♻️ Refactor organism
handling in curators
#2415
Merged
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Is part of a sequence of PRs that refactors the curators:
BaseCurator
asCurator
and introduceCatCurator
#2416CatCurator
#2413CellxGene
schema #2412PertCurator
fromwetlab
here and addCellxGene
Curator
test #2408CellxGene
Curator
fromcellxgene-lamin
here #2403DataFrameCurator
#2388Replace
self._kwargs
with explicit organism passing; remove ability to pass an organism ad-hoc in.validate()
etc.Gene.ensembl_gene_id
does not need it, whereasGene.symbol
needs itorganism
at any later stages of the workflow; it both opens up the door for integrity errors and makes the code complicated