Update and refactor pooling map EPP

[Karl-Svard]

Changed

• Added pool sorting to the pooling map
• Changed the color set
• Added new flag, -r/ --round-decimals for determining the amount of rounding
• Made the coloring truly container specific, and not pool-container as was before

Steps to consider while deploying

• Configuration changes:
• Documentation updates:
• Inform users by email:

Review:

• Code approved by
• Tests executed on stage by: (Document the test done with screen shots and description.)
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[Karl-Svard]

Example output generated from step https://cg-lims-stage.sys.scilifelab.se/clarity/work-details/553687

Old TWIST pooling script:

New script on the same TWIST step:

Note: The placement of the sample and pooling values are determined by the order in which they are added to the CLI

[Karl-Svard]

The command used to generate the TWIST pooling maps:

lims -c  <config path> epps -l <log path> -p <process ID> files pool-map -f <file name> -pu 'Volume H2O (ul)' -pu 'Total Amount (ng)' -pu 'Total Volume (ul)' -su 'Volume of sample (ul)' -su 'Amount taken (ng)' -su 'Amount (ng)' -r 2

The changes introduced shouldn't affect the syntax of the covid pooling map. So already configured EPPs will work out of the box

[AbiDalby]

Looks great!

[Karl-Svard]

The "Make TWIST pooling Map" EPP has been updated as well.

From:

bash -c "/home/glsai/miniconda3/envs/epp_master/bin/make_twist_pooling_map.py --pid {processLuid} --res {compoundOutputFileLuid1}"

To:

bash -c -l "conda activate cg_lims &&  lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} files pool-map -f  {compoundOutputFileLuid1} -pu 'Total Amount (ng)' -pu 'Total Volume (ul)' -pu 'Volume H2O (ul)' -su 'Volume of sample (ul)' -su 'Amount taken (ng)' -su 'Amount (ng)' -r 2"