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chanzuckerberg / single-cell

A collection of documents that reflect various design decisions that have been made for the cellxgene project.
MIT License
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Find and resolve all usages of/references to CL:0000003 and/or "native cell" across all repos #647

Closed danieljhegeman closed 7 months ago

danieljhegeman commented 9 months ago

See epic description

danieljhegeman commented 9 months ago

References to "native cell" and CL:0000003 in single-cell-curation have been resolved already

danieljhegeman commented 9 months ago

Confirmed no instances of 0000003 for native cell that do not also include CL: prefix in data portal

danieljhegeman commented 9 months ago

Changes will need to be merged immediately after migrations. FE filter compute script GHA should be run to regenerate ontology files for data portal from updated ontology version pins.

danieljhegeman commented 9 months ago

Data Portal changes are in dan/647-replace-native-cell (except for fixture updates, as addressed immediately above)

danieljhegeman commented 9 months ago

curation repo is clear

danieljhegeman commented 9 months ago

Explorer is clear

danieljhegeman commented 9 months ago

single-cell is clear

danieljhegeman commented 9 months ago

single-cell-analytics is clear

danieljhegeman commented 9 months ago

single-cell-ops-tools is clear

danieljhegeman commented 9 months ago

single-cell-infra is clear

danieljhegeman commented 9 months ago

cellxgene is clear

danieljhegeman commented 9 months ago

cellxgene-ontology-guide is clear

danieljhegeman commented 9 months ago

single-cell-annotation is clear

danieljhegeman commented 9 months ago

It looks like references to CL:0000003 occurring in cellxgene-census all fall into the category of notebook outputs, meaning that once the ontology updates are pushed to prod, the notebooks can be rerun and the resulting output committed. This is also recapitulated in the html docs pages for Census, specifically this one and this one.

brianraymor commented 9 months ago

I also see "native cell" referenced on a block list - https://github.com/chanzuckerberg/cellxgene-census/blob/aaccb5b472a7f83a472986b098[…]3c12eeed/tools/models/geneformer/finetune-geneformer.config.yml

@danieljhegeman It would be good to review your findings with @pablo-gar and @bkmartinjr. We've recently discovered some subtle census issues with schema 4.0.0 changes.

bkmartinjr commented 9 months ago

@mlin - we need to update GeneFormer config as part of this. I'll file a bug in Census tagging you.

brianraymor commented 7 months ago

Applications has a separate issue chanzuckerberg/single-cell-data-portal#6657 to address related changes.

Can this issue now be closed? CC: @danieljhegeman @metakuni

danieljhegeman commented 7 months ago

Since @atarashansky has ack'd my PR and is assuming ownership of it, which I imagine he'll transfer to the issue you've linked above, then yes.

danieljhegeman commented 7 months ago

Closing per discussion above cc @atarashansky