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DPL-916 PBMC Donor Pooling create plate #1582

Merged
merged 95 commits into from
Mar 11, 2024
Merged

DPL-916 PBMC Donor Pooling create plate #1582

merged 95 commits into from
Mar 11, 2024

Commits on Feb 13, 2024

  1. Added creator class to LRC PBMC Pools purpose

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    yoldas committed Feb 13, 2024
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  2. Added automatic state changer class to LRC PBMC Pools purpose

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    yoldas committed Feb 13, 2024
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  3. Added work completion request type to LRC PBMC Pools purpose

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    yoldas committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. Added pooling lookup table, same as Cardinal

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    yoldas committed Feb 14, 2024
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Commits on Feb 23, 2024

  1. Add creator_class configuration for LRC PBMC Pools purpose

    @yoldas
    yoldas committed Feb 23, 2024
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  2. Added pooling algorithm for donor pooling labware creator

    @yoldas
    yoldas committed Feb 23, 2024
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  3. Fixed split_single_group_by_donor_ids call

    @yoldas
    yoldas committed Feb 23, 2024
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  4. Added transfer requests and tag_depth info

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    yoldas committed Feb 23, 2024
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  5. Formatted labware creator code comments

    @yoldas
    yoldas committed Feb 23, 2024
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  6. Add donor pooling template for receving source plate barcodes

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    yoldas committed Feb 23, 2024
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  7. Add donor pooling plate purpose config factory

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    yoldas committed Feb 23, 2024
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  8. Prettier

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    yoldas committed Feb 23, 2024
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  9. Merge branch 'develop' into 1390-dpl-916-pbmc-donor-pooling-create-plate

    @yoldas
    yoldas committed Feb 23, 2024
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Commits on Feb 24, 2024

  1. Merged transfer_hash methods

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    yoldas committed Feb 24, 2024
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  2. Added initializer to load the lookup table

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    yoldas committed Feb 24, 2024
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Commits on Feb 25, 2024

  1. Add attribute readers for barcodes and minimal barcodes

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    yoldas committed Feb 25, 2024
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  2. Rubocop

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    yoldas committed Feb 25, 2024
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  3. Add test for source_plates method

    @yoldas
    yoldas committed Feb 25, 2024
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  4. Add test for source_wells_for_pooling method

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    yoldas committed Feb 25, 2024
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  5. Fix config name in number_of_pools method

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    yoldas committed Feb 25, 2024
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  6. Add test for number_of_pools method

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    yoldas committed Feb 25, 2024
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  7. Add tests for barcodes= and group_by_study_and_project methods

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    yoldas committed Feb 25, 2024
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  8. Add test for unique_donor_ids method

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    yoldas committed Feb 25, 2024
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  9. Fix unique_donor_ids method

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    yoldas committed Feb 25, 2024
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  10. Add test for split_single_group_by_donor_ids method

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    yoldas committed Feb 25, 2024
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  11. Fix split_single_group_by_donor_ids method

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    yoldas committed Feb 25, 2024
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  12. Rename donor_id split methods

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    yoldas committed Feb 25, 2024
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Commits on Feb 26, 2024

  1. Move helper methods to a separate module

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    yoldas committed Feb 26, 2024
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  2. Fix distribute_groups_across_pools method

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    yoldas committed Feb 26, 2024
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  3. Check nil in split_single_group_by_unique_donor_ids

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    yoldas committed Feb 26, 2024
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  4. Fix distribute_groups_across_pools call in build_pools

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    yoldas committed Feb 26, 2024
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  5. Add test for build_pools method

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    yoldas committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. Add tests for tag depth and transfer request attributes

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    yoldas committed Feb 27, 2024
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  2. Add test for transfer_material_from_parent! method

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    yoldas committed Feb 27, 2024
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  3. Add test for pools method

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    yoldas committed Feb 27, 2024
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  4. Prettier

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    yoldas committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. Change module name from helper to calculator

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    yoldas committed Feb 28, 2024
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  2. Rename file for donor pooling calculator

    @yoldas
    yoldas committed Feb 28, 2024
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  3. Update the include with the pooling calculator module name

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    yoldas committed Feb 28, 2024
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  4. Add donor pooling validations

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    yoldas committed Feb 28, 2024
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  5. Include validator in labware creator

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    yoldas committed Feb 28, 2024
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  6. Prettier

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  7. Updated message for number_of_pools_must_not_exceed_configured validator

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    yoldas committed Feb 28, 2024
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  8. Remove redundant include from validator

