chore: consolidated feature branch for ENVITED-X pipeline#14
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chore: consolidated feature branch for ENVITED-X pipeline#14
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Co-authored-by: Patrick Kalita <pkalita@lbl.gov>
…rrides Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>
fix(excelgen): move workbook.save outside loop
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> Signed-off-by: Carlo van Driesten <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> Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
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 new --message-template option that attaches sh:message literals to
each property shape using a user-defined template string.
Supported placeholders:
{name} — slot name (underscore-separated)
{title} — slot title (human-readable), falls back to name
{description} — slot description, falls back to empty string
{comments} — slot comments joined with "; ", falls back to empty string
{class} — enclosing class name
{path} — property IRI (compact or full)
The resulting message is stripped of leading/trailing whitespace and
omitted entirely when empty (avoids blank sh:message literals).
When --default-language is also set, the literal is language-tagged.
Example:
gen-shacl --message-template "{name} ({class}): {description} [{comments}]"
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 - 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>
The SHACL generator used Python truthiness checks for
minimum_cardinality and maximum_cardinality:
if s.minimum_cardinality: # 0 is falsy!
if s.maximum_cardinality: # 0 is falsy!
Since int(0) evaluates as False in Python, setting
maximum_cardinality: 0 (which should produce sh:maxCount 0,
meaning the property MUST NOT appear) silently emitted nothing.
This patch changes both checks to explicit `is not None`
comparisons, matching the pattern already used in the OWL
generator (owlgen.py lines 627-640) for the same attributes.
sh:maxCount 0 is valid per the W3C SHACL specification and means
"this property must not exist on any conforming node". This is
the standard mechanism for suppressing inherited properties on
subclasses via slot_usage with maximum_cardinality: 0.
Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
The SHACL generator translated any_of branches by dispatching
solely on `any.range` (class, type, enum, or simple datatype).
If a branch specified `pattern:` — either alone or combined
with a range — the constraint was silently dropped, producing
an empty blank node `[ ]` (trivially satisfied) instead of the
intended `[ sh:pattern "..." ]`.
This is a problem for schemas that use pattern alternatives in
`any_of`, such as the SPDX license field where valid values are
either members of a fixed enum (SPDX identifiers), IRIs, or
custom identifiers matching the LicenseRef- pattern defined in
SPDX Specification v2.3 Annex D (ABNF: license-ref =
["DocumentRef-"(idstring)":"]"LicenseRef-"(idstring)).
The fix adds a single check after the range dispatch:
if any.pattern:
g.add((range_list[-1], SH.pattern, Literal(any.pattern)))
This correctly handles:
- Pattern-only branches (no range): node gets only sh:pattern
- Range + pattern branches: node gets both sh:datatype and sh:pattern
- Range-only branches (no pattern): unchanged behaviour
The test suite now includes a dedicated schema exercising all
three cases, with assertions on both the generated RDF triples
and pyshacl validation of conforming/non-conforming data.
Signed-off-by: Carlo van Driesten <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> Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>
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Purpose
This PR exists solely to observe CI status for the combined feature branch used by the ENVITED-X asset pipeline. It is NOT intended to be merged.
Contents
9 commits stacked on upstream
main:DO NOT MERGE
This branch will be removed once all upstream PRs are merged.