Add a Sample grouping class in order to remove any_of range constraints

[sierra-moxon]

First PR towards removing any_of range constraints.
Sample is currently a grouping class for ProcessedSample and Biosample and is abstract.

[github-actions]

PR Preview Action v1.4.8
🚀 Deployed preview to https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-2244/
on branch gh-pages at 2024-11-27 20:50 UTC

[turbomam]

This is going to be great @sierra-moxon

Is there any connection with

• reduce dependence on any_of in range constraints - all planned proces… #2246

[sierra-moxon]

@turbomam - would like this to be a MaterialEntity. All classes should be descendent of one of the 3 subclasses of NamedThing - not additional NamedThing subclasses.

[sierra-moxon]

@sierra-moxon - fix this comment - it may be correct, but also should highlight parent vs. ancestor.

[eecavanna]

This looks good to me, @sierra-moxon. Thanks for implementing it (and walking us through it during today's meeting). The only thing I'm hesitant about is that the only is_a field that was modified here is for the Biosample class. Did you mean to do the same thing to the ProcessedSample class?

[sierra-moxon]

This looks good to me, @sierra-moxon. Thanks for implementing it (and walking us through it during today's meeting). The only thing I'm hesitant about is that the only is_a field that was modified here is for the Biosample class. Did you mean to do the same thing to the ProcessedSample class?

Hi @eecavanna! :) can you check the is_a hierarchy here again? -- I appreciate your review.

[sierra-moxon]

@turbomam - just a ping to say this is ready for review.

[eecavanna]

Here's a summary of my takeaways from reading the latest diff:

1. The DataGeneration class definition's has_input slot used to have an any_of constraint defined (whose members were: - range: Biosample and - range: ProcessedSample). This PR removes that any_of constraint and replaces it with range: Sample. The same is true about the MaterialProcessing, Extraction, SubSamplingProcess, MixingProcess, FiltrationProcess, and ChromatographicSeparationProcess class definitions.
2. This PR introduces a Sample class definition, which is_a: MaterialEntity.
3. The Biosample class definition used to have is_a: MaterialEntity on it. This PR replaces that with is_a: Sample. The same is true about the ProcessedSample class definition.