Support derived predicates between static predicates and plain predicates, as well as nested derived predicates

justin13601 commented 4 weeks ago

For #144

Summary by CodeRabbit

New Features
- Enhanced handling of static variables in derived predicates for improved output accuracy.
- Improved error messaging for unsupported data standards.
- Support for defining predicates in a separate configuration file, allowing for greater flexibility.
- Expanded predicates configuration language to include regular expressions and multi-column constraints.
- Added validation for predicate definitions to prevent misconfigurations.
- New logging feature to check the uniqueness of labels extracted from cohorts.
Documentation
- Added example usages in the documentation for better user guidance on new functionalities.
- Enhanced clarity and detail in the README and configuration documents regarding task setup and usage.
- Updated FAQs section to address common queries about static data handling.
- Clarified installation instructions and refined usage guidance for task configuration files.
Chores
- Updated code quality checks and test workflows for improved reliability and performance.
- Updated pre-commit hooks to the latest version for enhanced functionality.
- Improved error handling and validation in configuration loading processes.

coderabbitai[bot] commented 4 weeks ago

Walkthrough

The changes in this pull request involve enhancements to the get_predicates_df function in src/aces/predicates.py, improving the handling of static variables in derived predicates and refining error messaging. Additionally, several GitHub Actions workflow files have been updated to use newer versions of actions and to include additional steps for installing development packages. The .pre-commit-config.yaml has been updated to a newer version of pre-commit-hooks, while the pyproject.toml file restricts the pre-commit dependency to versions less than 4. The README.md and docs/source/configuration.md files have also been updated to improve documentation clarity and usability.

Changes

File	Change Summary
`src/aces/predicates.py`	Enhanced `get_predicates_df` to handle static variables in derived predicates; improved error handling; added example usages in docstring.
`.github/workflows/code-quality-main.yaml`	Updated `actions/checkout` and `actions/setup-python` to versions 4 and 5; added step to install dev packages; updated `pre-commit/action`.
`.github/workflows/code-quality-pr.yaml`	Similar updates as `code-quality-main.yaml`, including action version upgrades and new dev package installation step.
`.github/workflows/tests.yml`	Upgraded `actions/checkout` and `actions/setup-python`; changed package installation command.
`.pre-commit-config.yaml`	Updated `pre-commit-hooks` repository version from `v4.4.0` to `v5.0.0`.
`pyproject.toml`	Updated `pre-commit` dependency constraint from `"pre-commit"` to `"pre-commit<4"`.
`README.md`	Enhanced documentation for ACES, added details on new features, predicates configuration, and installation instructions.
`docs/source/configuration.md`	Clarified configuration language specification, added notes on memory optimization, and detailed field explanations.
`src/aces/config.py`	Improved error handling in `TaskExtractorConfig` for predicate definitions; updated docstring examples.
`src/aces/query.py`	Enhanced logging and error handling in `query` function for label extraction.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Predicates
    participant DataFrame

    User->>Predicates: Call get_predicates_df()
    Predicates->>DataFrame: Retrieve static variables
    DataFrame-->>Predicates: Return static variable values
    Predicates->>DataFrame: Process derived predicates
    DataFrame-->>User: Return updated DataFrame

🐇 "In code we hop and play,
With predicates bright as day,
Static values now align,
In our DataFrame, they shine!
With workflows fresh and neat,
Our coding journey's sweet!" 🐇

📜 Recent review details

**Configuration used: CodeRabbit UI** **Review profile: CHILL**

📥 Commits

Files that changed from the base of the PR and between f5b0dbcd3a7d68f5016e42a921c71500623a2d86 and 89023651b5d57e5faca0b85607083a4d2dc9783b.

