Automation Execution Environment

As of BaseSpace Clarity LIMS v5.0, several terms have been deprecated:

• External Program Integration Plug-in (EPP) has been replaced with automation

• EPP/AI node has been replaced with automation worker / AW node

• Parameter has been replaced with token

• User defined field (UDF) has been replaced with custom field

When a job is dispatched to the AI node/automation worker, the following steps occur:

1. A temporary working directory is created on the AI node / automation worker:

   • In AIInstallDirectory/temp/

   • With a unique name including the client process LIMS ID.

2. The command configured and selected as part of the step run in the LIMS is then sent to the AI node / automation worker, with any specified parameters / tokens replaced with actual values.

3. The command is executed on the AI node / automation worker, spawning step execution using the temporary working directory as the working directory context.

   • Script processing can use stdout, stderr, and return codes following standard shell programming packages.

4. When the script exits, the AI node/automation worker automatically retrieves any files with matching LIMS IDs from the temporary working directory. The files are attached to the appropriate output file placeholders.

How the API Infrastructure is Used

The automation API infrastructure can be used alone or with the REST API infrastructure.

For example:

• Simple scripts can use automation parameters/tokens and data files directly from the current working directory. They can write results back to the current working directory, associating them back to the relevant placeholders in Clarity LIMS.

• More advanced scripts can also use the REST API infrastructure to retrieve additional required information and place relevant data back into UDFs/custom fields. Advanced scripts can also attach and associate data files to placeholders, which may be in different locations, while the script is still running.