Automation Triggers and Command Line Calls

As of BaseSpace Clarity LIMS v5, the Operations Interface Java client, which is used by administrators to configure processes, consumables, user-defined fields, and users, has been deprecated. All configuration and administration tasks are now executed in the Clarity LIMS web interface.

In addition, several terms have been deprecated:

• External Program Integration Plug-in (EPP) has been replaced with automation.
• EPP/Automated Informatics (AI) node has been replaced with automation worker/AW node.
• Parameter has been replaced with token.

Use step automations to trigger a command-line call on a process/step or a file attachment event. The steps required differ depending on the LIMS version.

This article provides an overview of the steps required to configure automations and automation triggers. For detailed version-specific instructions, see the following documentation:

• Clarity LIMS v5: Add and Configure Automations
• Clarity LIMS v4.2 and earlier: Configuring Protocol Steps
1. On the main menu bar, select Configuration, then select the Automation tab.
2. On the Automation configuration screen on the Step Automation tab, add a new automation:
• Name the automation.
• Set the channel name.
• Define the command line.
• Enable the automation on the desired steps.
3. On the Master Step Settings or Step Settings screen of the related step, set the following:
• Trigger Location—The stage at which the script it is to be initiated (beginning of step, end of step, on entry to/exit from a screen, etc.).
• Trigger Style—How the script is to be initiated (automatically or manually when the user selects a button in the interface).

When running processes and protocol steps, note the following details:

• In the Clarity LIMS Operations Interface, processes are run on samples (analytes) or files.
• In the Clarity LIMS web interface, steps are run on samples only.

As of Clarity LIMS v5, the Operations Interface Java client has been deprecated.

1. In the Operations Interface, Select Configuration > Processes > Process Types and select the desired process.
2. On the External Programs tab, select the Process is associated with an external program checkbox, then add a new process parameter:
• Name the parameter.
• Set the channel name.
• Set the trigger mode (the default PostProcess trigger mode is recommended, see the following note).
• Define the command-line call.

While it is possible to set the trigger mode to PostProcess after each file attachment event, this mode is not supported in the Clarity LIMS web interface. As a result, it is not recommended. For details, see Advanced Mode: Multiple Triggers on Process Updates Including Each Input File Attachment .

3. In the Clarity LIMS web interface in the configuration area, modify the configuration of the step associated with the process previously configured. On the Automation tab, set the following:
• Behavior—How the script is to be initiated.
• Stage of Step—The stage at which the script it is to be initiated.
• Timing—When the script is initiated.

In the Operations Interface, a client process can be run on empty file placeholders many hours or days before that data is available. The client automatically dispatches and triggers the process completion event when the data becomes available.

When configuring a process, the trigger mode is controlled by the option chosen in the Add Process Parameter dialog, specifically the Trigger Mode drop-down list. There are two options to choose from:

• PostProcess (default mode)
• PostProcess after each file attachment event (advanced mode)

This mode is enabled when the PostProcess option is selected. This option is the default mode.

For event timing, consider the following details:

1. LIMS web interface:
• When running a step on samples, trigger the script by selecting a button in the interface. The script must be able to handle multiple invocations because users may select the button more than one time.
2. Operations interface:
• A process/step with sample artifact inputs that triggers the script after process/step completes.
• A process with file artifact inputs that triggers the script when all empty file placeholders have been populated with attached input files.
• A process run on previously populated file placeholders that triggers the script after a process/step completes.
• In this mode, the automation can transfer input files to the working directory for processing. Files created by the script in the temporary directory can be automatically attached to the output file placeholders.

This mode is enabled when the PostProcess after each file attachment event option is selected. This mode is the advanced, or verbose, mode.

• The PostProcess after each file attachment event mode is only supported in the Operations Interface. It is for advanced users, because the scripts triggered require more complexity.
• The Run each time a file attachment event occurs advanced mode requires REST. This mode requires the script to transfer files and limits the command-line parameter strings. The REST process, artifact, and file resources are used with this trigger.

For event timing, consider the following details:

• A process with sample artifact inputs triggers the completion event after a process completes.
• A process with file artifact inputs triggers each time a file placeholder is populated with an attached input file.
• The last input file attachment is the final trigger event. No other triggers fire after all file placeholders are populated, even if a file is later deleted and reimported or other process modifications occur.
• A process run on previously populated file placeholders triggers the completion event after a process/protocol step completes.

When attaching output files, consider the following information:

As there are many events being handled by the script in this mode, no assumptions are made about when to transfer input or output files. Therefore, no automatic attachment of output files is available in this mode.

Use the REST API to attach files (see Attach a File to a File Placeholder with REST for more information).

For more information, see API Training Videos.