Requeue Samples
Derived sample automations are automations that users can run on derived samples directly from the Projects Dashboard in Clarity LIMS.
The following example uses an automation to initiate a script that requeues samples to an earlier step in the workflow. The example also describes the main functions included in the script and demonstrates the configuration options that prompt the user for input. These options allow for greater flexibility during script runs. Before you follow the example, make sure that you have the following items:
A project containing samples assigned to a multi-stage workflow.
Samples that must be requeued. These samples must have completed at least one step in the workflow and must be available for requeue.
The purpose of the attached RequeueSamples.groovy script is to requeue selected derived samples to a previous step in the workflow with the derived sample automations feature.
Step 1. Get Sample Nodes
The getSampleNodes function is passed a list of derived sample LIMS IDs (as a command-line argument) to build a list containing the XML representations of the samples. The resulting sample URI list can then be used with a batchGET to return the sample nodes:
Step 2. Retrieve Workflow and Stage URIs
To retrieve the workflow name, you can URL encode the workflow name and use the result to query and retrieve the workflow URI:
The stage names are guaranteed to be unique for each workflow. However, they may not be unique in the Clarity LIMS system. As a result, the stage URI cannot be queried for in the same way as the workflow URI.
Instead, you can navigate through the workflow node to find the stage that matches the stage name specified using the getStageURI function. If a match is found, return the stage URI.
Step 3. Verify Each Sample Meets the Requeue Criteria
Next, you must make sure that each sample meets the criteria to be requeued using the canRequeue function. The following method checks all workflow stages for the samples:
If a match is found between a workflow stage URI and the stage URI specified, the sample node is added to a list of samples that can be requeued using the requeueList function.
If all the samples have this match and a status that allows for requeue, the list is returned. Otherwise, the script exits with an error message that states the first sample to cause failure.
Step 4. Check and Retrieve Workflow Stage for Sample Node
In this example, both unassignment from and assignment to a workflow stage must occur to complete the requeue. As the samples are requeuing to a previous stage in the workflow and can currently be queued for another stage, you must remove them from these queues.
The getCurrentStageURI and lastStageRun functions check the sample node for its most recent workflow stage. If the node is in a queued status, it returns that stage URI to be unassigned.
Step 5. Build the XML Assignment
Using the previous methods and their results, the following code uses Streaming Markup Builder and the assignmentXML function to build the XML to be posted:
The returned XML node is then posted using httpPOST.
Configuring and Running the Automation
Add and configure the automation
In Clarity LIMS, under Configuration, select the Automation tab.
Select the Derived Sample Automation tab.
Select New Automation and enter the following information:
Run the automation as follows.
Open the Projects Dashboard.
Select a project containing in-progress samples. Select In-progress samples.
In the sample list, you will see all of the submitted and derived samples that are currently in progress for this project.
In this example, the –w and -t {userinput} options invoke a dialog box on automation trigger. The user is required to enter two parameters: the full name of the stage and the workflow for which selected samples are to be requeued. The names must be enclosed in quotation marks.
Expected Output and Results
If the requeue is successful, each requeued sample is marked with a complete tag. Hovering over a sample shows a more detailed message.
RequeueSamples.groovy:
