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Update Server Passwords and Database Connection Details

This document describes the steps required to update the Clarity LIMS application configuration.

Two levels of user passwords are created in the Clarity LIMS system: one at the operating system level and one at the Clarity LIMS level.

Following are details on the user passwords, instructions for changing them, and instructions for updating Clarity LIMS with the new database connection details.

The following steps are only required if the passwords for glsftp and/or apiuser have been changed.

Update Operating System User Passwords

The user passwords created at the operating system level are for the glsai, glsjboss, and glsftp users.

  • glsai and glsjboss users:

    • These users have no configuration associated with them.

    • You may change their passwords at any time.

  • glsftp user:

    • After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util tool.

To change the glsftp password after installing Clarity LIMS, using SecretUtil:

  1. Change the glsftp user's password on the server.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh stop

  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update the password in the secret store.

    • For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.

    • For file-based secret storage, use Secret Management Util to update the password as follows:

      $ java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -u="new-password" app.ftp.password

  6. Start Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh start

Update Clarity LIMS User Passwords

The user passwords created at the Clarity LIMS level are for the admin, facility, and apiuser users.

  • admin and facility users:

    • These users have no configuration associated with them.

    • You may change their passwords at any time.

  • apiuser user:

    • After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util.

To change the apiuser password after installing Clarity LIMS:

  1. Check for any remote Automation Workers, and take note of their locations in your network. You will need to restart these after changing the password.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update the password in the secret store

    • For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.

    • For file-based secret storage, use Secret Management Util to update the password as follows:

  6. Start Clarity LIMS using the following command:

Update Database Connection Details

In some circumstances (such as security breaches/compromises), the database connection details (eg, database password) are updated, which prevents Clarity LIMS from connecting to the database. You can correct this issue by updating Clarity LIMS with the new database connection details as follows.

  1. Check for any remote Automation Workers.

  2. Update the existing tenant with the new details.

  3. Restart any Automation Workers.

To update database connection details:

  1. Check for any remote Automation Workers, and take note of their locations in your network.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update existing tenant with new details.

    • For vault-based secret storage, use either the Vault CLI or Vault UI to update the password.

    • For file-based secret storage, use the Secret Management Util to update the database password as the root user.

  6. Start Clarity LIMS using the following command:

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