Boyce Lab C-CDA and FHIR Data Converter

This Shiny application allows users to upload and parse C-CDA and FHIR text files. It extracts relevant elements and presents them in a tabular format for easy viewing and download.

Features

• Upload C-CDA and FHIR text files (up to 30MB)
• Parse and display the contents of C-CDA and FHIR files
• Download the parsed data as a CSV file

Installation

Prerequisites

Make sure you have R and RStudio installed on your system. You will also need the devtools package to install the app from GitHub.

1. Install R: Download R
2. Install RStudio: Download RStudio

Install Dependencies

Open RStudio and run the following commands to install the necessary packages:

install.packages(c("shiny", "xml2", "jsonlite", "dplyr", "tidyr", "DT", "devtools"))

Clone the Repository from GitHub

Open a terminal or command prompt and navigate to the directory where you want to clone the repository. Then, run the following command:

git clone https://github.com/BoyceLab/CDAtransformer.git

Install the App from GitHub

Use the devtools package to install the app from GitHub:

devtools::install_github("BoyceLab/CDAtransformer", force = TRUE)

Usage

1. Set the Working Directory:

   Open RStudio and set the working directory to where your app.R file is located:

   setwd("path/to/CDAtransformer")

   Replace "path/to/CDAtransformer" with the actual path to the cloned repository.

2. Run the App:

   Load the required packages and run the Shiny app:

   library(shiny)
   runApp(".")

3. Upload a File:

   • Click the "Choose CDA or FHIR Text File" button to upload your text file.
   • Select the file type (CDA or FHIR).
   • Click the "Parse Document" button to parse and display the contents.

4. Download Parsed Data:

   • Click the "Download CSV" button to download the parsed data as a CSV file.

Code Overview

UI

The UI is defined in the ui function and includes a title panel, file input, radio buttons for file type selection, a parse button, and a download button. The parsed data is displayed in a datatable.

Server

The server logic is defined in the server function and includes:

• File Parsing: Functions to parse CDA and FHIR files.
• Data Display: Render the parsed data in a datatable.
• Data Download: Allow users to download the parsed data as a CSV file.

Helper Functions

• parse_cda(file): Parses a CDA file and extracts relevant elements.
• flatten_list(x, name): Recursively flattens a list.
• parse_fhir(file): Parses multiple FHIR resources and flattens them.
• transpose_data(data): Transposes a data frame.

Contributing

Contributions are welcome! Please open an issue or submit a pull request for any changes.

License

This project is licensed under the MIT License - see the LICENSE file for details.