Install/Upgrade Secret Management for Integration Modules

This section describes the installation steps required for installing Secret Utility and integration packages.

As of Clarity LIMS v5.4, the method used for managing passwords (secrets) for Clarity LIMS integration modules has changed.

The following diagram shows the installation steps required for installing Secret Utility and integration packages with Clarity LIMS v5.4 and later.

For details on Compatibility of Releases with Integration Modules, see Integration > Compatibility.

1. Install Clarity LIMS v6.3.

   • Install Clarity LIMS-App 6.3 and complete pending script.

   • Secret Utility (secretutil) is installed as part of Clarity LIMS-App 6.3 dependency, and the Secret Utility configuration is part of Clarity LIMS pending scripts.

2. Install Secret Utility.

   • In the automated installation tooling for Clarity LIMS v6.3, the installation and configuration of Secret Utility is included. No further action is necessary.

   • For manual installation:

     1. Install Clarity LIMS-SecretUtil.

     2. Configure Secret Utility by running the following script:

        /opt/gls/clarity/config/pending/05_configure_claritylims_secretutil.sh.

        Refer to Guide to Secret Management for details on configuring Secret Utility.

3. Check usage of custom API username.

   • Check for any needs for custom API username, if any (eg novaseq_user). The documentation for the integration package provides the requirements for API username.

     NOTE: In a typical installation, a default API username (apiuser) is used. It is not necessary to add the default apiuser username, because it is configured as part of Clarity LIMS v6.3 installation. If no custom API username is required, skip step 4 and proceed to step 5.

4. Configure custom API username.

   • If a custom API username is not required, proceed to step 5.

   • If a custom API username is required, configure the user/password with Secret Utility as follows. Substitute the values enclosed in double quotes with your own values, keeping the double quotes.

     java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="password" "key"

     Example:

     java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="mypassword" "apiusers/novaseq_user"

   • For a custom api username, set the key to apiusers/{custom api username}

5. Install integration package.

   There is no change to the installation of the integration package. Follow existing installation instructions.

   NOTE:

   The new configuration script in the new integration package retrieves passwords directly from Secret Utility.

   For BSSH access token, follow the existing setup guide. There is no change in the configuration step.