Linkml conversion tooling

[yarikoptic]

This is an extract with amends from

• WiP: Branch with auto converted linkml model #381

which (branch linkml-auto-converted) would keep merging this branch into itself while reflecting on changes in the branch which could be rebased or gain merges from the master, and also can accumulate or drop "patch branches" from within its script defining what to patch with.

This way linkml-auto-converted would represent reflection of current state of conversion

TODO/PLAN

• Establish branch linkml-auto-converted -- that one in WiP: Branch with auto converted linkml model #381
• Made ‘hatch’ script (you could add pydantic2linkml as dependency there) to convert orig_models.py into dandischema/models.yaml : hatch ... TODO
• Translated the original models.py into dandischema/models.yaml and overlaid with an [dandischema/models_overlay.yaml] overlay file.
• script tools/linkml_conversion to convert into ‘linkml-auto-converted’
• define model_instances.yaml (or alike) which would define pre-populated records such as standards (bids, nwb, ...). aim for potentially multiple classes there.
• add a github workflow here which would react to changes into 'master' and this branch and with manual dispatch, which would first merge master into this branch, then run the script, and push results to linkml-auto-converted branch. This way we would always have 'up to date' and automatically updated state of that branch.
• address "notes" about failed conversions one way (changing current dandi-schema pydantic model) or another (pydantic2linkml) or !
  • we can add a custom script to "enhance" auto generate linkml model to address any changes needed programmatically!
  • we can have a branch (or just a .patch file) with changes to perform on top of converted linkml
• ...
• There you produce pydantic model out of this patched model sufficient (although potentially more relaxed) to replace current pydantic model.

[yarikoptic]

that is where we define branches from PRs to merge!

[codecov]

Codecov Report

❌ Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.83%. Comparing base (4b89e4f) to head (07e7d47).
⚠️ Report is 6 commits behind head on master.

Files with missing lines	Patch %	Lines
dandischema/models_importstab.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #387      +/-   ##
==========================================
- Coverage   97.92%   97.83%   -0.09%     
==========================================
  Files          18       19       +1     
  Lines        2405     2407       +2     
==========================================
  Hits         2355     2355              
- Misses         50       52       +2     

Flag	Coverage Δ
unittests	97.83% <0.00%> (-0.09%)	⬇️

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[yarikoptic]

Suggested change

	if [ "$status" -ne 0 ]; then
	if grep -qi 'failed' <<<"$out"; then
	echo "patch FAILED for branch $b — see rejects" >&2
	exit 1
	fi
	if ! grep -qiE 'previously applied|reversed|skipping patch' <<<"$out"; then
	echo "patch exited $status for branch $b without a recognized skip indicator; aborting" >&2
	exit 1
	fi
	fi
	if [ "$status" -ne 0 ]; then
	if grep -qiE 'previously applied|reversed|skipping patch' <<<"$out"; then
	echo "patch exited $status for branch $b but it was about applied patch, ignoring"
	else
	echo "patch FAILED for branch $b with exit $status — see rejects" >&2
	exit $status
	fi
	fi