feat(gen-shacl): add compositional fallback rule converters (M1-M5)

[jdsika]

Summary

Adds a compositional fallback to the rules → SHACL-SPARQL converter for
rule-operator combinations outside the three named patterns (boolean guard,
presence-implies-value, exclusive value). The fallback is tried only after
the named patterns, so their output is unchanged. It translates a conjunction
of precondition slot conditions plus a single postcondition into one
SELECT $this violation query. The safety contract is skip, never
mis-translate: any unsupported operator makes the converter return None
and the rule is logged at DEBUG and skipped.

Supported combinations

ID	Pattern	Violation SPARQL
M1	conditional-required: equals_string / value_presence: PRESENT precondition → required: true	precondition holds ∧ FILTER NOT EXISTS on the target slot
M2	conditional-absent: → value_presence: ABSENT	precondition holds ∧ the forbidden slot is present
M3	numeric threshold preconditions: minimum_value / maximum_value (inclusive, per the LinkML metamodel) on the trigger slot	numeric FILTER bound, combinable with any supported postcondition
M4	nested precondition: one hop into an inlined child via range_expression.slot_conditions (e.g. sun_position.elevation <= 0)	binds the child node, applies inner conditions via the shared _member_conditions emitter
M5	has_member list-membership: a multivalued slot must contain a member matching a nested range_expression	FILTER NOT EXISTS over the members

M4/M5 introduce _member_conditions (shared inner-condition emitter) and
_resolve_member_enum_ref, which resolves inner enum values against the
container slot's range class, so slot_usage-specialised enums pick the
correct permissible values.

Stack position

Base branch: feat/shaclgen-presence-implies-value-stacked — only the
fallback delta shows in the diff.

main
└─ feat/shaclgen-rules-sparql                      #11 (green)
   └─ feat/shaclgen-presence-implies-value-stacked   (PR: presence-implies-value)
      └─ feat/shaclgen-compositional-rule-fallback  ← this PR
         └─ fix/shaclgen-rule-converter-hardening     (follow-up)

Provenance

Squashed, content-identical, from the five M1–M5 commits on
feat/shacl-rule-converters (#18: 7566e30c, fac681e0, f8ea709d,
25f8cd28, 47769772), where the full CI matrix is green. Original
authorship preserved.

Areas of uncertainty

Skipped (never mis-translated), documented as follow-up candidates:

• equals → equals postconditions ("if A=x then B=y") are not yet composed.
• A precondition mixing a range_expression with scalar operators resolves
  via the nested branch only.
• Multiple postconditions (more than one slot condition) are skipped; a rule's
  postconditions are a conjunction, so the single-postcondition case covers
  the modeled cross-parameter rules.
• First-match operator dispatch on a single condition (e.g.
  {minimum_value, maximum_value} keeping only one bound) is a known defect
  fixed in the stacked follow-up fix/shaclgen-rule-converter-hardening,
  kept separate so the defect and its regression tests stay reviewable.

How was this tested?

• tests/linkml/test_generators/test_shaclgen.py on this branch:
  100 passed (base suites + 16 new tests; per converter: structural triple
  assertions, prepareQuery syntax validation, pyshacl end-to-end with
  advanced=True — conforming instances pass, crafted violations fail).
• ruff check and ruff format --check clean on both changed files.

Checklist

• My code follows the contributor guidelines
• I have added tests that prove my fix/feature works
• Existing tests pass locally with my changes

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[jdsika]

Adversarial audit findings (fallback converters, audited at stack tip incl. the hardening PR)

Findings demonstrated with pyshacl end-to-end probes against the stack tip; all apply equally to the consolidated branch of #18.

B1 — real bug: M4/M5 inner-slot paths resolve against the OUTER class.
_member_conditions calls self._slot_uri(sv, inner_name, cls) with the container class, but the inner slot lives on the container slot's range class (the neighboring _resolve_member_enum_ref gets this right for enums; the path resolution does not). Two demonstrated failure modes:

• False negative: child class overrides the inner slot's slot_uri via slot_usage → sh:path on the child shape uses the overridden IRI, the SPARQL body queries the base IRI → the constraint silently never fires.
• False positive: the inner slot name also exists on the outer class with a different slot_usage URI → the outer induced slot wins, the member pattern queries a predicate no member has, FILTER NOT EXISTS is vacuously true → conforming data flagged.
  Related: _resolve_member_enum_ref uses sv.get_slot(container_slot_name) (non-induced), so a slot_usage range-narrowing of the container slot on the outer class resolves enum values against the wrong enum.
  Fix direction: resolve inner_name (and the container range) against the container slot's induced range class, mirroring what _resolve_member_enum_ref does for enums.

B2 — real bug: recognized+unrecognized operator mixes are silently under-translated → false positives (contract violation).
The hardening PR fixed combining of recognized scalar operators, but a condition mixing a recognized with an unrecognized operator still translates with the unrecognized conjunct dropped: {equals_string: fog, pattern: "^f.*"} emits only the equals filter; expression-level any_of/all_of/none_of on pre/postconditions are ignored entirely (demonstrated: dropping an any_of precondition conjunct widened the trigger and pyshacl flagged a conforming instance). Postcondition side drops conjuncts too ({required: true, pattern: ...} → only required).
Fix direction: enumerate the set fields on each condition/expression and return None (skip) if anything outside the supported set is present.

B3 — real bug (artifact-poisoning edge): _sparql_number renders non-numeric bounds raw.
minimum_value/maximum_value have metamodel range Anything (the docstring's "LinkML parses as int or float" is incorrect). Demonstrated: minimum_value: "abc" → FILTER ( ?pre0 >= abc ) → pyshacl raises ParseException on every validation run against the generated shapes graph (one bad bound poisons validation of all data); a YAML date 2020-01-01 parses as the arithmetic expression 2020−01−01 = 2018 → constraint silently never fires; .nan/.inf also unparseable.
Fix direction: gate on isinstance(value, (int, float)) and not isinstance(value, bool) (covers the extended_* runtime subclasses) and propagate a skip otherwise.

B4 — edge case: elseconditions silently dropped.
bidirectional/open_world rules get explicit logger.warnings, but a rule with elseconditions is translated forward-only with no signal at all (the rule isn't skipped, so the DEBUG skip log doesn't fire). Demonstrated: a node failing only the else branch conforms.
Fix direction: warn (or skip) when elseconditions is set, consistent with the neighboring warnings.

Verified clean (attacked, held up): M2 conjunction semantics for multivalued slots (correct existential violation, deduplicated reports); M3 numeric promotion for well-typed data; M5 zero-member semantics (flagged, as "must contain a member" requires — though no test locks this in: suggest adding a zero-member violating instance); variable namespaces (?pre{i}/?post/?mem) are collision-free; deactivated/bidirectional handled before the fallback; pure value_presence: ABSENT preconditions are correctly rejected (skip).

Suggest addressing B1–B3 as a follow-up commit on this stack before upstreaming; the probe scripts are reusable as regression-test seeds.

[jdsika]

The substantive audit findings above are resolved in #22 (fix/shaclgen-rule-converter-audit-findings, stacked on this series) — one commit, 19 regression tests, 18 of which fail on the pre-fix source. See the finding→fix table in the #22 description.