Feat/us6.1 mapping utility

[ecarrenolozano]

This pull request introduces a new mapping lookup table (LUT) feature for ontology term translation, along with supporting utilities, API methods, and a demonstration notebook. It also updates pre-commit hooks and adds a new dependency. These changes make it easier to map and work with ontology terms across different databases.

Mapping LUT Feature and Utilities:

• Added a new MappingLUT class to represent mapping lookup tables for ontology IDs and database names, with utility methods for accessing mappings and database lists (ontograph/models.py).
• Implemented utility functions for reading mapping files, creating reverse mapping dictionaries, and translating term IDs using a LUT (ontograph/utils.py).

Client API Enhancements:

• Added methods to ClientOntology for loading mapping files, retrieving mapping LUTs, listing database names, and batch term retrieval (ontograph/client.py). [1] [2] [3] [4]
• Updated the ontology navigator to support batch retrieval of term objects and improved error handling (ontograph/queries/navigator.py).

Demonstration and Documentation:

• Added a new notebook chebi_mix_ontology.ipynb demonstrating the mapping LUT workflow and use cases.

Dependency and Tooling Updates:

• Added pandas as a dependency for mapping file operations (pyproject.toml).
• Updated pre-commit hook versions for ruff-pre-commit, pre-commit-hooks, and blacken-docs in .pre-commit-config.yaml. [1] [2] [3]

[Copilot]

Pull Request Overview

This pull request introduces a new mapping lookup table (LUT) feature for ontology term translation, enabling easier mapping and translation of ontology terms across different databases. The implementation includes comprehensive testing, utility functions, and API enhancements to support the new functionality.

• Adds MappingLUT class and utilities for reading mapping files and creating reverse mapping dictionaries
• Enhances ClientOntology with methods for loading mapping files, retrieving LUTs, and batch term retrieval
• Updates pre-commit hook versions and adds pandas dependency

Reviewed Changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
ontograph/utils.py	Core utilities for reading mapping files, creating reverse mappings, and translating term IDs
ontograph/models.py	New MappingLUT class to represent mapping lookup tables
ontograph/client.py	Client API enhancements for mapping operations and batch term retrieval
ontograph/queries/navigator.py	Updated navigator to support batch term retrieval with improved error handling
tests/test_utils.py	Comprehensive test suite for utility functions
tests/test_models.py	Test coverage for the new MappingLUT class
pyproject.toml	Adds pandas dependency
notebooks/chebi_mix_ontology.ipynb	Demonstration notebook showing mapping LUT workflow
.pre-commit-config.yaml	Updates pre-commit hook versions

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[Copilot]

Pull Request Overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated 1 comment.

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