Enhance OWL enum/permissible value handling and add comprehensive test coverage #2950
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…t coverage This commit improves the OWL generator's handling of permissible values and enums, with better type mapping support and comprehensive test coverage for different OWL representation strategies. ## Changes ### linkml/generators/owlgen.py - Add support for owl: and rdfs: prefixed default permissible value types in `_permissible_value_owl_type_for()` - Add metadata handling for enum definitions via `add_metadata()` call in `_add_enum()` - Add metadata handling for individual permissible value nodes when they are URIRefs - Improve type signature of `add_metadata()` to accept PermissibleValue objects - Add clarifying comment about non-null PV validation logic ### tests/test_generators/test_owlgen.py - Add comprehensive parameterized test `test_permissible_values()` covering: - Different default permissible value types (owl:Class, rdfs:Literal, owl:NamedIndividual) - Per-PV type overrides via implements field - Mixed URI/non-URI permissible value scenarios - Add detailed docstring documenting OWL mapping strategies and expected behaviors - Add PermissibleValueURIMixture enum for test parameterization - Test validates correct owl:unionOf vs owl:oneOf usage based on PV types ### linkml/utils/schema_builder.py - Fix bug in `add_enum()` where PermissibleValue objects weren't being added to enum definition ## Related Issues - Addresses TODO comments in owlgen.py lines 668, 929, 1186, 1205 regarding enum mapping - References #1841 for complex enum constraints The test suite now comprehensively validates that: - owl:Class permissible values generate owl:unionOf expressions with URIRef elements - rdfs:Literal permissible values generate owl:oneOf expressions with Literal elements - owl:NamedIndividual permissible values generate owl:oneOf expressions with URIRef elements - Mixed type scenarios work correctly or are skipped when undefined 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #2950 +/- ##
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+ Coverage 80.11% 83.95% +3.84%
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Files 141 141
Lines 15828 15835 +7
Branches 3210 3212 +2
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+ Hits 12680 13295 +615
+ Misses 2479 1830 -649
- Partials 669 710 +41 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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- Fix import sorting to comply with ruff formatting rules - Break long line in pytest parametrize decorator to stay under 120 character limit 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Add proper blank lines between class definitions - Fix parametrize decorator formatting - Fix indentation and spacing in permissible_values list - Add blank line after Collection import - Remove trailing whitespace and fix end-of-file formatting 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Replace modern union syntax (str | None) with typing.Union syntax to support Python 3.9 where the | operator for types was not yet available. - Add typing.Union import - Replace str | None | tuple[str, str] with Union[str, None, tuple[str, str]] - Update docstring to use Union syntax as well This fixes the TypeError: unsupported operand type(s) for |: 'type' and 'NoneType' error in Python 3.9 CI runs. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
The snapshots now include metadata (skos:definition, etc.) for enum definitions and permissible values, which is the expected behavior after the OWL generator enhancements in the previous commits. Changes reflect: - Addition of metadata properties for enum definitions - Addition of metadata properties for permissible value nodes (when URIRefs) - Proper skos:definition properties from enum and PV descriptions These changes improve the semantic richness of generated OWL output by preserving documentation and metadata from the LinkML schema. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Add comprehensive documentation to owl.rst covering: - CLI options for controlling enum/permissible value generation - Schema-level annotations using `implements` for fine-grained control - Examples of enum-level vs per-PV control - OWL output patterns for different PV types (Class, NamedIndividual, Literal) - Mixed type enums and URI vs text-based representations - Advanced usage examples with external vocabularies The documentation now clearly explains: 1. How to use --default-permissible-value-type CLI option 2. How to use implements annotations at enum and PV level 3. The semantic differences between owl:unionOf vs owl:oneOf 4. How URIs/meanings affect the OWL representation 5. Advanced patterns for semantic web integration 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
amc-corey-cox
requested changes
Oct 20, 2025
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@cmungall just let me know if it's okay to remove those print statements and I'll do so and get this merged. |
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go ahead and remove the prints, you can trim excess verbiage from the docstring but for nuanced combinatorial logic I favor n the side of exhaustiveness |
amc-corey-cox
approved these changes
Oct 21, 2025
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This commit improves the OWL generator's handling of permissible values and enums,
with better type mapping support and comprehensive test coverage for different
OWL representation strategies.
Changes
linkml/generators/owlgen.py
_permissible_value_owl_type_for()add_metadata()call in_add_enum()add_metadata()to accept PermissibleValue objectstests/test_generators/test_owlgen.py
test_permissible_values()covering:linkml/utils/schema_builder.py
add_enum()where PermissibleValue objects weren't being added to enum definitionRelated Issues
rangeand apatternresults in generated OWL that won't pass validation (like with jena riot, loading into a triplestore) #1841 for complex enum constraintsThe test suite now comprehensively validates that:
🤖 Generated with Claude Code
Co-Authored-By: Claude [email protected]