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justin13601 / ACES

ACES: Automatic Cohort Extraction System for Event-Streams
https://eventstreamaces.readthedocs.io/en/latest/
MIT License
21 stars 1 forks source link

Adding more comprehensive tests across the API. #28

Closed mmcdermott closed 4 months ago

mmcdermott commented 4 months ago

Still in draft mode. Some minor changes to the API expected.

Summary by CodeRabbit

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Commits Files that changed from the base of the PR and between e35d5a439e4b0e856c88fdb9a374673dc353c669 and 5ddfc1e89aa0f7adfeb7fc353946e4bf8afd511a.

Walkthrough

This update introduces a comprehensive overhaul to the configuration and querying system for extracting data from structured EHR data. Key changes include the addition of new dependencies, enhancements to constraint validation, and significant refactoring of predicate generation and query functions. The update also includes new utility functions, updated sample configurations, and improved documentation.

Changes

File/Path Change Summary
config_str_language.md Introduced detailed specification for the configuration language for EHR data extraction.
pyproject.toml Added "networkx == 3.3" to the list of dependencies.
src/esgpt_task_querying/constraints.py Added check_constraints function with new parameters and logic for constraints validation.
src/esgpt_task_querying/extract_subtree.py Updated extract_subtree function with new parameter subtree_root_offset.
src/esgpt_task_querying/predicates.py Refactored generate_predicate_columns to generate_predicates_df with new parameters and logic.
src/esgpt_task_querying/query.py Updated query function with new parameter names and imports, added type validation.
src/esgpt_task_querying/types.py Introduced TemporalWindowBounds and ToEventWindowBounds named tuples with methods for Polars ops.
sample_configs/01-inhospital-mortality.yaml Restructured predicates and windows sections, updated admission, discharge, death, and gap definitions.
src/esgpt_task_querying/utils.py Added parse_timedelta function for parsing time strings into timedelta objects.
terminology.md Introduced terminology and design details for the algorithm extracting valid time windows from event data.
.gitignore Added result.csv to ignored files.
run.py Renamed and restructured functions for loading data, updated logic for different file formats.
run.yaml Updated data_path configuration from sample_data/esgpt_sample to sample_data/sample.csv.

🐇 Code changes come and go, like springtime's gentle breeze, With predicates and windows, we query with such ease. Constraints now stand tall, in the forest of our code, And data flows like rivers, down a well-defined road. So here's a rabbit's cheer, for the updates that we see, May our queries be swift, and our data ever free! 🌸

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codecov-commenter commented 4 months ago

Codecov Report

Attention: Patch coverage is 94.44444% with 12 lines in your changes are missing coverage. Please review.

Files Coverage Δ
src/esgpt_task_querying/constraints.py 100.00% <100.00%> (ø)
src/esgpt_task_querying/types.py 100.00% <100.00%> (ø)
src/esgpt_task_querying/extract_subtree.py 94.11% <94.11%> (ø)
src/esgpt_task_querying/aggregate.py 93.97% <93.97%> (ø)
src/esgpt_task_querying/summarize.py 37.50% <64.28%> (-3.07%) :arrow_down: