feat(generators): enforce has_member alike in SHACL and JSON Schema

[jdsika]

2026-10-14: rebased onto the rebased #30; no code change.

Stacked on #30. Covers upstream linkml#2465 (gen-shacl ignores has_member).

Change

has_member asks for "at least one member satisfying the condition" of a multivalued slot. Both generators now read it the same way: a member is one value, which must satisfy the value operators, range and range_expression of the expression.

slots:
  tags:
    range: string
    multivalued: true
    has_member: {equals_string: reviewed}

tags	before: SHACL	before: JSON Schema	now: both
absent	valid	valid	invalid
[]	valid	invalid	invalid
[pending]	valid	invalid	invalid
[reviewed, pending]	valid	valid	valid

• gen-shacl ignored has_member. It now emits sh:qualifiedValueShape with sh:qualifiedMinCount 1 (SHACL §4.7.3), on slots and in slot conditions of class-level expressions.
• gen-json-schema applied only the member's value operators, accepted an absent slot, and ignored has_member in class-level expressions. It now emits contains on a required slot. For a slot inlined as a dict it emits not: {additionalProperties: {not: <member>}}, because contains doesn't apply to objects.
• In a slot condition, has_member decides presence (an absent slot fails it), and the member takes the form of the condition: "definitely true" under none_of.

Decisions

• A slot without a value has no member, so an absent slot and [] both fail. The evidence:

  • the metamodel: "at least one member"; and value_presence says that for lists, ABSENT means empty;
  • the compliance suite: has_member on [] is invalid;
  • gen-owl's owl:someValuesFrom.

  gen-json-schema accepted an absent slot but rejected [], a distinction RDF can't express.

• This changes gen-json-schema: an optional slot with has_member is now required. The has_member cases of jsonschema_multivalued_element_constraints.yaml move to jsonschema_multivalued_has_member.yaml, which adds the absent, empty and null cases.

• Skipped by SHACL, with a warning:

  • has_member on a single-valued slot; the metamodel says "the value of the slot is multivalued";
  • a member with presence or slot operators (minimum_cardinality, any_of, …);
  • equals_string on a reference; that is fork issue gen-shacl rules: translate equals_string on IRI- and typed-literal-valued ranges (follow-up to linkml/linkml#3989) #37.

• Dropped from the earlier version: comparing equals_string with class references by IRI (issue gen-shacl rules: translate equals_string on IRI- and typed-literal-valued ranges (follow-up to linkml/linkml#3989) #37), equals_expression (see fix(generators): enforce range_expression on each value alike in SHACL and JSON Schema #30), raising on unsupported input, and the changes to rules, which keep their own reading (feat(gen-shacl): translate presence-implies-value rules to SHACL-SPARQL linkml/linkml#3989).

Other generators

• gen-owl: owl:someValuesFrom under open-world semantics; unchanged.
• ShEx, Python, Pydantic: no has_member support; unchanged.
• Rules: on this base, neither generator's rule translation handles has_member; the rules stack (feat(gen-shacl): translate presence-implies-value rules to SHACL-SPARQL #19/feat(gen-shacl): add a compositional fallback for rule-to-SPARQL conversion #20) adds it to gen-shacl's composed rule translation.

Validation

• test_has_member.py: 48 cases. They validate the same instance with both generated artifacts (RDF through the generated JSON-LD context), plus SHACL-only and JSON-only cases. 34 fail on fix(generators): enforce range_expression on each value alike in SHACL and JSON Schema #30.
• Out-of-tree check during development: 480 random schemas and 5,760 instances (has_member on slots and in class-level conditions, with member range_expression). gen-shacl, gen-json-schema and an independent three-valued model agreed on all of them. That harness is not part of this PR.
• Mutation: 21 mutants of the new code, all killed; one by the doctest of states_presence.
• Sweep: across 387 schemas in the repository, SHACL and JSON Schema output is unchanged, with identical errors and warnings.
• Compliance: test_membership now expects SHACL to implement has_member, except on references.
• Tests: the agreement harness of fix(generators): enforce range_expression on each value alike in SHACL and JSON Schema #30's tests moves to tests/linkml/utils/generator_agreement.py, shared with these tests.
• CI: see the checks on the current head.