NC File Processor

This tool processes NC files, either directly or within PJNZ files, updating coverage rates based on a provided configuration.

Prerequisites

• Python 3.6 or higher
• Required Python packages (install via pip install -r requirements.txt):
  • csv
  • json
  • logging
  • typing
  • zipfile

File Structure

.
├── src/
│   ├── main.py
│   └── nc_processor.py
├── data/
│   ├── constants.csv
│   └── mapped_risk_ids.csv
├── config/
│   └── your_config_file.json
├── tmp/
│   └── (output files will be saved here)
└── README.md

Usage

The tool can be used in two modes:

1. Processing PJNZ Files

To process a PJNZ file, extracting and updating its NC content:

python -m src.main pjnz <path_to_pjnz_file> <path_to_config_file>

Example:

python -m src.main pjnz ./data/example.PJNZ ./config/all_scenarios.json

2. Processing NC Files Directly

To process an NC file directly:

python -m src.main nc <path_to_nc_file> <path_to_config_file>

Example:

python -m src.main nc ./data/example.NC ./config/all_scenarios.json

Running the tool for multiple countries and scenarios

This repository contains scripts for processing configuration templates and generating outputs. Here's a quick guide on how to use it:

Main Components

1. create_and_run_configurations.sh: The main shell script that orchestrates the entire process.
2. scripts/create_configurations.py: Python script for creating configurations from templates.
3. scripts/batch_individual_json_configs.sh: Shell script for processing individual JSON configs.

How to Run

1. Open a terminal and navigate to the repository root.

2. Run the main script:

   ./create_and_run_configurations.sh
   

3. Follow the prompts to select a configuration template.

What Happens

1. The script lists available templates from ./templates/*.json.
2. You select a template.
3. The script runs python -m scripts.create_configurations with your selected template.
4. It then processes the baseline configurations using ./scripts/batch_individual_json_configs.sh.
5. Finally, it processes the scaleup configurations using the same script.

Directory Structure

• Templates: ./templates/*.json
• Output: ./config/{scenario}/{config_type}/

Tips

• Ensure all scripts are executable (chmod +x script_name.sh).
• Check that Python and required dependencies are installed.
• Make sure your template JSON files are in the ./templates/ directory.

Remember, this script automates the entire process from template selection to final output generation. If you need to run individual steps, you can use the component scripts directly.

Output

The tool will generate the following outputs in the ./tmp directory:

• For PJNZ processing: An updated PJNZ file and a log file
• For direct NC processing: An updated NC file and a log file

Output files are named based on the input file or configuration file name.

Configuration

The configuration file (JSON format) should specify:

• Treatment associations
• Prevention associations
• Risk factors

Refer to the existing configuration files in the config/ directory for the correct structure.

Data Files

Ensure that constants.csv and mapped_risk_ids.csv are present in the data/ directory. These files are used for lookups during processing.

Logging

Detailed logs of the processing are saved alongside the output files in the ./tmp directory.

Contributing

For bug reports or feature requests, please open an issue on the project's GitHub repository.