Handle LinkML migration issue of pydantic2linkml: Impossible to generate slot usage entry for the #389

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1. candleindark

   added a parent issue on Mar 27, 2026

   • Establish at least 8 issues for specific groups of problems in converted linkml #388
2. candleindark commented on May 8, 2026

   

   candleindark

   on May 8, 2026

   MemberAuthor

   More actions

   Note: Inline definition of a slot via the attributes meta slot does
   not change its behavior under inheritance. All slots are inherited the
   same way regardless of whether they are defined inline within a class
   (via attributes) or at the schema level (via top-level slots
   referenced by the class's slots list).

   Concretely, in a child class declared with is_a: Parent:

   • Inherited slots are required if the parent declared them required.
   • Inherited slots carry their parent-declared range and other
     constraints.
   • The child can add new slots, and can extend inherited ones via
     slot_usage under the same rules that apply to schema-level slots.

   Verified with linkml-validate against a minimal schema and three data
   instances.

   schema.yaml

   id: https://example.org/inherit-demo
   name: inherit_demo
   prefixes:
     linkml: https://w3id.org/linkml/
     ex: https://example.org/
   default_prefix: ex
   default_range: string
   imports:
     - linkml:types
   
   classes:
     Person:
       attributes:
         name:
           required: true
         age:
           range: integer
   
     Employee:
       is_a: Person
       attributes:
         employer:
           required: true

   employee_ok.yaml — valid Employee

   name: Alice
   age: 30
   employer: Acme

   $ linkml-validate -s schema.yaml -C Employee employee_ok.yaml
   No issues found
   

   employee_missing_inherited.yaml — missing inherited required slot name

   employer: Acme
   age: 30

   $ linkml-validate -s schema.yaml -C Employee employee_missing_inherited.yaml
   [ERROR] [.../employee_missing_inherited.yaml/0] 'name' is a required property in /
   

   employee_bad_inherited_type.yaml — violates inherited range on age

   name: Bob
   age: not-a-number
   employer: Acme

   $ linkml-validate -s schema.yaml -C Employee employee_bad_inherited_type.yaml
   [ERROR] [.../employee_bad_inherited_type.yaml/0] 'not-a-number' is not of type 'integer', 'null' in /age
   
3. yarikoptic commented on May 8, 2026

   

   yarikoptic

   on May 8, 2026

   Member

   More actions

   try to just make it more restrictive (to go from required: False into required: True to be ok). If it works for json schema and pydantic -- let's proceed that way and just add a test which checks that it remains so with current version of linkml.

   If it all of a sudden stops working, which we detect via CI like we do in dandi-cli running against dev

       - name: Install dev versions of select dependencies
         if: matrix.mode == 'dev-deps'
         run: |
           pip install git+https://github.com/jaraco/keyring
           pip install git+https://github.com/NeurodataWithoutBorders/nwbinspector
           pip install git+https://github.com/NeurodataWithoutBorders/pynwb \
               git+https://github.com/hdmf-dev/hdmf \
               git+https://github.com/hdmf-dev/hdmf-zarr
   

   then we will look into a "solution" (like screaming at upstream for breaking behavior) or come with a workaround. Let's just establish version ceiling for linkml dependency right away within e.g. major version.
4. candleindark

   added sub-issues on May 12, 2026

   • Handle Impossible to generate slot usage entry complaints about changes in the required metadata slot #405
   • Handle Impossible to generate slot usage entry complaints about changes in the range metadata slot #406
   • Handle Impossible to generate slot usage entry complaints about changes in the pattern metadata slot #407
5. candleindark commented on May 15, 2026

   

   candleindark

   on May 15, 2026

   MemberAuthor

   More actions

   try to just make it more restrictive (to go from required: False into required: True to be ok). If it works for json schema and pydantic -- let's proceed that way and just add a test which checks that it remains so with current version of linkml.

   If it all of a sudden stops working, which we detect via CI like we do in dandi-cli running against dev

       - name: Install dev versions of select dependencies
         if: matrix.mode == 'dev-deps'
         run: |
           pip install git+https://github.com/jaraco/keyring
           pip install git+https://github.com/NeurodataWithoutBorders/nwbinspector
           pip install git+https://github.com/NeurodataWithoutBorders/pynwb \
               git+https://github.com/hdmf-dev/hdmf \
               git+https://github.com/hdmf-dev/hdmf-zarr
   

   then we will look into a "solution" (like screaming at upstream for breaking behavior) or come with a workaround. Let's just establish version ceiling for linkml dependency right away within e.g. major version.

   This issue is codified as #405. The proposed translation to LinkML is implemented in pydantic2linkml via dandi/pydantic2linkml#66 and the continuous verification of the LinkML behavior against regression has been implemented via #408.
6. candleindark

   added a sub-issue on May 19, 2026

   • Handle Impossible to generate slot usage entry complaints about missing readonly metadata slot #413
7. candleindark

   added a sub-issue on Aug 6, 2026

   • Revisit the #406 solution once #437 is merged #438
8. candleindark

   added a commit that references this issue on Aug 7, 2026

   fix: drop `schemaKey` `MANUAL_NOTE` entries from `models_merge.yaml`

   ...

   09730f8
9. yarikoptic-gitmate

   added a commit that references this issue on Sep 29, 2026

   Require non-empty `name` for Contributor and BaseType (schema 0.8.1)

   ...

   742cc63