Multirun capabilities and other improvements

[mmcdermott]

Summary by CodeRabbit

• Documentation

  • Enhanced installation instructions and detailed steps for running the MEDS extraction ETL process.
  • Added a README for the eICU-CRD v2.0 dataset extraction example.

• New Features

  • Introduced a batch script for job execution with defined resource allocations.
  • Added integration tests to verify ETL pipeline correctness.
  • Added new configuration files for various pipeline stages and data processing.

• Bug Fixes

  • Updated file handling and processing conditions to improve reliability.

• Refactor

  • Restructured configuration files to define stages and parameters more clearly.
  • Adjusted extraction configuration keys and values for consistency.

• Chores

  • Updated pre-commit hooks for code cleanup and unused import removal.

[coderabbitai]

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Walkthrough

The changes primarily enhance the MEDS data extraction and preprocessing pipeline, adding new configurations, scripts, and instructions for handling MIMIC-IV and eICU datasets. Key updates include improved installation commands, parallel processing options, and detailed guidance for running ETL processes locally, in parallel, or over Slurm. Additionally, new configuration files and scripts streamline the data processing stages, ensuring efficient and accurate data handling.

Changes

File(s)	Change Summary
.pre-commit-config.yaml	Added arguments --in-place and --remove-all-unused-imports to the autoflake hook.
MIMIC-IV_Example/README.md	Updated installation and MEDS extraction ETL process instructions, including local, parallel, and Slurm options.
MIMIC-IV_Example/joint_script.sh	No changes to exported entities; script processes MIMIC-IV data through various steps.
MIMIC-IV_Example/joint_script_slurm.sh	No changes to exported entities; script processes MIMIC-IV data using submitit Hydra launcher.
MIMIC-IV_Example/pre_MEDS.py	Modified fix_static_data function, added conditional checks and file handling logic in main.
MIMIC-IV_Example/sbatch_joint_script.sh	Introduced a batch script for running jobs with defined resource allocations and output configurations.
README.md	Enhanced MEDS data extraction and preprocessing pipeline instructions, added integration tests, updated configuration files, and provided details on running the pipeline in parallel.
configs/extraction.yaml	Restructured to define a pipeline for extracting raw MEDS events, added stages, and updated configurations.
configs/pipeline.yaml	Introduced configurations for a MEDS pipeline ETL process, defining global IO settings and Hydra settings for job execution.
configs/preprocess.yaml	Restructured pipeline stages, introduced new stages, and updated parameters.
eICU_Example/README.md	Provided steps for extracting a MEDS dataset from eICU-CRD v2.0 dataset, outlining installation, data preparation, and ETL process.
eICU_Example/configs/event_configs.yaml	Introduced structured configuration for various patient events and data points in eICU datasets.
eICU_Example/configs/pre_MEDS.yaml	Introduced configuration settings for data processing pipeline, including Hydra configuration for job naming and logging.
eICU_Example/configs/table_preprocessors.yaml	Introduced configurations for medical data tables, specifying offset and pseudotime columns, output data columns, and warning items.
eICU_Example/joint_script.sh	No changes to exported entities; script automates processing of eICU data through various steps.
eICU_Example/joint_script_slurm.sh	No changes to exported entities; script facilitates processing of eICU data using submitit Hydra launcher.
eICU_Example/pre_MEDS.py	Added functions for pre-MEDS data wrangling for eICU datasets, utilizing Hydra for configuration management and logging.
tests/test_extraction.py	Modified extraction configuration kwargs, updated directory paths and assertions, adjusted directory names, and error handling in test logic.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Script
    participant ETL_Process
    participant Slurm
    User->>Script: Initiate ETL Process
    Script->>ETL_Process: Start Local/Parallel Processing
    Script->>Slurm: Submit Job (if Slurm)
    Slurm->>ETL_Process: Execute ETL Stages
    ETL_Process->>Script: Process Data
    Script->>User: Completion Notification

Loading

Poem

In data's maze, we find our way,
With scripts and configs, night and day.
From MIMIC to eICU's embrace,
Extraction flows with newfound grace.
Parallel paths and Slurm's might,
Data's journey, a wondrous flight.
Through pipelines clear, our goals in sight.
🌟🐇✨

---

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