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In cases where an external web application authenticates a user and redirects to a LabKey Server instance, you can use the API loginApi.api.

In its simplest form you can post JSON like the following to login-loginApi.api:

{
email: "myemail@test.test",
password: "xxxxxxx"
}

The response JSON will indicate success or failure, and provide helpful details in the success case.

A more complex use case is shown by the default LabKey login page, and its handler JS file below:

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