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feat: add cellxgene schema 3.0.0 fields to Standard Categories #412

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merged 1 commit into from
Aug 23, 2022

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@nayib-jose-gloria nayib-jose-gloria commented Aug 22, 2022

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Functional:

Readability:


Changes

  • Add 'donor_Id' to Standard Categories
  • Add 'suspension_type' to Standard Categories
  • Add 'self_reported_ethnicity' and 'self_reported_ethnicity_ontology_term_id' to Standard Categories.
  • Note: in the interim, we will support both 'ethnicity' and 'self_reported_ethnicity' fields in Standard Categories. Once the data portal is migrated over to 3.0.0, we will remove support for ethnicity as a Standard Category (as it will be a deprecated column name in cellxgene schema 3.0.0 in favor of self_reported_ethnicity)

QA

  • Will test locally with a 3.0.0 and 2.0.0 dataset, to ensure expected new behavior and no regressions

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codecov bot commented Aug 22, 2022

Codecov Report

Merging #412 (e73eddc) into main (90f976e) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #412   +/-   ##
=======================================
  Coverage   75.86%   75.86%           
=======================================
  Files          90       90           
  Lines        6778     6778           
=======================================
  Hits         5142     5142           
  Misses       1636     1636           
Flag Coverage Δ
frontend 75.86% <ø> (ø)
javascript 75.86% <ø> (ø)
smokeTest ?
unitTest 75.86% <ø> (ø)

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@nayib-jose-gloria nayib-jose-gloria marked this pull request as ready for review August 23, 2022 16:20
@nayib-jose-gloria nayib-jose-gloria changed the title feat: add cellxgene schema 3.0.0 fields to Standard Categories [WIP] feat: add cellxgene schema 3.0.0 fields to Standard Categories Aug 23, 2022
@nayib-jose-gloria nayib-jose-gloria merged commit b265fcf into main Aug 23, 2022
@nayib-jose-gloria nayib-jose-gloria deleted the nayib/schema-3-0-0-updates branch August 23, 2022 17:16
danieljhegeman pushed a commit that referenced this pull request Aug 30, 2022
* chore: updating logo (#389)

* chore: updating logo

* feature: Added loading spinner to geneset average color-by and fixed a continuous legend bug (#384)

* added loading spinner to mean colorby and fixed legend async bug

* revert prettier

* temp fix tsc emit

* typed

* fix

* fixed bugs

Co-authored-by: atarashansky <[email protected]>

* typed obs crossfilter (#420)

Co-authored-by: atarashansky <[email protected]>

* typed categorical selection reducer (#417)

Co-authored-by: atarashansky <[email protected]>

* typed differential reducer (#419)

Co-authored-by: atarashansky <[email protected]>

* typed annoMatrix reducer (#416)

Co-authored-by: atarashansky <[email protected]>

* chore: purge autosave from codebase (#425)

* chore: typed genesetsUI reducer

* fix tsc error

* chore: purge autosave

* delete nameNewAnnotation

* remove unused

Co-authored-by: atarashansky <[email protected]>

* chore: typed controls reducer (#418)

* typed controls reducer

* refine scatterplot accessor type to be string or false

* address revisions

* type level return function

Co-authored-by: atarashansky <[email protected]>

* typed point dilation (#421)

Co-authored-by: atarashansky <[email protected]>

* Revert "feat: add cellxgene schema 3.0.0 fields to Standard Categories (#412)" (#428)

This reverts commit b265fcf.

* typed graph selection reducer (#422)

Co-authored-by: atarashansky <[email protected]>

* chore: typed cascade reducer (#426)

* test

* update cascade reducer

* add map as possible type for cascade

* refactor(cascadeReducer): Quick feedback (#427)

* revert changes

* Update client/src/reducers/cascade.ts

Co-authored-by: Severiano Badajoz <[email protected]>

* remove as string

* refactor(cascadeReducer): Quick feedback 2 (#430)

Co-authored-by: atarashansky <[email protected]>
Co-authored-by: Timmy Huang <[email protected]>
Co-authored-by: Severiano Badajoz <[email protected]>

* chore: typed genesetsUI reducer (#423)

* chore: typed genesetsUI reducer

* fix tsc error

Co-authored-by: atarashansky <[email protected]>

* chore: typed config reducer (#424)

* chore: typed config reducer

* restrict error type

Co-authored-by: atarashansky <[email protected]>

Co-authored-by: ashin-czi <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: Nayib Gloria <[email protected]>
Co-authored-by: Timmy Huang <[email protected]>
Co-authored-by: Severiano Badajoz <[email protected]>
danieljhegeman pushed a commit that referenced this pull request Sep 1, 2022
* chore: updating logo (#389)

* chore: updating logo

* feature: Added loading spinner to geneset average color-by and fixed a continuous legend bug (#384)

* added loading spinner to mean colorby and fixed legend async bug

* revert prettier

* temp fix tsc emit

* typed

* fix

* fixed bugs

Co-authored-by: atarashansky <[email protected]>

* typed obs crossfilter (#420)

Co-authored-by: atarashansky <[email protected]>

* typed categorical selection reducer (#417)

Co-authored-by: atarashansky <[email protected]>

* typed differential reducer (#419)

Co-authored-by: atarashansky <[email protected]>

* typed annoMatrix reducer (#416)

Co-authored-by: atarashansky <[email protected]>

* chore: purge autosave from codebase (#425)

* chore: typed genesetsUI reducer

* fix tsc error

* chore: purge autosave

* delete nameNewAnnotation

* remove unused

Co-authored-by: atarashansky <[email protected]>

* chore: typed controls reducer (#418)

* typed controls reducer

* refine scatterplot accessor type to be string or false

* address revisions

* type level return function

Co-authored-by: atarashansky <[email protected]>

* typed point dilation (#421)

Co-authored-by: atarashansky <[email protected]>

* Revert "feat: add cellxgene schema 3.0.0 fields to Standard Categories (#412)" (#428)

This reverts commit b265fcf.

* typed graph selection reducer (#422)

Co-authored-by: atarashansky <[email protected]>

* chore: typed cascade reducer (#426)

* test

* update cascade reducer

* add map as possible type for cascade

* refactor(cascadeReducer): Quick feedback (#427)

* revert changes

* Update client/src/reducers/cascade.ts

Co-authored-by: Severiano Badajoz <[email protected]>

* remove as string

* refactor(cascadeReducer): Quick feedback 2 (#430)

Co-authored-by: atarashansky <[email protected]>
Co-authored-by: Timmy Huang <[email protected]>
Co-authored-by: Severiano Badajoz <[email protected]>

* chore: typed genesetsUI reducer (#423)

* chore: typed genesetsUI reducer

* fix tsc error

Co-authored-by: atarashansky <[email protected]>

* chore: typed config reducer (#424)

* chore: typed config reducer

* restrict error type

Co-authored-by: atarashansky <[email protected]>

Co-authored-by: ashin-czi <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: Nayib Gloria <[email protected]>
Co-authored-by: Timmy Huang <[email protected]>
Co-authored-by: Severiano Badajoz <[email protected]>

Co-authored-by: ashin-czi <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: atarashansky <[email protected]>
Co-authored-by: Nayib Gloria <[email protected]>
Co-authored-by: Timmy Huang <[email protected]>
Co-authored-by: Severiano Badajoz <[email protected]>
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2 participants