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Emit warnings for abstract class covering axiom edge cases: - Zero children: warn that no covering axiom will be generated - One child: warn that the covering axiom degenerates to an equivalence (Parent = Child), recommending --skip-abstract-class-as-unionof-subclasses Both axioms are still emitted when applicable (semantically correct per OWL 2), but warnings alert users who extend the ontology downstream. Tests verify warnings are logged, flag suppression works, the single-child covering axiom triple is correctly asserted, plus negative tests for multi-child and concrete class cases, and the mixin-only children edge case. Refs: linkml#3309, linkml#3219 Signed-off-by: jdsika <carlo.van-driesten@bmw.de>
… consistency JSON-LD processors treat xsd:anyURI as an opaque string literal, so range:uri/uriorcurie slots get xsd:anyURI coercion instead of proper IRI node semantics (@type:@id, owl:ObjectProperty, sh:IRI). Add an opt-in --xsd-anyuri-as-iri flag that promotes xsd:anyURI ranges to IRI semantics across all three generators: - JSON-LD context: @type: xsd:anyURI → @type: @id - OWL: DatatypeProperty → ObjectProperty (no rdfs:range restriction) - SHACL: sh:datatype xsd:anyURI → sh:nodeKind sh:IRI The flag only affects types whose XSD mapping is xsd:anyURI (uri and uriorcurie). The curie type (xsd:string) is correctly excluded via is_xsd_anyuri_range() to maintain cross-generator consistency. Standards basis: - OWL 2 §5.3-5.4 (ObjectProperty vs DatatypeProperty) - SHACL §4.8.1 (sh:nodeKind sh:IRI) - JSON-LD 1.1 §4.2.2 (type coercion with @id) - RDF 1.1 §3.2-3.3 (IRIs as first-class nodes, not string literals) Signed-off-by: jdsika <carlo.van-driesten@bmw.de>
…lib serialization Add a --deterministic / --no-deterministic CLI flag (default off) to OWL, SHACL, JSON-LD Context, and JSON-LD generators that produces byte-identical output across invocations. Three-phase hybrid pipeline for Turtle generators: 1. RDFC-1.0 canonicalization (W3C Recommendation) via pyoxigraph 2. Weisfeiler-Lehman structural hashing for diff-stable blank node IDs 3. Hybrid rdflib re-serialization for idiomatic Turtle (inline blank nodes, collection syntax, prefix filtering) JSON generators use deterministic_json() with recursive deep-sort and JSON-LD-aware key ordering that preserves conventional @context structure. Collection items (owl:oneOf, sh:in, sh:ignoredProperties) are sorted when --deterministic is set to ensure reproducible RDF list order. pyoxigraph >= 0.4.0 is imported lazily only when --deterministic is used. Tests skip gracefully when pyoxigraph is unavailable. Refs: linkml#1847 Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de> Signed-off-by: jdsika <carlo.van-driesten@bmw.de>
… names Add an opt-in --normalize-prefixes flag to OWL, SHACL, and JSON-LD Context generators that normalises non-standard prefix aliases to well-known names from a static prefix map (derived from rdflib 7.x defaults, cross-checked against prefix.cc consensus). Key design decisions: - Static frozen map (MappingProxyType) instead of runtime Graph().namespaces() lookup eliminates rdflib version dependency - Both http://schema.org/ and https://schema.org/ map to 'schema' - Shared normalize_graph_prefixes() helper used by OWL and SHACL - Two-phase graph normalisation: Phase 1 normalises schema-declared prefixes, Phase 2 cleans up runtime-injected bindings - Collision detection: skip with warning when standard prefix name is already user-declared for a different namespace - Phase 2 guard prevents overwriting HTTPS bindings with HTTP variants The flag defaults to off, preserving existing behaviour. Tests cover OWL, SHACL, and context generators with sdo->schema, dce->dc, http/https edge case, custom prefix preservation, flag-off backward compatibility, cross-generator consistency, prefix collision detection, schema1 regression prevention, Phase 2 HTTPS guard, empty schema edge case, and static map integrity. Signed-off-by: jdsika <carlo.van-driesten@bmw.de>
