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.

Recommendations

• 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.

Proposed solution

• 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, and so it is saved in a sample UDF.

The following pseudo code 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:

   • Rename the SampleName to a desired name (see Recommendations section, above).

   • Finally, PUT the Sample XML back.