Wizard for creating linkml2sheets templates

[turbomam]

Will revert to draft after discussing with CJM 2022-07-15

No related issue?

This branch also contains some makefile rules illustrating round tripping from schema to sheets and back

[turbomam]

make -f mam.makefile gen_and_pop

oops has hardcoded path to the NMDC schema

there are a lot of todo comments in schemasheets/template_wizard.py

[turbomam]

can you remove all unnecessary files from the commit?

Thanks for looking at this again.

Shoot, I thought this was one of my tidier PRs. Can you give an example of what I should remove?

[turbomam]

I wasn't planning on using this for the schemasheets part of the workshop, if that makes any difference in the priority.

[joshmoore]

Some feedback:

• Firstly, thanks! 💐 This is precisely what I was looking for today.
• Copying the template_wizard.makefile into a new directory was a solid starting point
  • I uncommented the slot.tsv and schema.yaml targets. They additionally need dependencies on all the other tasks.
  • I replaced the ndmc.yaml links with $(SCHEMA) and all references to ndmc with $(PREFIX) which worked well.
  • I replaced biosample with my target class.
• project_source in list_element_slots.py needs configuring and the use of "work" needs replacing with "target" (for this Makefile)
• A few code changes were needed:
  • schema_exporter.py line 171 needs a check for a SlotDefinition (for my model)
  • A few places don't seem to detect all the internal columns (e.g. 'attributes', 'class_uri', 'description', 'class', 'from_schema', 'mixins')
  • schemamaker.py line 145 is getting a dict rather than a list in my case. This is a weird one.
• Round-tripping failed with ValueError: Enter an interpretation for attributes but since I primarily wanted to get to a TSV (or actually, a google sheet) this was more than enough. Thanks again.

[sierra-moxon]

@joshmoore @turbomam - do you think we can close this PR and the associated ticket? Or instead, should we get it to a point where we can merge it into the repository? :)

[joshmoore]

I discussed briefly with @cmungall in February and I think there was another path forward that was preferred. But in general, big :+1: from my sides to having some form of command or recipe to create the necessary pieces here.

I have switched from using this custom code of mine to just hand-creating linkml2sheets templates.

I could provide some notes on how to set up the templates with a minimal amount of effort.

I am inclined to close this PR.