Routing Output Artifacts to Specific Workflows/Stages

This example provides the user with the opportunity to route samples individually to the HiSeq, MiSeq, or both stages from the Record Details screen.

Step configuration

The step is configured to display two checkbox analyte UDFs / derived sample custom fields. The fields are used to select the destination workflow/stages for each derived sample. You can choose to queue the sample for HiSeq, MiSeq, or both.

In this example, you select the following:

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Two samples to be queued for HiSeq

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Two samples for MiSeq

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Two that are not routed

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Two samples for both HiSeq and MiSeq

Parameters

The script accepts the following parameters:

-u	The username of the current user (Required)
-p	The password of the current user (Required)
-s	The URI of the step that launches the script - the {stepURI:v2} token (Required)

An example of the full syntax to invoke the script is as follows:

bash -c "/usr/bin/python /opt/gls/clarity/customextensions/Route_to_HiSeq_MiSeq.py -u {username} -p {password} -s {stepURI:v2}"

On the Record Details screen, you use the analyte UDF / derived sample custom field checkboxes to decide which workflow/stage combination to send each derived sample.

The first important piece of information required is the URI of the destination stage.

A stage URI can change across LIMS instances (such as switching from Dev to Prod). Therefore, the script gathers the stage URI from the workflow and stage name. This process occurs even when the workflows are identical.

The main method in the script is routeAnalytes. This method in turn carries out several operations:

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Gathers the information for the process / master step that triggered the script, including output analytes.

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For each analyte, evaluates which UDFs / custom fields have been set, and adds the analyte to a list of analytes to route.

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Creates the XML message for each stage.

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Does a POST to the REST API to add the analytes to the queue in Clarity LIMS.

Modifications

This script can be modified to look for a process level UDF (master step custom field). Modified in this way, all outputs from the step would be routed to the same step.

This example also serves to demonstrate a more general concept. Routing artifacts is valuable in any situation where a sample must be queued for a stage outside of the usual order of a workflow. This routing approach is valuable even when routing newly submitted samples to the first stage in a workflow.

For more information on using the artifact/route endpoint, refer to the REST API Reference, available from the API Portal.

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You are running a version of Python supported by BaseSpace Clarity LIMS. For details, refer to the Technical Requirements provided in the Clarity LIMS Core Functionality documentation section.

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The attached file is placed on the Clarity LIMS server, in the /opt/gls/clarity/customextensions folder.

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The Python API Library (glsapiutil.py) is placed on the Clarity LIMS server, in the /opt/gls/clarity/customextensions folder. You can download the latest glsapiutil library from Illumina GitHub.

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The example code is provided for illustrative purposes only. The example code does not contain sufficient exception handling for use 'as is' in a production environment.

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Samples can be inadvertently duplicated in the next step. This duplication occurs if:

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The sample is being routed at the last step of a protocol and;

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If the action of next steps is Mark Protocol as Complete.

This duplication is due to:

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The next step is routing the artifact to its default destination and;

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The script is routing the same artifact.

The solution here is to set the default next steps action to Remove from Workflow instead. This solution can be automated using Lab Logic Toolkit or the API.

Route_to_HiSeq_MiSeq.py.txt