Overview

Building upon the Submissions Pilot 2 in which a Shiny application created as an R package was successfully transferred to the FDA using the eCTD gateway protocol, the objective of Pilot 4 is to explore novel technologies to bundle the application along with the necessary execution dependencies and streamline the transfer and execution procedures. The specific technologies targeted in this pilot are the following:

• Containers: A mechanism to encapsulate a piece of software alongside the environment used for its dependencies and execution. The end user simply needs a container runtime installed on their system to execute a container.
• WebAssembly: A framework inspired by assembly in which applications developed in languages such as JavaScript, Python, and now R can be compiled into a self-contained native bundle that can be executed directly in a user's modern web browser, without requiring additional software on their host system.

This repository addresses the container version of the application.

Important Links

TBD

Development Setup

How to Clone Repository

This repository leverages the concept of Git Submodules to dynamically obtain the Pilot 2 Shiny Application source code. To ensure your local clone of the repository obtains the submodule, run the following commands in Git, depending on which method you prefer:

# HTTP method
git clone --recurse-submodules https://github.com/RConsortium/submissions-pilot4-container

# SSH method
git clone --recurse-submodules [email protected]:RConsortium/submissions-pilot4-container.git

For reference, the submodule was initialized with the following:

git submodule add [email protected]:RConsortium/submissions-pilot2.git submissions-pilot2

Container Runtime

This pilot uses the Docker containerization engine to create and execute the Shiny application used in Pilot 2 as a container. There are multiple ways to use Docker on your system:

• Docker Desktop provides a GUI interface to manage containers and associated images. The utility is available on all operating systems: Windows (Intel and ARM), MacOS (Intel and Arm), and Linux.
• Specific to Linux, you can install Docker Engine, also known as Docker Community Edition. Complete details on supported Linux distributions and installation procedures can be found in the aforementioned link.

Building Application Container

Navigate to the root directory of the repository on your system, and run the following command:

docker build -t RConsortium/submissions-pilot4-container:latest .

Running Application Container

Run the following command in a terminal:

docker run -it --rm -p 8787:8787 RConsortium/submissions-pilot4-container:latest

Next, open a new browser tab and visit the following address: localhost:8787. You should see the Pilot 2 application appear in the browser tab.

When you are finished using the application, close the browser tab and then stop the Docker container process by visiting the terminal running the container and pressing Ctrl+C on your keyboard.

Additional notes:

• If you prefer to use a different port on your host system to serve the application, you can change the first port number in the -p 8787:8787 flag of the run command. For example, if you wish to use the port number 7777 on your host system, the run command would be the following:

docker run -it --rm -p 7777:8787 RConsortium/submissions-pilot4-container:latest

Assembling eCTD Bundle

TBD

Automation

TBD

Acknowledgement

The instrascture to create and execute the container version of the Shiny application was initially developed by the engineers at Appsilon and documented in the following GitHub repository: github.com/Appsilon/experimental-fda-submission-4-podman.