Using the admin console, administrators can control many server configuration options via the Site Settings page. During installation of LabKey Server, you have the option to immediately specify site settings, or you may accept defaults and return to customize them later.

  • Select (Admin) > Site > Admin Console.
  • Under Configuration, click Site Settings.


Set Site Administrators

  • Primary site administrator. Use this dropdown to select the primary site administrator. This user must have the Site Administrator role. This dropdown defaults to the first user assigned Site Administrator on the site. LabKey staff may contact this administrator to assist if the server is submitting exception reports or other information that indicates that there is a problem.

URL Settings

  • Base Server URL: Used to create links in emails sent by the system and also the root of Short URLs. The base URL should contain the protocol (http or https), hostname, and port if required. The webapp context path should never be added. Examples: "" or "" (but not "").
  • Use "path first" urls (/home/project-begin.view): See LabKey URLs

Automatically Check for Updates and Report Usage Statistics

Check for updates to LabKey Server and report usage statistics to the LabKey team.

Checking for updates helps ensure that you are running the most recent version of LabKey Server. Reporting anonymous usage statistics helps the LabKey team improve product quality for the features you are using. All data is transmitted securely over SSL.

For a complete list of usage statistics that are reported, see Usage/Exception Reporting.

  • OFF - Do not check for updates or report any usage data.
  • ON - Check for updates and report system information, usage data, and organization details.
At any time, you can click the View button to display the information that would be reported. Note that this is for your information only and no data will be submitted to LabKey when you view this information locally.

Automatically Report Exceptions

Reporting exceptions helps the LabKey team improve product quality. All data is transmitted securely over SSL.

There are three levels of exception reporting available. For a complete list of information reported at each level, see Usage/Exception Reporting.

  • Low level: Include anonymous system and exception information, including the stack trace, build number, server operating system, database name and version, JDBC driver and version, etc.
  • Medium level: All of the above, plus the exception message and URL that triggered it.
  • High level: All of the above, plus the user's email address. The user will be contacted only to ask for help in reproducing the bug, if necessary.
After selecting an exception reporting level, click the View button to display the information that would be reported for the given level (except for the actual stack trace). Note that this is for your information only and no data will be submitted to LabKey when you view this sample.

Reporting exceptions to the local server may help your local team improve product quality. Local reporting is always at the high level described above.

Customize LabKey System Properties

Log memory usage frequency: If you are experiencing OutOfMemoryErrors with your installation, you can enable logging that will help the LabKey development team track down the problem. This will log the memory usage to <CATALINA_HOME>/logs/labkeyMemory.log. This setting is used for debugging, so it is typically disabled and set to 0.

Maximum file size, in bytes, to allow in database BLOBs: LabKey Server stores some file uploads as BLOBs in the database. These include attachments to wikis, issues, and messages. This setting establishes a maximum file size to be stored as a BLOB. Users are directed to upload larger files using other means, which are persisted in the file system itself.

Require ExtJS v3.4.1 to be loaded on each page: Optional.

Require ExtJS v3.x based Client API be loaded on each page: Optional.

The above options to load ExtJS v3 on each page are provided to support legacy applications which rely on Ext3 without explicitly declaring this dependency. The performance impact on LabKey Server may be substantial. See Dependencies on Ext3 for more information.

Configure Security

Require SSL connections: Specifies that users may connect to your LabKey site only via SSL (that is, via the https protocol). Learn more here: Installation: Tomcat Configuration

SSL port: Specifies the port over which users can access your LabKey site over SSL. The standard default port for SSL is 443. Note that this differs from the Tomcat default port, which is 8443. Set this value to correspond to the SSL port number you have specified in the <tomcat-home>/conf/server.xml file. Learn more about configuring SSL here: Installation: Tomcat Configuration.

Configure API Keys

Allow API Keys: Enable to make API keys (i.e. tokens) available to logged in users for use in APIs. This enables client code to perform operations under a logged in user's identification without requiring passwords or other credentials to appear in said code. See API Keys for more details.

Expire API Keys: Configure how long-lived any API keys generated will be. Options include:

    • Never
    • 7 days
    • 30 days
    • 90 days
    • 365 days
Allow session keys: Enable to make available API keys which are attached only to the user's current logged-in session. See Compliant Access via Session Key for more details.

Note: You can choose to independently enable either API Keys or Session Keys or enable both simultaneously.

Configure Pipeline Settings

Pipeline tools. A list of directories on the web server which contain the executables that are run for pipeline jobs. The list separator is ; (semicolon) or : (colon) on a Mac. It should include the directories where your TPP and XTandem files reside. The appropriate directory will entered automatically in this field the first time you run a schema upgrade and the web server finds it blank.

Ribbon Bar Message

Display Message: whether to display the message defined in Message HTML in a bar at the top of each page.

Admin-only Mode

Admin only mode: If checked, only site admins can log into this LabKey Server installation.

Message to users when site is in admin-only mode: Specifies the message that is displayed to users when this site is in admin-only mode. Wiki formatting is allowed in this message.

HTTP Security Settings


Controls whether or not a browser may render a server page in a <frame> , <iframe> or <object>.

  • Same Origin - Pages may only be rendered in a frame when the frame is in the same domain.
  • Allow - Pages may be rendered in a frame in all circumstances.

CSRF Checking

Note: Beginning with release 19.1, CSRF (Cross Site Request Forgery) Checking is no longer a configurable option. CSRF enforcement is applied to all POST requests. For details see: Cross-Site Request Forgery (CSRF) Protection

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