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LabKey Server supports SAML (Security Assertion Markup Language) authentication, acting as a service provider to authenticate against a SAML 2.0 identity provider. You can configure LabKey Server to authenticate against a single SAML identity provider (IdP). LabKey Server supports either plain text or encrypted assertion responses from the SAML identity provider. Note that nameId attribute in the assertion must match the email address in the user's LabKey Server account.

SAML Terminology

  • IdP: Identity Provider. The authenticating SAML server. This may be software (Shibboleth and OpenAM are two open source software IdPs), or hardware (e.g., an F5 BigIp appliance with the APM module). This will be connected to a user store, frequently an LDAP server.
  • SP: Service Provider. The application or server requesting authentication.
  • SAML Request: The request sent to the IdP to attempt to authenticate the user.
  • SAML Response: The response back from the IdP that the user was authenticated. A request contains an assertion about the user. The assertion contains one or more attributes about the user. At very least the nameId attribute is included, which is what identifies the user.

How SAML Authentication Works

From a LabKey sign in page, or next to the Sign In link in the upper right, a user clicks the admin-configured "SAML" logo. LabKey generates a SAML request, and redirects the user's browser to the identity provider's SSO URL with the request attached. If a given SAML identity provider is configured as the default, the user will bypass the sign in page and go directly to the identity provider.

The identity provider (IdP) presents the user with its authentication challenge. This is typically in the form of a login screen, but more sophisticated systems might use biometrics, authentication dongles, or other two-factor authentication mechanisms.

If the IdP verifies the user against its user store, a signed SAML response is generated, and redirects the browser back to LabKey Server with the response attached.

LabKey Server then verifies the signature of the response, decrypts the assertion if it was optionally encrypted, and verifies the email address from the nameId attribute. At this point, the user is considered authenticated with LabKey Server and directed to the server home page (or to whatever page the user was originally attempting to reach).

Auto Create Authenticated Users

If a user is authenticated by the SAML server but does not already have an account on the LabKey Server, the system can create one automatically. This is enabled by default but can be disabled using a checkbox in the global settings of the authentication page.

Set Up Steps

Before you begin, ensure that you can log in using standard database configuration (i.e. that you have not disabled this default login mechanism). You may need it to recover if you make a configuration error.

Step 1: First, you will set up your SAML Identity Provider and obtain an IdP signing certificate, and provide other details including the full ACS URL where the login will redirect for authentication. This URL is composed of these elements:

  • The base server URL, sometimes also referred to as the "Entity" or the "Identifier".
  • The "configuration" parameter which must match the configuration on LabKey Server. This parameter is an incrementing integer (beginning at 1). Unless you know that you have already configured other SAML configurations on LabKey, you will start by using "1".
Make your best guess at what this full ACS URL will be and provide it on your IdP. For example, using the information in the screen image below, the full ACS URL would be:

Depending on your IdP, you may have various requirements or terms for the same URLs, such as "Reply URL", "Sign-on URL", "Destination URL", and/or "Recipient URL". All of these that are required must include the "/saml-validate.view?configuration=#" with the correct parameter value.

Step 2: Next, you will log in to LabKey Server and create the SAML Authentication Configuration as described before, using the certificate you obtained in step 1, and other required details. When you save this configuration, you should immediately reopen it for editing (before logging out) in order to confirm that all the ACS URL components, especially the configuration parameter, match what you provided to your IdP in step 1 above.

Step 3: If the configuration parameters do not match, you must go back to your SAML Identity Provider and edit the configuration there, so that the ACS URL matches the one shown in the LabKey configuration panel.

Upgrade Note for Switching to a Root Deployment

Upgrade note: When upgrading to use embedded Tomcat, we strongly recommend that you deploy LabKey at the root. If you were previously using a configuration file named "labkey.xml", you will have been using a "labkey" context path. This was previously part of the ACS URL but will now be removed. You'll need to update the configuration of your SAML Identity Provider to remove the "labkey" context path so that the ACS URL matches the one now shown in the upgraded LabKey Server's configuration panel.

Create a New SAML Authentication Configuration

  • Go to (Admin) > Site > Admin Console.
  • In the Configuration section, click Authentication.
  • On the Primary tab of the Configurations panel, select Add New Primary Configuration > SAML...
  • In the popup, configure the properties as described below.
  • Click Finish to save.

You can create multiple SAML configurations on the same server.

Note that the configuration settings make use of the encrypted property store, so in order to configure/use SAML, an Encryption Key must be set in the file. If a key is not set, attempting to go to the SAML configuration screen displays an error message, directing the administrator to fix the configuration.

