Work with the Steps Pooling Endpoint
Pooling steps require that each input analyte artifact (derived sample) in the step be inserted into a pool. You can automate this task by using the API steps pooling endpoint. Automation of pooling allows you to reduce error and user interaction with Clarity LIMS.
In this example, a script pools samples based on the value of the pool id user-defined field (UDF)/custom field of the artifact.
As of Clarity LIMS v5, the term user-defined field (UDF) has been replaced with custom field in the user interface. However, the API resource is still called UDF.
Master step fields—Configured on master steps. Master step fields only apply to the following:
The master step on which the fields are configured.
The steps derived from those master steps.
Global fields—Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.
To keep this example simple, the script does not handle samples with reagent labels.
Before you follow the example, make sure that you have the following items:
A configured analyte UDF/derived-sample custom field named pool id in Clarity LIMS.
Groovy that is installed on the server and accessible at /opt/groovy/bin/groovy
The GLSRestApiUtils.groovy file is stored in /opt/groovy/lib/
Step 1. Add Master Step, Protocol, and Library Pooling Step
In Clarity LIMS, under Configuration, select the Lab Work tab.
Select an existing Pooling master step or add a new one.
On the master step configuration form, select the Pooling milestone.
Step 2. Configure Step Automation and Trigger
In Clarity LIMS, under Configuration, select the Automation tab.
Add a new step automation. Associate the automation with the WorkingWithStepsPoolingEndpoint.groovy script. The command line used in this example is as follows.
bash -c "/opt/groovy/bin/groovy -cp /opt/groovy/lib /opt/gls/clarity/customextensions/WorkingWithStepsPoolingEndpoint.groovy -u {username} -p {password} -s {stepURI:v2:http}"
Step 3. Configure Protocol and Add Pool ID Step
In Clarity LIMS, under Configuration, select the Lab Work tab.
Select the pooling protocol containing the Library Pooling step.
Add the Add Pool ID step that sets the pool id custom field of the samples. Move this step to the top of the Steps list.
Step 4. Create Workflow and Add Samples
In Clarity LIMS, under Configuration, select the Lab Work tab.
Create a workflow containing the configured pooling protocol. Activate the workflow.
On the Projects and Samples screen, create a project and add samples to it. Assign the samples to your pooling workflow.
Step 5. Run Samples Through the Steps
Begin working on the samples. In the first step, enter values into the pool id custom field.
Continue to the Library Pooling step and add samples to the Ice Bucket. Select Begin Work to execute the script.
How the script works
The script is passed the URI of the pooling step. Then, using the URI, the pool node of the step is retrieved. This node contains an available-inputs node that lists the URIs of the available input artifacts.
The script retrieves all available input artifacts, and then iterates through the list of retrieved artifacts. For each artifact, the script looks for the pool id custom field. If the field is not found, the script moves on to the next artifact. If the field is found, its value is stored in the poolID variable.
When the script encounters a new pool ID, it creates a new pool with a name equal to that ID. Input artifacts are sorted into pools based on the value of its pool id field, and as they are inserted into pools they are removed from the list of available inputs.
After all of the available inputs are iterated through, the updated pool node is sent back to Clarity LIMS:
Expected Output and Results
Artifacts with the same Pool ID UDF / custom field will be automatically added to the same pool.
WorkingWithStepsPoolingEndpoint.groovy:
GLSRestApiUtils.groovy:
