Automations (formerly referred to as EPP triggers or automation actions) allow lab scientists to invoke scripts as part of their workflow. These scripts must successfully complete for the lab scientist to proceed to the next step of the workflow.
EPP automation/support is compatible with API v2 r21 and above.
The API documentation includes the terms External Program Integration Plug-in (EPP) and EPP node.
As of BaseSpace Clarity LIMS v5.0, these terms are deprecated. The term EPP has been replaced with automation. EPP node is referred to as the Automation Worker or Automation Worker node. These components are used to trigger and run scripts, typically after lab activities are recorded in the LIMS.
Automations have various uses, including the following:
Workflow enforcement—Makes sure that samples only enter valid protocol steps.
Business logic enforcement—Validates that samples are approved by accounting before work is done on them. This automation can also make sure that selected samples are worked on together.
Automatic file generation—Automates the creation of driver files, sample sheets, or other files specific to your protocol and instrumentation.
Notification—Notifies external systems of lab progress. For example, you can notify Accounting of completed projects so that they can then bill for services rendered.
Configuration
You can enable automations on master steps in two configuration areas of Clarity LIMS:
On the Automations tab, when adding or configuring an automation. For more information, see #add-and-configure-automations.
After it is enabled on a master step, the automation becomes available for use on all steps derived from that master step.
You can configure the automation trigger on the master step, or on the steps derived from that master step.
Script Messages
Progress Message
While executing a script, if more than one script would be triggered for a single user action, they are reported in sequence. This reporting continues until all scripts complete, or one of them fails.
An example scenario would be a step that is configured to execute the following:
One script upon exit of the Placement screen.
A second script upon entry of the Record Details screen.
In this scenario, when the lab scientist advances their protocol step from the Placement screen to the Record Details screen, the scripts are executed in sequence.
The parameter string/automation name configured on the master step is displayed in a progress message. You can use this feature by giving your parameter strings/automations meaningful names that provide you with context about what the script is doing. The following is an example of a progress message.
You cannot proceed until the script completes successfully.
Non-Responsive Scripts Message
You can request to cancel a script that is not responsive. While canceling abandons the monitoring of script execution, it does not stop the execution of the script.
After canceling a script, follow up with the Clarity LIMS administrator to determine if the AI node/automation worker must be restarted.
Non-Blocking Success and Warning Message
The scientific programmers in your facility can provide you with a message upon successful execution of a script. There are two possible non-fatal messages: OK and WARNING. These messages can be set using the step program status REST API endpoint.
Message boxes display the script name, followed by a message that is set by the script using the step program status REST API endpoint. Line breaks are permitted in the custom message. The following is an example of a success message:
After you select OK, you are permitted to proceed in the workflow.
Blocking Script Failure Message
When a script fails, a message box displays. There are two ways to produce fatal messages:
By using the step program status REST API endpoint (informing FAILURE as the status)
By generating output to the console and returning a non-zero exit code
For example, when beginning a step, if the script does not allow you to work on the samples together in Ice Bucket, the samples will be returned to Ice Bucket after acknowledging the error message. In this case, the step is prevented from being tracked. The following is an example of a failure message:
If you attempt to advance a step from the Pooling screen, but an error is detected, the error state prevents you from continuing. The following is an example of this type of message:
After you select OK, you are prevented from proceeding in the workflow. Instead, you must return to the Pooling screen and address the problem before proceeding.
