AMP SCZ Form Quality Control Trackers

This repository contains a quality control (QC) framework developed for the Accelerating Medicines Partnership for Schizophrenia (AMP SCZ) project—a large-scale, longitudinal study on schizophrenia.

Overview

The QC system:

• Analyzes datasets for missing, unexpected, or inconsistent values
• Detects mismatches between variable values and form specifications
• Flags potential outliers and tracks resolved errors
• Generates detailed reports for quality tracking over time

Project Structure

form_qc_trackers/
├── run_qc.py                     # Main entry point
├── config.json                   # Customizable parameters for each run
├── logging_config.py             # Logging setup
├── main/
│   ├── analyze_dataset/          # Analyzes structure of data
│   ├── discover_errors/          # Searches for anomalies and potential errors
│   └── generate_reports/         # Creates and uploads output to Dropbox
├── README.md
└── LICENSE

Getting Started

3. Configure your run

   • Modify config.json to define paths.
   • download packages specified in requirements.txt
   • Include dependencies listed below in dependencies folder that you define in the config file

4. Run the pipeline

   • Files Needed (all other dependencies will be generated) dependencies./

     ├── dropbox_credentials.json
     ├── scid_diagnosis_vars.json
     ├── forms_per_timepoint.json
     ├── data_dictionary/
     │ └── current_data_dictionary.csv

   • Execute the "run_qc.py" file