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cellannotation / cell-annotation-schema

General, open-standard schema for cell annotations
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Name tweaks #31

Closed dosumis closed 8 months ago

dosumis commented 8 months ago

Fixes #30 - please see ticket for justification.

@mfutey & @evanbiederstedt - to review the effect of this PR please just review examples/Siletti_expression_evidence.json + README.

(This turned out to be more hassle to complete than I expected, but was a useful exercise in testing new infrastructure and editing SOPs.)

github-actions[bot] commented 8 months ago

Validation Passes.

github-actions[bot] commented 8 months ago

Validation Fails. Check action report for details.

github-actions[bot] commented 8 months ago

Validation Fails. Check action report for details.

github-actions[bot] commented 8 months ago

Validation Passes.

dosumis commented 8 months ago

@hkir-dev @ubyndr - schema is good. Not sure why unit tests are failing. Surely unit tests should be for code only and so independent of changes to schema and test examples?

github-actions[bot] commented 8 months ago

Validation Passes.

dosumis commented 8 months ago

Update - partly fixed by updating key BICAN extension.

github-actions[bot] commented 8 months ago

Validation Passes.

github-actions[bot] commented 8 months ago

Validation Passes.

github-actions[bot] commented 8 months ago

Validation Passes.

dosumis commented 8 months ago

I think this is too strict for a test. The schema should do the work.

image. in schema_manager_test.py

I will fix for now to ensure PR passes.

github-actions[bot] commented 8 months ago

Validation Passes.

hkir-dev commented 8 months ago

I think there is a bug in the merge logic. I am trying to fix it now. You don't need to change your schema.

dosumis commented 8 months ago

I think there is a bug in the merge logic. I am trying to fix it now. You don't need to change your schema.

I looks to me like the problem was with overly strict the tests - see #34

hkir-dev commented 8 months ago

Unit tests should only test the behaviour of the code. Updating the schema shouldn't fail unit tests. Code should work with any schema. So I am trying to test the code with the schemas located in the test_data folder.

However, there is a bug in the schema merging, so test_data/*_extension.json schemas are accidentally merged with the ./general_schema.json instead of the test_data/general_schema.json.

github-actions[bot] commented 8 months ago

Validation Fails. Check action report for details.

github-actions[bot] commented 8 months ago

Validation Passes.

evanbiederstedt commented 8 months ago

Let's run spellcheck on all of this please

github-actions[bot] commented 8 months ago

Validation Passes.

evanbiederstedt commented 8 months ago

@dosumis We really should run this through spellcheck