Express DANDI data models in LinkML

[candleindark]

The goal of this PR is to provide representations of DANDI data models in LinkML.

The initial representations in LinkML are generated with https://github.com/candleindark/linkml-aind-model a fork of https://github.com/DailyDreaming/linkml-aind-model.

Incremental targets:

• Develop the tool at https://github.com/candleindark/linkml-aind-model to produce more correct and complete conversion from Pydantic models to a LinkML schema
• Set up a CI project to check various existing data instances against the produced LinkML schema
• Use the produced LinkML schema to produce Pydantic models to replace the existing Pydantic models in the dandi-schema project and check how well the existing tests in the project pass.
• Repeat the above steps to obtain a more complete and accurate LinkML schema if needed

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.81%. Comparing base (dc15401) to head (55992f0).

Additional details and impacted files

@@              Coverage Diff              @@
##           to-linkml     #240      +/-   ##
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+ Coverage      87.39%   91.81%   +4.41%     
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  Files             16       16              
  Lines           1722     1722              
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+ Hits            1505     1581      +76     
+ Misses           217      141      -76     

Flag	Coverage Δ
unittests	91.81% <ø> (+4.41%)	⬆️

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[djarecka]

@candleindark - can you point me to the newest version of the linkml schema. The links posints to versions that are 5-8months old

[candleindark]

@djarecka You can generate the current schema using https://github.com/candleindark/pydantic2linkml/tree/enh (make sure it is the enh branch), by running pydantic2linkml -o dandi-linkml-schema.yml dandischema.models.

I will also make the latest DANDI LinkML schema available on https://github.com/dandi/dandisets-linkml-status, as part of the report directory, later today as well.

[djarecka]

perhaps you can add it to github (even if it's not final), so I can point someone to it

[candleindark]

I will provide a link to it at https://github.com/dandi/dandisets-linkml-status/blob/main/dandi-reports/summary.md. https://github.com/dandi/dandisets-linkml-status/tree/main will provide some the up-to-date info on the conversion of Dandi models to LinkML.

[candleindark]

@djarecka The latest generated DANDI LinkML schema is now referenced on https://github.com/dandi/dandisets-linkml-status/blob/main/dandi-reports/summary.md.

[candleindark]

I am closing this PR. It is no longer relevant. An up-to-date DANDI LinkML schema is now always referenced at https://github.com/dandi/dandisets-linkml-status/blob/main/dandi-reports/summary.md along with the validation results of dandiset metadata against it.