Generating a Hierarchical Sample History

Often, workflows do not have a linear configuration. Even in those cases, samples progressing through workflows may be re-queued, replicated, or submitted into a number of parallel workflows.

Attempts to align downstream results with submitted samples may get hindered when trying to account for sample replicates or the dynamic decisions made in the lab.

A visual representation of a samples complete history presented in a clear hierarchical format allows for a digestible report of the work done on the sample. This format provides at-a-glance understanding of the any of the branching or re-queuing of a sample.

Solution

This example describes a python script which, given an artifact, recursively finds all the processes for which that artifact was an input, then finds all the associated output artifacts of that process. This continues for all processes all the way down to the most downstream artifact.

A clear visual representation of the entire history of work on a sample, similar to what was available in the Ops interface, can allow a user to see all the processes and derivations of a sample. This is especially of use for troublesome samples that have branched into numerous downstream replicates which may end up in the same or different sequencing protocol.

Parameters

The script accepts the following parameters:

-a

The LIMSID of the artifact (Required)

-u

The username of the current user (Required)

-p

The password of the current user (Required)

-s

The API steps URI {stepURI:v2}. (Required)

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

bash -l -c "/usr/bin/python /opt/gls/clarity/customextensions/sample_history.py -a DAN2A4PA1 -s {stepURI:v2} -u {username} -p {password}"

Script output example:

Sibling artifacts will appear aligned vertically with the same indentation. In the above example, 122-1650 Library Pooling (MiSeq) 5.0 created two replicate Analytes, 2-4110 and 2-4111. Analyte 2-4111 was the input to the subsequent step ( 24-1952 ) and no additional work was performed on 2-4110.

Processes performed on an artifact will appear underneath with a tab indentation. In the above example, the first 4 processes ( 3 QC processes and Fragment DNA ) are all using the Root Analyte (CRA201A1PA1) as an input.

Adding Colours with termcolor

Install package termcolor for colour printing support. Entity colours can be configured within the script. Globally turn off colours by changing the variable use_colours to False ( line 16 ).

Assumptions and Notes

Your configuration conforms with the script's requirements, as documented in Solution.
You are running a version of Python that is supported by Clarity LIMS, as documented in the Clarity LIMS Technical Requirements.
The glsapiutil.py file is placed in the working directory.
The example code is provided for illustrative purposes only. It does not contain sufficient exception handling for use 'as is' in a production environment.