Add low volume warning to aliquot volume EPP

[Karl-Svard]

Connected to the feature request in issue #435

Added

• New exception for low volumes, LowVolumeError
• New Click option for minimum volume threshold, minimum_volume

Changed

• Restructured aliquot_volume.py EPP

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]

Tests on stage

Test with some samples missing UDFs

Test with some samples having aliquots below the given threshold

Test with all samples passing the threshold check

Summary

The scripts passed all tests and the resulting aliquots are identical to those calculated by the previous script

[idalindegaard]

Bra jobbat!👏💯

[Karl-Svard]

Current usage of the script in prod:

INFO:cg_lims.scripts.check_config:Button: Calculate Volume
INFO:cg_lims.scripts.check_config:Bash string: bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}  udf calculate aliquot-volume --concentration-udf 'Concentration' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)' --amount-ng-udf 'Amount needed (ng)'"
INFO:cg_lims.scripts.check_config:Processes: [('1357', 'Aliquot samples for enzymatic fragmentation TWIST v2')] 

INFO:cg_lims.scripts.check_config:Button: Calculate Aliquotation Volume from Average concentration (ng/ul) Saphyr
INFO:cg_lims.scripts.check_config:Bash string: bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}   udf calculate aliquot-volume --concentration-udf 'Initial Concentration (ng/ul)' --amount-ng-udf 'Amount needed (ng)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)'"
INFO:cg_lims.scripts.check_config:Processes: [('1909', 'Labelling & Staining (Saphyr)')] 

Current usage of script in stage

INFO:cg_lims.scripts.check_config:Button: Calculate Volume
INFO:cg_lims.scripts.check_config:Bash string: bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}  udf calculate aliquot-volume --concentration-udf 'Concentration' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)' --amount-ng-udf 'Amount needed (ng)' --min-volume 1"
INFO:cg_lims.scripts.check_config:Processes: [('1357', 'Aliquot samples for enzymatic fragmentation TWIST v2')] 

INFO:cg_lims.scripts.check_config:Button: Calculate Aliquotation Volume from Average concentration (ng/ul) Saphyr
INFO:cg_lims.scripts.check_config:Bash string: bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}   udf calculate aliquot-volume --concentration-udf 'Initial Concentration (ng/ul)' --amount-ng-udf 'Amount needed (ng)' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume H2O (ul)' --total-volume-udf 'Total Volume (ul)'"
INFO:cg_lims.scripts.check_config:Processes: [('1909', 'Labelling & Staining (Saphyr)')] 

INFO:cg_lims.scripts.check_config:Button: Calculate EB Volume
INFO:cg_lims.scripts.check_config:Bash string: bash -c -l "conda activate cg_lims &&  lims -c  /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid}  udf calculate aliquot-volume --concentration-udf 'Concentration' --volume-udf 'Sample Volume (ul)' --buffer-udf 'Volume Buffer (ul)' --total-volume-udf 'Total Volume (ul)' --amount-ng-udf 'Amount needed (ng)'"
INFO:cg_lims.scripts.check_config:Processes: [('2022', 'Aliquot samples for WGS fragmentation v1'), ('2034', 'Aliquot samples for DNA size selection (SRE) v1')] 

Only the TWIST and Watchmaker steps will have to be updated as --min-volume is fully optional and it will behave as normal without it (default is 0ul). Both TWIST and Watchmaker will use 1ul as the lower threshold.