Adds Metadata specifications to tasks, datasets, and models. by mmcdermott · Pull Request #168 · Medical-Event-Data-Standard/MEDS-DEV

mmcdermott · 2025-03-05T20:39:24Z

Closes We need a codified way to indicate what datasets are suitable for what tasks #60
Closes We need to track some metadata about tasks #151
Add documentation to README
Closes We need to track metadata about each model #152
Closes We need to track some metadata about each dataset #65
Closes [MIMIC-IV] What Metadata should be tracked for MIMIC-IV? #155

I've added @tompollard, @Jwoo5, @Oufattole, @ChaoPang, and @teyaberg as contact people for various tasks and models in this PR. Please affirm or deny that you are comfortable with this when you have a chance.

… supported dataset. Closes #60 and #151. Still need to apply to datasets and models.

coderabbitai · 2025-03-05T20:39:32Z

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

Review comments: Directly reply to a review comment made by CodeRabbit. Example:
- I pushed a fix in commit <commit_id>, please review it.
- Generate unit testing code for this file.
- Open a follow-up GitHub issue for this discussion.
Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
- @coderabbitai generate unit testing code for this file.
- @coderabbitai modularize this function.
PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
- @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
- @coderabbitai read src/utils.ts and generate unit testing code.
- @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
- @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

@coderabbitai pause to pause the reviews on a PR.
@coderabbitai resume to resume the paused reviews.
@coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
@coderabbitai full review to do a full review from scratch and review all the files again.
@coderabbitai summary to regenerate the summary of the PR.
@coderabbitai generate docstrings to generate docstrings for this PR.
@coderabbitai resolve resolve all the CodeRabbit review comments.
@coderabbitai configuration to show the current CodeRabbit configuration for the repository.
@coderabbitai help to get help.

Other keywords and placeholders

Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (`.coderabbit.yaml`)

You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
Please see the configuration documentation for more information.
If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

Visit our Documentation for detailed information on how to use CodeRabbit.
Join our Discord Community to get help, request features, and share feedback.
Follow us on X/Twitter for updates and announcements.

codecov · 2025-03-05T20:41:37Z

Codecov Report

Attention: Patch coverage is 97.16981% with 3 lines in your changes missing coverage. Please review.

Project coverage is 95.29%. Comparing base (098ab79) to head (3012935).

✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/MEDS_DEV/datasets/__init__.py	96.29%	1 Missing ⚠️
src/MEDS_DEV/tasks/__init__.py	95.45%	1 Missing ⚠️
src/MEDS_DEV/utils.py	98.14%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #168      +/-   ##
==========================================
+ Coverage   94.78%   95.29%   +0.50%     
==========================================
  Files          11       11              
  Lines         345      446     +101     
==========================================
+ Hits          327      425      +98     
- Misses         18       21       +3

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

README.md

src/MEDS_DEV/models/cehrbert/model.yaml

src/MEDS_DEV/models/meds_tab/tiny/model.yaml

README.md

Co-authored-by: Kamilė Stankevičiūtė <33470490+kamilest@users.noreply.github.com>

Oufattole

LGTM

kamilest

Looks good to me!

ChaoPang

Looks good to me!

Added a metadata specification and corrected task metadata, including…

16033ce

… supported dataset. Closes #60 and #151. Still need to apply to datasets and models.

corrected typo

d5227b9

mmcdermott requested review from Jwoo5 and Oufattole March 5, 2025 20:50

Added model metadata.

809365b

mmcdermott requested a review from ChaoPang March 5, 2025 20:53

Added dataset metadata and README descriptions

a221108

mmcdermott requested a review from tompollard March 5, 2025 21:27

kamilest reviewed Mar 5, 2025

View reviewed changes

Jwoo5 approved these changes Mar 6, 2025

View reviewed changes

prockenschaub mentioned this pull request Mar 6, 2025

[Dataset] Adds dataset AUMCdb #147

Open

mmcdermott and others added 4 commits March 6, 2025 10:20

Update README.md

44313aa

Co-authored-by: Kamilė Stankevičiūtė <33470490+kamilest@users.noreply.github.com>

Update README.md

820969c

Co-authored-by: Kamilė Stankevičiūtė <33470490+kamilest@users.noreply.github.com>

Apply suggestions from code review

ed356be

Co-authored-by: Kamilė Stankevičiūtė <33470490+kamilest@users.noreply.github.com>

Added information about the access policy enum

3012935

mmcdermott requested a review from kamilest March 6, 2025 17:04

mmcdermott linked an issue Mar 6, 2025 that may be closed by this pull request

[MIMIC-IV] What Metadata should be tracked for MIMIC-IV? #155

Closed

Oufattole approved these changes Mar 6, 2025

View reviewed changes

kamilest approved these changes Mar 6, 2025

View reviewed changes

ChaoPang approved these changes Mar 7, 2025

View reviewed changes

mmcdermott merged commit c6dbb4b into dev Mar 8, 2025
8 checks passed

mmcdermott mentioned this pull request Mar 8, 2025

Added GenHPF model #170

Merged

mmcdermott deleted the add_metadata branch March 12, 2025 20:20

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Adds Metadata specifications to tasks, datasets, and models.#168

Adds Metadata specifications to tasks, datasets, and models.#168
mmcdermott merged 8 commits intodevfrom
add_metadata

mmcdermott commented Mar 5, 2025 •

edited

Loading

Uh oh!

coderabbitai bot commented Mar 5, 2025

Review skipped

Chat

CodeRabbit Commands (Invoked using PR comments)

Other keywords and placeholders

CodeRabbit Configuration File (`.coderabbit.yaml`)

Documentation and Community

Uh oh!

codecov bot commented Mar 5, 2025 •

edited

Loading

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Oufattole left a comment

Uh oh!

kamilest left a comment

Uh oh!

ChaoPang left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

Conversation

mmcdermott commented Mar 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

coderabbitai bot commented Mar 5, 2025

Review skipped

Chat

CodeRabbit Commands (Invoked using PR comments)

Other keywords and placeholders

CodeRabbit Configuration File (.coderabbit.yaml)

Documentation and Community

Uh oh!

codecov bot commented Mar 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Oufattole left a comment

Choose a reason for hiding this comment

Uh oh!

kamilest left a comment

Choose a reason for hiding this comment

Uh oh!

ChaoPang left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

mmcdermott commented Mar 5, 2025 •

edited

Loading

CodeRabbit Configuration File (`.coderabbit.yaml`)

codecov bot commented Mar 5, 2025 •

edited

Loading