x-atlas-consortia / hs-ontology-api

Ontology API built on top of the UBKG API and shared by HuBMAP and SenNet projects
1 stars 0 forks source link

[DO NOT MERGE] Add Segmentation Masks, GeoMx, RNAseq (with probes) and Xenium assay types #139

Closed shirey closed 4 weeks ago

shirey commented 1 month ago

Add Segmentation Masks, GeoMx, RNAseq (with probes) and Xenium assay types to interim/dev assayclasses.json file.

yuanzhou commented 1 month ago

Alert, @shirey @jpuerto-psc we can't merge this PR into main. jpuerto/rules-engine-integration branch was created off dev-integrate and will pollute the commit history of main.

Screenshot 2024-11-01 at 4 28 17 PM
jpuerto-psc commented 1 month ago

Thanks @yuanzhou - I think we were planning on just deleting this branch since these changes carried in to #147.

AlanSimmons commented 4 weeks ago

I think that we overcomplicated things.

  1. The change to the "dev server" was one file--the ontologies.json.
  2. We wanted to make sure that the ontologies.json was identical to the changes to the response from the production assayclasses endpoint--i.e., that if you called assayclasses, you'd get the same content as what's in ontologies.json.

At this point, I think that we can resolve this by just manually copying the ontologies.json over to the hs-ontology-api dev branch.

We might want to consider moving the "dev server" thingy into its own repo.

yuanzhou commented 4 weeks ago

I agree with @AlanSimmons. Any future changes to the dev/assayclasses.json should be branched off the latest main then PR into dev-integrate rather than using dev-integrate as the base branch. This will prevent us from messing up the commit history of main.

AlanSimmons commented 4 weeks ago

Another option would be to move the files in the dev folder path into a separate repo, with the understanding that any PRs would merge only with dev-integrate. That would keep the static dev server separate from the hs-ontology-api. The dev server shares no files with hs-ontology-api, so it really shouldn't be in this repo, anyway.

jpuerto-psc commented 4 weeks ago

@AlanSimmons - feel free to discuss this w/ @shirey I have no opinion on where the code for this should live. Just need a server to hit against for testing