Add definition method to OLS implementation #831
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- Added definition and definitions methods to OLS implementation - Added LANGUAGE_TAG type to types.py - Fixed MRO issue by correcting inheritance hierarchy - Added tests for the new methods This change completes the BasicOntologyInterface implementation in OLS adapter. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Remove trailing whitespace to fix ruff check issues. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
- Remove unused imports - Fix exception handling that doesn't use exception variable - Fix import sorting 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Split long lines into multiple lines using parenthesized multi-line strings. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
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Pull Request Overview
This PR adds new definition methods to the OLS implementation, updates the inheritance order for the base class, and adjusts related tests and configuration files.
- Introduces the definition and definitions methods with a dedicated definition cache.
- Fixes the MRO issue by reordering base classes and updates tests to mock new functionality.
- Updates YAML configuration files for typos and improves type definitions.
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/oaklib/implementations/ols/ols_implementation.py | Added definition methods, updated caching mechanism, and restructured inheritance order. |
| tests/test_implementations/test_ols.py | Added and modified tests to cover the new definition methods and adjusted mock setups. |
| src/oaklib/datamodels/value_set_configuration.yaml | Fixed a typo in the description and added missing descriptions to attributes. |
| src/oaklib/types.py | Introduced a new LANGUAGE_TAG type. |
| src/oaklib/conf/lexmatch-rules-oboinowl-default.yaml | Updated rule keys and corrected descriptions; potential issue in the regex for matching box brackets. |
Comments suppressed due to low confidence (1)
src/oaklib/conf/lexmatch-rules-oboinowl-default.yaml:73
- The regex for matching content in box brackets may be incorrect: using [^)] excludes a closing parenthesis rather than a closing bracket. Consider changing it to r'[[^\]]*]' to properly match text inside square brackets.
match: r'\[[^)]*\]'
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This change completes the BasicOntologyInterface implementation in OLS adapter.
🤖 Generated with Claude Code
Co-Authored-By: Claude [email protected]