MedtronicCSVtoFHIR is a Python SCRIPT that facilitates the conversion of Medtronic CSV data to FHIR (Fast Healthcare Interoperability Resources) bundles for interoperability with healthcare systems.

This library processes Medtronic CSV data containing patient information and generates FHIR-compliant data bundles. It includes functions for handling glucose observations, carbohydrate observations, and insulin medication administration, allowing seamless integration of data into healthcare systems.

• Conversion of Medtronic CSV data to FHIR bundles ( in main.py).
• Generation of glucose observations ( in conversion.py).
• Generation of carbohydrate observations ( in conversion.py).
• Creation of insulin medication administration bundles ( in conversion.py).
• Integration with FHIR-compatible systems [VERSION R4] (customizable via environment variables (at .env)

We've included anonymized patient data produced between October and November 2023 in a separate folder for testing purposes.

The data is in the Demo folder.

Additionally, associated FHIR bundles have been generated based on the provided data using the following format:

• Glucose bundles (e.g., bundle_year_2023_month_10_week_1_part_1.json, )
• Carbohydrate bundles (e.g., carbs_bundle_year_2023_month_10_week_1_part_1 )
• Medication Administration bundles (Insulin) (e.g., insulin_bundle_year_2023_month_11_week_2_part_2.json )

Note: Some weekly data may be divided into multiple parts, especially larger bundles that could potentially exceed the processing capacity of an FHIR server.

1. Clone the repository:

git clone https://github.com/pra008/Medtronic-csv-FHIR

cd Medtronic-csv-FHIR

2. Run the installation script for macOS (and other Unix-like systems like iOS):

./install.sh

2. Run the installation script for Windows:

install.bat

This script will perform the following tasks:

• Checks if Python is installed. If not, it provides instructions to download and install Python.
• Creates a virtual environment named venv in the project directory.
• Activates the virtual environment.
• Installs the required dependencies specified in requirements.txt.
• Once the setup is complete, you can start using the project by following the usage instructions or running your desired commands.

To run the application, a convenience script is provided which takes care of setting up the necessary environment variables and starting the application.

1. Open the Command Prompt or PowerShell in the directory where your project is located.
2. Execute the provided batch script run.bat by typing the following command and pressing Enter:

run.bat

This will load the environment variables from the .env file, activate the virtual environment if available, and run the Python script. Ensure that your .env file is in the same directory as the script.

3. The script will attempt to execute the Python application and will provide feedback in the command line interface. If there are any errors, the script will display a message with "Failed to run Python script."

Make sure you have Python installed and that the path to your Python executable is correctly set in your system's PATH environment variable before running the script.

For Unix-based systems, ensure you have the appropriate permissions to execute the script by running:

python3 main.py

If you haven't installed Python, you can download it from the official [a https://www.python.org/downloads/](Python website) and follow the installation instructions based on your operating system.

While not mandatory, it's recommended to use a virtual environment to isolate project dependencies. To set up a virtual environment:

1. Open a terminal or command prompt.
2. Navigate to the project directory.

cd /path/to/Medtronic-csv-FHIR

3. Run the following command to create a virtual environment (replace venv with your preferred environment name):

python3 -m venv venv

4. Activate the virtual environment:

• On Windows:

venv\Scripts\activate

• On macOS and Linux:

source venv/bin/activate

Once Python is installed and a virtual environment (if desired) is set up, you can install the required packages:

1. Ensure you're in the project directory and the virtual environment is activated.
2. Run the following command to install the required dependencies using pip:

pip install -r requirements.txt

This will install all the necessary dependencies specified in the requirements.txt file for the Medtronic CSV to FHIR conversion library.

This will install all the necessary dependencies specified in the requirements.txt file for the Medtronic CSV to FHIR conversion library.

Please be aware that some of these constants are defined by Medtronic and they MAY CHANGE

Refer to the Medtronic CSV Documentation for more details.

Please note that the documentation for Medtronic CSV files is incomplete. As a result, some variables were guessed based on the available information.

For example, for glucose data:

• BG_SENT_FOR_CALIB: They use these values and report the manual glucose values

• USER_ACCEPTED_REMOTE_BG: They use these values and report the manual glucose values

Note: The official documentation lacks explicit details for variables that distinguish between BOLUS, BASAL, and CORRECTION types in Medtronic data. We've defined several constants to fill this gap. These constants are crucial for interpreting the data accurately, particularly in the auto_bolus column and similar fields. Here's how we've defined and used these variables:

These variables are set as environment variables in our code, allowing for dynamic adjustment and easier management of the constants used in data processing.

You can customize these as well.