Renaming Samples to Add an Internal ID
When a lab takes in samples, they are named by the lab scientist who supplies them. As such, samples may be named in any way imaginable. Conversely, the research facilities processing the samples often have strict naming conventions.
When these two situations occur, there is a need for the sample to renamed with the strict nomenclature of the processing lab. However, in order for the final data to be meaningful for the scientist who supplied the samples, the original name must also be retained.
In this example, the attached script may be used to rename samples, while retaining their original names in a separate field.
The original name of the sample is saved in a user-defined field (UDF) called Customer's Sample Name, .
The Sample Name for the submitted sample is overwritten, using the specific naming convention of the customer.
It is recommended that the script be launched by a process/protocol step as early as possible in the sample lifecycle.
The script is invoked with just three parameters:
An example of the full syntax to invoke the script is as follows:
Once the command-line parameters have been harvested, and the API object set up ready to handle API requests, the renameSamples() method is called.
This method implements the following pseudo code:
Assumptions and Notes
Both of the attached files are placed on the Clarity LIMS server, in the /opt/gls/clarity/customextensions folder.
A user defined field, named Customer's Sample Name has been created at the analyte (sample) level.
The Customer's Sample Name field is visible within the LabLink Collaborations Interface.
renameSamples.py: