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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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(NEW) Fix range of slot compound on SolutionComponent #1666

Closed mslarae13 closed 3 months ago

mslarae13 commented 6 months ago

Discovered while writing ADR

Refer to

JamesTessmer commented 6 months ago

Here is a branch for the issue https://github.com/microbiomedata/berkeley-schema-fy24/tree/Fix-compound-range

JamesTessmer commented 6 months ago

Update: The enums are being enforced which I confirmed by adding an invalid data file and testing the valid ones with different values. The issue seems to be with the generated documentation saying the range is a string (which is technically true) but it doesn't show the enums being used to enforce the values.

mslarae13 commented 6 months ago

@sujaypatil96 can you help sort out why the generated documentation is wrong? https://microbiomedata.github.io/berkeley-schema-fy24/SolutionComponent/

ssarrafan commented 6 months ago

@sujaypatil96 can you help sort out why the generated documentation is wrong? https://microbiomedata.github.io/berkeley-schema-fy24/SolutionComponent/

Should this issue be re-assigned to @sujaypatil96? @mslarae13

ssarrafan commented 6 months ago

I'm going to remove this issue from the sprint and add the backlog label to it. If it should be active in the next sprint let me know. If it should be re-assigned to @Sujay Patil let me know.

sujaypatil96 commented 6 months ago

@mslarae13 @JamesTessmer this appears to be a schema issue?

The definition for SolutionComponent has the slot compound asserted on it, but it’s range needs to be modified to ProteolyticEnzymeEnum in a _slotusage statement underneath slots.

turbomam commented 5 months ago

I would like for us to review the overall modeling of solutions and reagents. The range slot_usages for compound sound relatively safe to me.

turbomam commented 5 months ago

see also (eventually!):

anastasiyaprymolenna commented 4 months ago

The documentation generation will be resolved with the release of LinkML version 1.7.6, until then the issue will remain open

mslarae13 commented 4 months ago

@anastasiyaprymolenna does this have relevance for the re-working of ChemicalConversionProcess?

turbomam commented 4 months ago

I'm working on a refactoring of everything solution related for Wednesday

turbomam commented 3 months ago

compound has been replaced by substances_used