gen-sqlvalidation rules: not inherited, lost on abstract classes and mixins, value_presence unsupported #44

What

On upstream main 5aa87ad, gen-sqlvalidation:

• checks only a class's own rules;
• skips rules declared on abstract classes and mixins;
• doesn't translate value_presence.

Reproduction

id: https://example.org/x
name: x
prefixes: {linkml: https://w3id.org/linkml/, ex: https://example.org/}
default_prefix: ex
default_range: string
imports: [linkml:types]
classes:
  P:
    # abstract: true   (or mixin: true with C: {mixins: [P]})
    attributes: {guard: {}, kind: {}, target: {}}
    rules:
      - preconditions: {slot_conditions: {guard: {equals_string: g}}}
        postconditions: {slot_conditions: {target: {equals_string: x}}}
  C: {is_a: P}

Run gen-sqlvalidation --no-include-comments schema.yaml, then run the output on SQLite tables created with gen-sqltables.

1. Concrete P: there is only a FROM "P" rule query, so row C(guard='g', target='y') is not reported.
2. Abstract or mixin P: there is no rule query at all, although tables P and C exist.
3. Precondition guard: {value_presence: PRESENT}: the rule is skipped with "preconditions exist but produced no SQL conditions".
4. Precondition {guard: {value_presence: ABSENT}, kind: {equals_string: k}}: the query is WHERE kind = 'k' AND (target != 'x' OR target IS NULL), with no warning. A row with guard set is reported, which is a false positive.

References

• Metamodel rules: "the collection of rules that apply to all members of this class".
• jsonschemagen applies ancestor rules since Traverse class ancestors looking for rules to apply in JSON Schema output linkml/linkml#1805, and shaclgen does the same in feat(gen-shacl): translate presence-implies-value rules to SHACL-SPARQL linkml/linkml#3989.
• The spec gap is tracked in Specification: state that a class's rules include those of its ancestors and mixins (additive) #45.

Proposed fix

• For every non-abstract, non-mixin class, collect rules from class_ancestors(class_name) (mixins included), and translate them against that class's table and columns.
• Translate value_presence: PRESENT / ABSENT as IS NOT NULL / IS NULL, negated in postconditions.
• When any condition can't be translated, skip the rule with a warning instead of dropping that condition.

Acceptance criteria

SQLite-executed tests cover:

• the concrete-parent, abstract-parent and mixin cases;
• value_presence in both pre- and postconditions;
• a mixed precondition with an untranslatable operator.