Standardizing Sample Naming via the API

A lab may receive samples submitted from various sources. This can pose a problem with regards to sample names.There may be duplicate sample names, and/or various name formats, all of which make it hard for lab scientists to recognize a sample.

Clarity LIMS programmers often rename all incoming samples to a certain naming convention.

This section provides an example to address this problem.

• When accepting a project and its samples, the receiving lab scientist runs a Clarity LIMS step named Receive Samples.
• The underlying Receive Samples process type/master step is configured with analyte (sample) inputs and no analyte outputs.
• A shared result file output is configured to capture logging from the script.
• The sample name could be a derivative of the Sample LIMSID with a prefix:
– Because the LIMSID is guaranteed to be unique, this approach mitigates any need to maintain an external sequence of numbers.
– The Sample LIMSID is derived from the Project LIMSID, which is configurable.
• The Receive Samples process is configured to trigger a script that renames the samples that are input to the process.
• This trigger also passes the OriginatingProcessURI to the script. This example assumes that the original submitted sample name must be preserved, so it is saved in a sample UDF.

The following pseudocode shows how one might implement the sample renaming script:

1. Connect to the API, using the OriginatingProcessURI.
2. Retrieve the OriginatingProcessXML and store it in a variable.
3. Iterate through the inputoutput map of the OriginatingProcessXML and for each InputArtifact:
• GET the InputArtifactURI and store the input ArtifactXML in a variable.
• From this ArtifactXML, GET the SourceSampleXML and store it in another variable.
• Modify the SourceSampleXML. To do this modification, copy the original SampleName to an OriginalSampleNameUDF.
• Rename the SampleName to a desired name (see Recommendations).
• Finally, PUT the Sample XML back.