feat(gen-shacl): translate presence-implies-value rules to SHACL-SPARQL

[jdsika]

Summary

Adds the presence-implies-value pattern to the rules → SHACL-SPARQL
converter: a precondition asserting value_presence: PRESENT on a guard slot
plus a postcondition constraining another slot with equals_string /
equals_string_in becomes a sh:SPARQLConstraint that flags focus nodes where
the guard is present but the target does not hold an allowed value.

It reads as "if the guard slot is present, the target slot must be present and
hold one of the allowed values" and generalises the existing boolean guard to
arbitrary enum values. Enum permissible values resolve to their meaning IRIs;
values without meaning compare as string literals. $this is pre-bound per
SHACL §5.3.1.

Example from the modeled use case: if sun_altitude is present, daytime must
be day or twilight — cross-parameter consistency that per-slot SHACL
property shapes cannot express.

Bug fixed along the way

The pre-existing boolean guard was not gated on the target slot's range. A slot
of range string carrying equals_string: "true" was translated as a boolean
comparison, which does not match the string "true" in the data — so conforming
instances were reported as violations. The guard now requires range boolean,
and string-ranged slots fall through to the presence-implies-value pattern and
compare as strings.

Translation contract: skip, never mis-translate

Pattern matching is exact. Each converter requires its conditions to set
precisely the operators it translates. A rule carrying anything further — extra
scalar operators, or expression-level any_of / all_of / none_of /
exactly_one_of — is skipped rather than partially translated, because dropping
a term would either widen the precondition (false positives) or weaken the
postcondition (false negatives).

Slot resolution goes through induced slots, so slot_usage overrides,
slot_uri overrides and alias-form keys all resolve to the same IRI that
sh:path emits.

Stack position

main
└─ #19  presence-implies-value      ← this PR
   └─ #20  compositional fallback (M1–M5)
      └─ #23  documentation

Note

No dependencies. This PR applies directly to main. The rules → SPARQL
framework it extends (_add_rules, _rule_to_sparql, the boolean-guard and
exclusive-value patterns) is already in main via linkml#3451.

Testing

pytest tests/linkml/test_generators/test_shaclgen.py — 105 passed, with
the full generator suite green (1774 passed, 52 skipped, 3 xfailed).
Coverage includes SPARQL syntax validation and pyshacl end-to-end conforming
/ violating round-trips for each pattern, plus negative tests asserting that
unsupported operator combinations are skipped rather than mis-translated.

Review notes

This PR was re-cut from an earlier five-PR stack. The corrections that were
previously separate follow-ups are folded into the feature they correct, so
there is no longer a PR that introduces a defect and another that fixes it.
Two defects found during that re-cut are fixed here: the boolean-guard range
gate above, and a duplicate test_rule_with_elseconditions_warns definition
that silently shadowed the existing test of the same name.

[jdsika]

Adversarial audit findings (PIV converter, audited at stack tip incl. the hardening PR)

Two substantive findings, both empirically demonstrated with pyshacl end-to-end probes and cross-checked against LinkML's reference rule semantics (gen-json-schema if/then realization):

A1 — real bug: greedy dispatch drops extra pre/postcondition operators → false positives.
_rule_to_sparql dispatches to presence-implies-value whenever the precondition has value_presence: PRESENT and the postcondition has equals_string/equals_string_in — without requiring these to be the only operators set. A precondition {value_presence: PRESENT, minimum_value: 100} loses the threshold: data with temp 50 (precondition unsatisfied, rule vacuously satisfied — LinkML's own JSON-Schema realization accepts it) is flagged as violating. Dual: extra postcondition operators are dropped too (equals_string alongside equals_string_in — the _in list silently wins). This widens/narrows the rule instead of skipping — a mis-translation, not a safe skip.
Fix direction: dispatch only when the pre/post conditions set exactly the pattern's operators; otherwise fall through (the fallback PR's _scalar_filters already does this accounting per-operator — the named patterns need the same exhaustiveness check).

A2 — edge case: boolean-guard shadows PIV for equals_string: "true" on non-boolean slots.
The boolean-guard branch keeps dispatch priority but never checks that the target slot's range is boolean. A rule "if opt present, status (range string) must equal "true"" is hijacked into a boolean comparison; both status "true" (conforming) and status "false" are flagged. Pre-existing in the framework, but this PR codifies the priority order, and PIV is the handler that would translate this rule correctly.
Fix direction: gate the boolean-guard branch on the induced post-slot range being boolean.

Verified clean (attacked, held up): absent-target semantics (violation via !BOUND, matches the JSON-Schema required realization); multivalued-target ∀ semantics (matches items:{const}); multivalued guards; mixed meaning/no-meaning equals_string_in sets (matches rdflib_dumper's IRI-vs-literal convention exactly).

Test gaps (cosmetic): test_presence_implies_value_no_meaning_falls_back_to_literal's "<Manual>" not in query assertion is vacuous (an erroneous emission would be a full IRI, never matching that string); no tests for combined operators (would have caught A1) or equals_string: "true" on a non-boolean slot (would have caught A2).

These findings equally apply to the consolidated branch of #18. Suggest addressing A1/A2 as a follow-up commit on this stack before upstreaming.

[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.

[jdsika]

Mirrored upstream as linkml#3989.