📒 Files selected for processing (1)

* src/aces/config.py (6 hunks)

🧰 Additional context used

🪛 GitHub Check: codecov/patch

src/aces/config.py
[warning] 1378-1378: src/aces/config.py#L1378 Added line #L1378 was not covered by tests

🔇 Additional comments (5)

src/aces/config.py (5)
`1077-1077`: **LGTM! Improved error message clarity.** The error message now clearly indicates the number of missing relationships and provides better context. --- `1169-1169`: **Excellent documentation improvements!** The added examples effectively demonstrate: 1. Configuration loading with predicates 2. Static and plain predicate joining 3. Complex nested derived predicates This significantly improves the understanding of the configuration system. Also applies to: 1199-1258 --- `1399-1404`: **LGTM! Enhanced input validation.** The added validation properly catches incorrect string-based predicate definitions and provides clear guidance on the correct format. --- `1454-1454`: **LGTM! Consistent error message formatting.** The error message formatting maintains consistency with the codebase style and improves readability. --- `1339-1339`: **LGTM! Robust predicate handling implementation.** The changes effectively: 1. Merge predicates from multiple sources 2. Recursively validate nested derived predicates 3. Build a comprehensive set of referenced predicates However, there's an uncovered code path. Let's verify the test coverage: Also applies to: 1353-1391

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codecov[bot] commented 4 weeks ago

Codecov Report

Attention: Patch coverage is 95.00000% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/aces/config.py	93.75%	1 Missing :warning:

Files with missing lines	Coverage Δ
src/aces/predicates.py	`83.59% <100.00%> (-0.41%)`	:arrow_down:
src/aces/query.py	`72.09% <ø> (-23.66%)`	:arrow_down:
src/aces/config.py	`97.22% <93.75%> (-0.41%)`	:arrow_down:

... and 4 files with indirect coverage changes

justin13601 commented 4 weeks ago

@mmcdermott I tried to implement a way to allow for derived predicates joining static and plain predicates - basically I just copy over the static predicate values from the null timestamp rows throughout the same subject_id if they exist since these are static and do not change. Then the logic for the evaluation of the derived predicates shouldn't need to change. Does this seem reasonable?

justin13601 commented 4 weeks ago

Might be a bit difficult to properly test the new error/warning messages in query.py...

mmcdermott commented 3 weeks ago

@justin13601, can you add tests to get the codecov up to the desired target?

justin13601 commented 3 weeks ago

Also closes #94

justin13601 commented 3 weeks ago

@mmcdermott I realized nested derived predicates will most likely be needed for creating these different reference ranges so I tried to enable that. Let me know if the following seems reasonable:

To create different reference ranges (for illustration purposes, not following actual clinical guidelines):

Different normal ranges:

  normal_spo2_male_range:
    code: lab_name//O2 saturation pulseoxymetry (%)
    value_min: 90
    value_max: 120
    value_min_inclusive: True
    value_max_inclusive: True
  normal_spo2_female_range:
    code: lab_name//O2 saturation pulseoxymetry (%)
    value_min: 80
    value_max: 110
    value_min_inclusive: True
    value_max_inclusive: True
  normal_spo2_male:
    expr: and(normal_spo2_male_range, male)
  normal_spo2_female:
    expr: and(normal_spo2_female_range, female)

Different abnormal ranges (may be worth looking into not() logic...:

  abnormally_low_spo2_male:
    code: lab_name//O2 saturation pulseoxymetry (%)
    value_max: 90
    value_max_inclusive: False
  abnormally_low_spo2_female:
    code: lab_name//O2 saturation pulseoxymetry (%)
    value_max: 80
    value_max_inclusive: False
  abnormally_high_spo2:
    code: lab_name//O2 saturation pulseoxymetry (%)
    value_min: 120
    value_min_inclusive: False
  abnormal_spo2_male_range:
    expr: or(abnormally_low_spo2_male, abnormally_high_spo2)
  abnormal_spo2_male:
    expr: and(abnormal_spo2_male_range, male)
  abnormal_spo2_female_range:
    expr: or(abnormally_low_spo2_female, abnormally_high_spo2)
  abnormal_spo2_female:
    expr: and(abnormal_spo2_female_range, female)
  abnormal_spo2:
    expr: or(abnormal_spo2_male, abnormal_spo2_female)

mmcdermott commented 3 weeks ago

@justin13601 this LGTM, so merge at your leisure.

justin13601 / ACES