a test user, and click Evaluate. In the section below, select the Generated Access Token tab to examine the JWT structure.

A sample JWT might look like this:

  "exp": 1234567891,
  "iat": 1234567892,
  "jti": "transient-id",
  "iss": "issuer",
  "sub": "subject",
  "typ": "Bearer",
  "session_state": "sessionstate",
  "acr": "1",
  "realm_access": {
    "roles": [
  "scope": "openid"

The jwtRolesPath in this case would be realm_access::roles. Double check this against the jwtRolesPath value set in application.properties.