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Emit @type: @vocab with a scoped @vocab namespace for enum-ranged slots whose permissible values all have meaning IRIs that share a single namespace and whose text matches the meaning local name. This enables bare string enum values (e.g. "RoadTypeMotorway") to expand to full IRIs via JSON-LD 1.1 type coercion (section 4.2.3) combined with scoped contexts (section 4.1.8). The combined context preserves backward compatibility with structured {text, description, meaning} objects via the existing SKOS mappings. Enums that don't meet the eligibility criteria (missing meanings, mixed namespaces, or text/local-name mismatches) fall back to the existing ENUM_CONTEXT behavior. Refs: linkml#2497 Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
…erals Add a `--default-language` CLI option to both gen-owl and gen-shacl that emits BCP 47 language-tagged string literals for human-readable annotations. gen-owl changes: - New `default_language` field on OwlSchemaGenerator - `_LANGUAGE_TAGGABLE_RANGES` frozenset (string, ncname) guards tagging - `_resolve_language()` checks element-level in_language first, then default - `_literal()` helper creates properly tagged Literal objects - `add_metadata()` tags string-range and fallback-range literals - `add_enum()` PV labels respect language tags - New `--default-language` Click option gen-shacl changes: - New `default_language` field on ShaclGenerator - NodeShape rdfs:label / rdfs:comment get language tags - PropertyShape sh:name / sh:description get language tags via prop_pv_text() - Numeric literals (sh:order, sh:minCount, etc.) are never tagged - New `--default-language` Click option Tests: - 3 new OWL tests: tagged labels, backward-compat plain literals, URI ranges - 4 new SHACL tests: NodeShape, PropertyShape, plain literals, numeric guard Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
…apes
Add a --message-template CLI option to gen-shacl that generates
sh:message literals on every property shape from a user-supplied
template string.
Supported placeholders:
- {name} - slot name (underscore-separated LinkML identifier)
- {title} - slot title (human-readable), falls back to name
- {class} - enclosing class name
- {path} - property IRI
Example usage:
gen-shacl --message-template 'Validation of {name} failed!' schema.yaml
This enables SHACL validators (e.g. pyshacl) to produce human-friendly
error messages identifying the specific constraint that was violated.
Changes:
- New message_template field on ShaclGenerator dataclass
- Template expansion after sh:name / sh:description emission
- Uses prop_pv_text for language tag support when combined with
--default-language (sh:message gets language tag per SHACL 2.1.5)
- Invalid/positional placeholders and format specs raise ValueError
with helpful message (catches KeyError, IndexError, ValueError)
- Empty and whitespace-only templates normalised to None (no emission)
- New --message-template Click CLI option
- 10 new tests: basic, title/class placeholders, backward-compat,
invalid/positional/format-spec errors, empty/whitespace, combined
Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
Implement SHACL-SPARQL constraint generation for the boolean-guard pattern commonly used in conditional validation rules. When a LinkML class has rules: blocks with preconditions (value_presence: PRESENT) and postconditions (equals_string: true), the generator now emits sh:SPARQLConstraint nodes on the corresponding sh:NodeShape. Features: - New _add_rules() method translates recognised rule patterns to SPARQL - Boolean-guard pattern: if value present then flag must be true - Rule description mapped to sh:message on the constraint - Language-tagged sh:message when --default-language is set - Deactivated rules are skipped - Warnings emitted for bidirectional/open_world rule flags - New --emit-rules/--no-emit-rules CLI flag (default: enabled) - Full URI references in SPARQL (no PREFIX declarations needed) The generated SPARQL follows W3C SHACL Section 5 and uses the pre-bound \ variable per Section 5.3.1. Constraints are validated by pyshacl with advanced=True. Refs: linkml#2464 Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
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