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    yoldas committed Feb 28, 2024
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  9. Add comments to validation methods

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    yoldas committed Feb 28, 2024
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  10. Prettier

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    yoldas committed Feb 28, 2024
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  11. Add tests for validations

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Commits on Mar 1, 2024

  1. Add test for wells_with_aliquots_must_have_donor_id

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    yoldas committed Mar 1, 2024
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  2. Add validation wells_with_aliquots_must_have_donor_id

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    yoldas committed Mar 1, 2024
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Commits on Mar 7, 2024

  1. Rename labware creator argument to max_number_of_source_plates

    @yoldas
    yoldas committed Mar 7, 2024
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  2. Fix typo in labware_wells method doc

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    yoldas committed Mar 7, 2024
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Commits on Mar 10, 2024

  1. Use number_of_pools and default_number_of_pools from purpose_config

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  2. Add pooling and default_number_pools to labware creator arguments

    @yoldas
    yoldas committed Mar 10, 2024
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  3. Updated docs with config:generate

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    yoldas committed Mar 10, 2024
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  4. Load pooling configurations with config task

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    yoldas committed Mar 10, 2024
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  5. Add labware creator arguments to donor_pooling_plate_purpose_config f… 

    …actory
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  6. Update test with default_number_of_pools from purpose config

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    yoldas committed Mar 10, 2024
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  7. Reset Settings.poolings in spec_config to allow testing with custom s… 

    …etup
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  8. Add config loader for poolings

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    yoldas committed Mar 10, 2024
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  9. Add donor_pooling_config factory for testing pooling configurations f… 

    …rom Settings
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  10. Add interim scrna donor pooling config YAML file (lookup table; copy … 

    …of cardinal)
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  11. Add fixtures for testing with pooling configurations

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    yoldas committed Mar 10, 2024
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  12. Add test for poolings config loader

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    yoldas committed Mar 10, 2024
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  13. Add well_at_location method to Plate

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    yoldas committed Mar 10, 2024
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  14. Use plate.well_at_location method instead of get_well_for_plate_location

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    yoldas committed Mar 10, 2024
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  15. Remove get_well_for_plate_location method from labware creator

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  16. Remove test for get_well_for_plate_location method

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    yoldas committed Mar 10, 2024
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  17. Update config rake task stdout progress with pooling config

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    yoldas committed Mar 10, 2024
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  18. Add method to compute all tag depths at once into a hash

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    yoldas committed Mar 10, 2024
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  19. Use pre-computed tag depths (as strings) in request_hash

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    yoldas committed Mar 10, 2024
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  20. Remove per well tag_depth method because they are pre-computed now

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    yoldas committed Mar 10, 2024
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  21. Replace tag_depth test with tag_depth_hash test

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  22. Fix caching the result of tag_depth_hash computation

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    yoldas committed Mar 10, 2024
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  23. Use less strong wording in the view as suggested in code-review

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    yoldas committed Mar 10, 2024
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  24. Update instructions with the conditions of pooling

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    yoldas committed Mar 10, 2024
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  25. Apply doc suggestion for DonorPoolingCalculator

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    yoldas committed Mar 10, 2024
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  26. Add to doc: only one aliquot is expected per well

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    yoldas committed Mar 10, 2024
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  27. Remove redundant nil-check

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    yoldas committed Mar 10, 2024
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  28. Use counter instead of empty check for the while loop condition

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  29. Prettier

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  30. Add examples in the comments for methods

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    yoldas committed Mar 10, 2024
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  31. Add missing source plate barcodes to the error message

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    yoldas committed Mar 10, 2024
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  32. Update test with missing source plate barcodes

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    yoldas committed Mar 10, 2024
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  33. Rubocop

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  34. Separate assigment statement from the chain

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    yoldas committed Mar 10, 2024
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  35. Update error message strings

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  36. Remove redundant source_plate param from locations_with_missing_donor_id

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  37. Add a method to map source wells to their plates

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    yoldas committed Mar 10, 2024
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  38. Ensure validator uses the same filtered wells as the labware creator

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  39. Add test for source_wells_to_plates method

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  40. Update code documentation of locations_with_missing_donor_id method

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    yoldas committed Mar 10, 2024
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  41. Remove pooling config CSV file

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  42. Remove CSV config file loader

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Commits on Mar 11, 2024

  1. Prettier

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  2. Merge branch 'develop' into 1390-dpl-916-pbmc-donor-pooling-create-plate

    @yoldas
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