added storage functionality for raw windows #121

Oufattole · 2024-08-27T19:18:12Z

Resolves issue #97

Summary by CodeRabbit

New Features
- Introduced configuration options for specifying a directory and filename for exporting window statistics.
- Enhanced functionality to export window statistics to a specified location based on user configuration.
Tests
- Added a new test function to validate the command-line interface functionality for processing medication data.

coderabbitai · 2024-08-27T19:18:19Z

Walkthrough

The changes introduce new configuration options for specifying a directory and filename for storing window statistics, enhancing output handling capabilities. The main function has been updated to include logic for creating directories and writing the result DataFrame to a Parquet file when specified paths are provided. Additionally, a new test function has been implemented to validate the command-line interface for processing medication data and ensure the correct functionality of output file generation.

Changes

File	Change Summary
`src/aces/__main__.py`	Added conditional blocks to check for `window_stats_filepath` and `window_stats_dir`, writing `result` DataFrame to a specified Parquet file.
`src/aces/configs/aces.yaml`	Introduced `window_stats_dir`, `window_stats_filename`, and modified `window_stats_filepath` for configurable output file handling.
`tests/test_meds.py`	Added `test_meds_window_storage` function to validate CLI handling of medication data and output file generation.

Poem

🐇 In the fields where data flows,
A new path for stats now grows.
With files that gleam in Parquet's light,
Our rabbit code hops to new heights.
Testing the meds with joy and cheer,
Output's clear, the vision's near! 🥕✨

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coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 28bf935 and 410468d.

Files selected for processing (3)

src/aces/main.py (1 hunks)
src/aces/configs/aces.yaml (1 hunks)
tests/test_meds.py (1 hunks)

Additional comments not posted (5)

src/aces/configs/aces.yaml (2)

15-15: LGTM!

The comment is clear and provides necessary context for the new configuration option.

The code changes are approved.

16-16: LGTM!

The new configuration option window_stats_filepath is correctly added and follows the existing structure.

The code changes are approved.

src/aces/__main__.py (2)

176-176: LGTM!

The conditional check for cfg.window_stats_filepath is correctly implemented and follows the existing structure.

The code changes are approved.

177-177: LGTM!

The logic to write the result DataFrame to a Parquet file if cfg.window_stats_filepath is specified is correctly implemented and follows the existing structure.

The code changes are approved.

tests/test_meds.py (1)

373-458: LGTM!

The new test function test_meds_window_storage is comprehensive and correctly validates the functionality of the CLI related to processing medication data. The use of a temporary directory for managing input and output files is a good practice.

The code changes are approved.

src/aces/__main__.py

tests/test_meds.py

src/aces/configs/aces.yaml

…s check file directories

coderabbitai

Actionable comments posted: 3

Outside diff range, codebase verification and nitpick comments (1)

tests/test_meds.py (1)

373-376: Consider adding a docstring.

Adding a docstring to the function will improve readability and maintainability by explaining the purpose and functionality of the test.

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 410468d and 76a1ca2.

Files selected for processing (3)

src/aces/main.py (1 hunks)
src/aces/configs/aces.yaml (1 hunks)
tests/test_meds.py (1 hunks)

Files skipped from review as they are similar to previous changes (2)

src/aces/main.py
src/aces/configs/aces.yaml

Additional context used

Ruff

tests/test_meds.py

409-409: Use key in dict instead of key in dict.keys()

Remove .keys()

(SIM118)

Additional comments not posted (2)

tests/test_meds.py (2)

384-388: LGTM!

The setup of input files, task configurations, and expected outputs is correctly implemented.

389-425: LGTM!

The logic for managing the temporary directory, writing input files, and task configurations is correctly implemented. The command setup is also appropriate.

Tools

Ruff

409-409: Use key in dict instead of key in dict.keys()

Remove .keys()

(SIM118)

tests/test_meds.py

…necessary .keys() from loop

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 76a1ca2 and fa413de.

Files selected for processing (1)

tests/test_meds.py (2 hunks)

Files skipped from review as they are similar to previous changes (1)

tests/test_meds.py

src/aces/configs/aces.yaml

tests/test_meds.py

justin13601 · 2024-08-27T23:44:43Z

~~This is meant to save the original structs for the contrastive learning use case mentioned earlier right?~~

Edit: oops sorry, I missed this at the top, yes it resolves #97.

…toring window stats

coderabbitai

Actionable comments posted: 0

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Commits

Files that changed from the base of the PR and between fa413de and 41f8bde.

Files selected for processing (3)

src/aces/main.py (1 hunks)
src/aces/configs/aces.yaml (1 hunks)
tests/test_meds.py (3 hunks)

Files skipped from review as they are similar to previous changes (3)

src/aces/main.py
src/aces/configs/aces.yaml
tests/test_meds.py

added storage functionality for raw windows

410468d

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mmcdermott requested a review from justin13601 August 27, 2024 19:40

made shard specific file names for window stats storage and made test…

76a1ca2

…s check file directories

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addressed formatting changes (moved imports to the top and removed un…

fa413de

…necessary .keys() from loop

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Oufattole added 2 commits August 28, 2024 03:18

changed from window_stats_filename to window_stats_filepath

353d8a5

added thorough tests for checking the actual outputted windows when s…

41f8bde

…toring window stats

coderabbitai bot reviewed Aug 28, 2024

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justin13601 approved these changes Aug 28, 2024

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mmcdermott approved these changes Aug 28, 2024

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mmcdermott merged commit 3006041 into justin13601:main Aug 28, 2024
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added storage functionality for raw windows #121

added storage functionality for raw windows #121

Oufattole commented Aug 27, 2024 •

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added storage functionality for raw windows #121

added storage functionality for raw windows #121

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Oufattole commented Aug 27, 2024 • edited by coderabbitai bot Loading

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