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:
Connect to the API, using the OriginatingProcessURI.
Retrieve the OriginatingProcessXML and store it in a variable.
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.
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