Elevation should be required in the soil template

[pvangay]

For reference, see DH link - admin privileges required.

Elevation is required in the MIxS soil package (confirmed in v6). During the GSP workshop, we demo'd it as required (see last page of solutions for attendees). Currently, validation only flags entries with missing units, but does not flag empty cells.

[turbomam]

OK, I need to set it's LinkML required attribute to True

For which environments should it be required? Should I just check with MIxS :-) ?

I'm confused about why it's in the MIxS modified section already... nothing has been modified. I think that section membership is declared in the Google Sheet now instead of being detected by inspection.

[turbomam]

Confirming that elev is required for the soil environmental package within the MIxS LinkML model

[mslarae13]

Check sheets and friends elevation is required in modifications long & this slot is required in the submission portal.

[turbomam]

I am confirming that SoilInterface entries in the new submission schema require elev entries now. I will link the files that demonstrate that fact.

[turbomam]

https://github.com/microbiomedata/submission-schema/blob/main/src/data/valid/SampleData-soil-data-exhaustive.yaml contains two SoilInterfaces, captured in the soil_data slot.

• source_mat_id: x:1
• source_mat_id: x:2

Both have elev values of 123.

Note the absence of any units. We should ensure that this column is entitled "elevation in meters". @cmungall has some long term solutions so we won't have to manually manage slot names, title and validation rules, esp. with regards to measurements that have explicit or implicit units.

That file is converted into https://github.com/microbiomedata/submission-schema/blob/main/examples/output/SampleData-soil-data-exhaustive.json by the the examples/output/README.md Makefile target. If it were invalid to assign an elev to a SoilInterface, then that JSON file would not have been generated.

[turbomam]

I also created

• a simpler SampleData-soil-data-minimal.yaml sampel data file
• an invalid src/data/invalid/SampleData-soil-data-missing-elev.yaml, which lacks elev. The Makefile expects files in src/data/invalid to be invalid. If there are valid, then the build process fails.

This demonstrates that elev is both available and required for SoilInterfaces

@sujaypatil96 @pkalita-lbl and I can help colleagues create valid and invalid test files like these to check their expectations