Configure the properties for SAML authentication:

  • Configuration Status: Click the Enabled slider to toggle whether this configuration is active.
  • Description: Provide a unique description of this provider.
  • IdP Signing Certificate (Required): Either drag and drop or click to select a pem file.
  • Encryption Certificate (Optional): The encryption certificate for the service provider (SP). Use this field and the SP Private Key field (below) if you want the assertion in the SAML response to be encrypted. These two fields work together: they either must both be set, or neither should be set.
  • SP Private Key (Optional): The private key for the service provider (SP). Use this field and the Encryption Certificate field (above) if you want the assertion in the SAML response to be encrypted. These two fields work together: they either must both be set, or neither should be set.
  • IdP SSO URL (Required): The target IdP (identity provider) URL for SSO authentication, where the SAML identity provider is found.
  • Issuer URL: The issuer of the service provider SAML metadata. Some IdP configurations require this, some do not. If required, it's probably the base URL for the LabKey Server instance.
  • NameID Format (Optional): This is the NameIdformat specified in the SAML request. Options are:
    • Email Address (Default)
    • Transient
    • Unspecified
  • Force Authorization: If checked, require the user to login again via IdP, even if they are already logged in via an SSO provider.
  • Default to this SAML Identity Provider: Check the box to redirect the login page directly to this SAML identity provider instead of requiring the user to click on a logo first.
  • Validate XML Responses: We strongly recommend validating XML responses from the IdP. Uncheck this only if your network infrastructure blocks the server's access to
  • Associated Email Domain: Email domain that indicates which users are expected to authenticate using this configuration. For example, if set to '', all users who enter are presumed to authenticate using this configuration. This is often left blank, but if provided, LabKey will suggest this authentication method to users with the specified domain if they fail an authentication attempt using a different configuration. LabKey will also not create database logins when administrators add user accounts with this email domain.
  • Page Header Logo / Login Page Logo: Provide a logo image to use in the page header or on the login page, or both.
    • These logos will be presented as quick links to access your authentication system.
    • Learn more about logo fields for Single Sign-On authentication here: Single Sign-On Logos.
  • Click Finish in the popup to save.

EntityId / entity_id (Base Server URL)

Note that the Base Server URL is included in the SAML request as the EntityId / entity_id. To control the Base Server URL, use the "Customize Site page" link in the UI or:

  • Go to (Admin) > Site > Admin Console.
  • Under Configuration, click Site Settings.
  • On the Customize Site page, change the Base Server URL as necessary.
Note that changing this setting will affect links in emails sent by the server, as well as any short URLs you generate. For details see Site Settings.

Assertion Customer Service (ACS) URL

The ACS URL you'll provide in the LabKey Server configuration UI must match that expected by the SAML Identity Provider.

It is a combination of the base server EntityID, a possible "/labkey" context-path, and "saml-validate.view?configuration=" followed by a "configuration" parameter that will be supplied for you when you save.

  • When you first create a SAML configuration, the word "configuration" is shown as the value of this parameter, but it will be replaced with an integer upon save.
  • Immediately after saving, edit the configuration to see the final URL and the configuration parameter value that was assigned.
  • Your SAML identity provider must be configured to redirect to this URL at the end of the authentication process.
If when you configured your SAML Identity Provider, you provided a different configuration parameter, you must now go back and edit that on the IdP so that the ACS URL is the same in both places. This may need to be defined in multiple places, such as "Reply URL", "Sign-on URL", "Destination URL", and/or "Recipient URL".

Edit an Existing SAML Configuration

  • Go to (Admin) > Site > Admin Console.
  • In the Configuration section, click Authentication.
  • Click the (pencil) next to the target SAML configuration to edit the configuration.
  • After making changes, click Apply in the popup, then Save and Finish to exit the authentication page.


Configuration ID

If you see a message similar to "Unable to validate authentication. SAML configuration id not found." you may be able to work around it by clearing cookies in your browser.

If that is not effective, log into your LabKey Server directly (via standard database authentication), and check the SAML configuration page. Edit the configuration to see the configuration parameter supplied for the ACS URL field, as well as the Base Server URL. Configure your SAML identity provider to include this parameter in whichever URLs your IdP requires, such as "Reply URL", "Sign-on URL", "Destination URL", and/or "Recipient URL".

Using SAML with Load Balancers

If you are using a Load Balancer (e.g. AWS Application Load Balancer, Nginx, Apache, etc), you may need to edit your server.xml file to configure the expected ports.

For instance, if the load balancer is configured to work on port 443, but in your server.port is set to use 8080, you'd need to update that setting to 443 so it matches your load balancer.

SAML Functionality Not Currently Supported

  • Metadata generation - LabKey Server supports only static service provider metadata xml.
  • Metadata discovery - LabKey Server does not query an IdP for its metadata, nor does the server respond to requests for its service provider metadata.
If your IdP requires Service Provider XML Metadata, you can generate the XML using a tool such as:
  • Federation participation is not supported.
  • More complex scenarios for combinations of encrypted or signed requests, responses, assertions, and attributes are not supported. For example, signed assertions with individually encrypted attributes.
  • Processing other attributes about the user. For example, sometimes a role or permissions are given in the assertion; LabKey Server ignores these if present.
  • Interaction with an independent service provider is not supported.
  • Single logout (SLO)

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