Dash FDA

A Dash app to visualize data from the openFDA elasticsearch API.

App on CapRover.

Built with:

• Plotly Dash
• openFDA /device endpoint

Data from openFDA.

API keys

This project requires to get some API keys from external services.

• PLOTLY_USERNAME, PLOTLY_API_KEY: get them at chart-studio.plotly.com.
• OPEN_FDA_API_KEY: get it at openFDA

Installation

This project uses pyenv and pyenv-virtualenv to manage the Python virtual environment, and poetry to manage the project dependencies.

If you don't already have it, install python 3.8.5.

pyenv install 3.8.5

Create a virtual environment and activate it.

pyenv virtualenv 3.8.5 dash_fda
pyenv activate dash_fda

Remember to activate the virtual environment every time you work on this project.

Install all the dependencies from the poetry.lock file.

poetry install

Tasks

This project uses the task runner Poe the Poet to run poetry scripts.

Non-dockerized app

Run the app locally using a development server (Dash uses a Flask development server):

poetry run poe dev

# or, in alternative
python app.py

Run the app locally using a production server (gunicorn):

poetry run poe prod

Run all tests with pytest:

poetry run poe test

Format all code with black:

poetry run poe format

Dockerized app

Build the Docker image and give it a name and a version tag:

docker build -t dash-fda:v0.1.0 .

Run the Docker container:

docker run --env-file ./dash_fda/.env -p 5001:5000 dash-fda:v0.1.0

Deploy the dockerized app on CapRover (running on my DigitalOcean Droplet):

./deploy.sh

Troubleshooting

If you are on Ubuntu you might get ModuleNotFoundError: No module named '_bz2' and/or UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. These errors are caused by pandas when it tries to import these compression libraries. If you get these errors you need to install the libbz2-dev package and the liblzma-dev package, then re-compile your python interpreter.

Here is how you can do it:

# deactivate and remove the virtual environment
pyenv deactivate
pyenv virtualenv-delete dash_fda

# remove the "broken" python interpreter
pyenv uninstall 3.8.5

# install the compression libreries
sudo apt-get install libbz2-dev liblzma-dev

# download and compile the python interpreter
pyenv install 3.8.5

# re-create the virtual environment and activate it
pyenv virtualenv 3.8.5 dash_fda
pyenv activate dash_fda

# re-install all the dependencies
poetry install

Disclaimer

This app is just an independent project, and it has not been evaluated by the Food and Drug Administration. This app is not intended to diagnose, treat, cure, or prevent any disease. Do not rely on this app to make any decision regarding medical care.