remove horizon_method slot

[bmeluch]

remove horizon_method slot from waterinterface

MAM 2023-09-27: added a link to the issue here:

• "soil horizon method" appears in submission portal for water samples #148

[pkalita-lbl]

Hey thanks for taking a crack at this! However the submission schema is, for lack of a better word, weird. Specifically, the file you've changed actually gets built based on other files. The file you want to look at is sheets_and_friends/tsv_in/import_slots_regardless.tsv. In particular this line says "take the horizon_method slot from the nmdc_schema and plop it into the following classes of the submission_schema: AirInterface, BiofilmInterface, etc". So you'd want to remove WaterInterface from that list. Then you can regenerate all the generated files (there will be a lot!) and run tests with make all.

[turbomam]

Thanks @bmeluch !

Let's set up a conversation between you and either @pkalita-lbl or me about "what files to commit" Sorry, I haven't set this repo to be especially helpful in that regard!

You PRs will be easiest to review if you only commit the files you have changed. It looks like you are either doing the build process on your own or at least getting ready for it. That's great.

Please don't commit changes to examples/output/ or project/. In fact, it's unlikely that you will need to commit files from any path other than src/data/ or sheets_and_friends/

[turbomam]

It also looks like you updated the valid data files. That's great too. Please also add a new invalid example file that shows the illegal use of whatever slots/columns you are removing. @pkalita-lbl , @brynnz22 and I can help you with that too.

[pkalita-lbl]

a conversation between you and either @pkalita-lbl or me about "what files to commit"

You know that conversation with me will start with "we should have drastically fewer generated files checked in in the first place" 😂

Please also add a new invalid example file that shows the illegal use of whatever slots/columns you are removing

I have mixed feelings about this. I understand what the point would be, but where do we draw the line? It's impractical to test every slot that shouldn't be there.

[turbomam]

Thanks @pkalita-lbl. Let me ponder what value I think we're getting out of having the examples/output files. I would like for the repo to include a worked example of data being converted between LinkML JSON or YAML, TSV and DH JSON. But I guess what we are checking in now doesn't really help with that.

I can do the same thing for the project files. I do want to generate OWL for inclusion in the triplestore.

I agree that we shouldn't try to cover every exhaustive invalid case, but I would like to add a new invalid case each time some expressiveness is removed form the schema.

[bmeluch]

Thank you so much @pkalita-lbl !
@mslarae13 helpful notes from Patrick about how to edit the submission schema