pydhis2 0.2.1

Reproducible DHIS2 Python SDK for LMIC scenarios

pydhis2

A modern Python SDK for DHIS2, designed for robust and reproducible scientific workflows.

pydhis2 is a next-generation Python library for interacting with DHIS2, the world's largest health information management system. It provides a clean, modern, and efficient API for data extraction, analysis, and management, with a strong emphasis on creating reproducible workflows—a critical need in scientific research and public health analysis, especially in Low and Middle-Income Country (LMIC) contexts.

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✨ Why pydhis2?

• 🚀 Modern & Asynchronous: Built with asyncio for high-performance, non-blocking I/O, making it ideal for large-scale data operations. A synchronous client is also provided for simplicity in smaller scripts.
• reproducible Reproducible by Design: From project templates to a powerful CLI, pydhis2 is built to support standardized, shareable, and verifiable data analysis pipelines.
• 🐼 Seamless DataFrame Integration: Natively convert DHIS2 analytics data into Pandas DataFrames with a single method call (.to_pandas()), connecting you instantly to the PyData ecosystem.
• 🔧 Powerful Command Line Interface: Automate common tasks like data pulling and configuration directly from your terminal.

🚀 Getting Started

1. Installation

Install pydhis2 directly from PyPI:

pip install pydhis2

2. Verify Your Installation

Use the built-in CLI to run a quick demo. This will connect to a live DHIS2 server, fetch data, and confirm that your installation is working correctly.

# Check the installed version
pydhis2 version

# Run the quick demo
pydhis2 demo quick

A successful run will produce the following output:

============================================================
pydhis2 Quick Demo
============================================================
=== Testing: https://demos.dhis2.org/dq ===
   Found working API endpoint!
   System: Data Quality
   Version: 2.38.4.3
Found working server: https://demos.dhis2.org/dq

2. Querying Analytics data...
Retrieved 1 data records
...
Demo completed successfully!

📖 Basic Usage

Here is a simple example of how to use pydhis2 in a Python script to fetch analytics data and load it into a Pandas DataFrame.

Create a file named my_analysis.py:

import asyncio
import sys
from pydhis2 import get_client, DHIS2Config
from pydhis2.core.types import AnalyticsQuery

# pydhis2 provides both an async and a sync client
AsyncDHIS2Client, _ = get_client()

async def main():
    # 1. Configure the connection to a DHIS2 server
    config = DHIS2Config(
        base_url="https://demos.dhis2.org/dq",
        auth=("demo", "District1#")
    )
  
    async with AsyncDHIS2Client(config) as client:
        # 2. Define the query parameters
        query = AnalyticsQuery(
            dx=["b6mCG9sphIT"],   # Data element: ANC 1 Outlier Threshold
            ou="qzGX4XdWufs",    # Org unit: A-1 District Hospital
            pe="2023"            # Period: Year 2023
        )

        # 3. Fetch data and convert it directly to a Pandas DataFrame
        df = await client.analytics.to_pandas(query)

        # 4. Analyze and display the results
        print("✅ Data fetched successfully!")
        print(f"Retrieved {len(df)} records.")
        print("\n--- Data Preview ---")
        print(df.head())

if __name__ == "__main__":
    # Standard fix for asyncio on Windows
    if sys.platform == 'win32':
        asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
    asyncio.run(main())

Run your script from the terminal:

python my_analysis.py

🔧 Server Configuration

While you can pass credentials directly in your script, we recommend using environment variables for better security and flexibility.

1. Environment Variables (Recommended)

export DHIS2_URL="https://your-dhis2-server.com"
export DHIS2_USERNAME="your_username"
export DHIS2_PASSWORD="your_password"

pydhis2 will automatically detect and use these variables.

2. In-Script Configuration

from pydhis2 import DHIS2Config

config = DHIS2Config(
    base_url="https://your-dhis2-server.com",  
    auth=("your_username", "your_password")
)

3. Using the CLI The CLI provides a convenient way to set and cache your credentials.

pydhis2 config --url "https://your-dhis2-server.com" --username "your_username"

🏗️ A Reproducible Workflow: Project Templates

Beyond being a library, pydhis2 promotes a standardized workflow that is essential for scientific research. To jumpstart your analysis, we provide a project template powered by Cookiecutter.

Why use the template?

• Standardization: Ensures every project starts with a clean, logical structure.
• Rapid Start: Generate a fully functional project skeleton in a single command.
• Best Practices: Includes pre-configured settings for DHIS2 connections, data quality pipelines, and environment management.
• Focus on Analysis: Spend less time on boilerplate setup and more time on your research.

How to Use

1. Install Cookiecutter:

   pip install cookiecutter
   

2. Generate your project: Point Cookiecutter to the pydhis2 template. It will prompt you for project details.

   cookiecutter gh:HzaCode/pyDHIS2 --directory pydhis2/templates
   

   You'll be prompted for details like your project name and author:

   project_name [My DHIS-2 Analysis Project]: Malaria Analysis Malawi
   project_slug [malaria_analysis_malawi]:
   author_name [Your Name]: Dr. Evans
   

3. Get a complete, ready-to-use project structure:

   malaria-analysis-malawi/
   ├── configs/          # DHIS-2 & DQR configurations
   ├── data/             # Raw and processed data
   ├── pipelines/        # Analysis pipeline definitions
   ├── scripts/          # Runner scripts
   ├── .env.example      # Environment variable template
   └── README.md         # A dedicated README for your new project
   

You can now cd into your new project directory and begin your analysis immediately!

🖥️ Command Line Interface

pydhis2 provides a powerful CLI for common data operations. (Note: Implementation is in progress)

# Pull analytics data and save as Parquet
pydhis2 analytics pull --dx "b6mCG9sphIT" --ou "qzGX4XdWufs" --pe "2023" --out analytics.parquet

# Pull tracker events
pydhis2 tracker events --program "program_id" --out events.parquet

# Run a data quality review
pydhis2 dqr analyze --input analytics.parquet --html dqr_report.html

For a full list of commands, run pydhis2 --help.

📊 Supported Endpoints

Endpoint	Read	Write	DataFrame	Pagination	Streaming
Analytics	✅	-	✅	✅	✅
DataValueSets	✅	✅	✅	✅	✅
Tracker Events	✅	✅	✅	✅	✅
Metadata	✅	✅	✅	-	-

📋 Compatibility

• Python: ≥ 3.9
• DHIS2: ≥ 2.36
• Platforms: Windows, Linux, macOS

🤝 Contributing

Contributions are welcome and highly encouraged! pydhis2 is a community-driven project, and we believe that collaboration is key to building robust and useful tools for the open-science community.

Please see our Contributing Guide for details on how to get started. Also, be sure to review our Code of Conduct.

📞 Community & Support

• 📖 Documentation: For in-depth guides and API references.
• 🐛 GitHub Issues: To report bugs or request new features.
• 💬 GitHub Discussions: For questions, ideas, and community conversation.
• 📝 Changelog: Version history and release notes.

📄 License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.