HuBMAP Pancreas Data Explorer

This site visualizes pancreas data collected as part of the HuBMAP project, which aims to collect cell-level data for every organ in the human body.

Prerequisites

Docker/ Docker Compose

Getting Started with development

1. Clone this repo

   git clone https://github.com/james-labyer/HuBMAP-pancreas-data-explorer.git
   

2. Some of the files in this project are too large to check into GitHub. The GitHub repo includes representative examples that use smaller files. If you want to view the larger files, download them and move them into the appropriate subfolders in:

   app/assets/optical-clearing-czi
   

3. Build the image

   cd app
   docker compose -f docker-compose-dev.yaml build
   

4. Run the image

   docker compose -f docker-compose-dev.yaml up
   

   Running the image starts the app at localhost:8050. Hot reloading within the Docker container does not work currently, but since the dev image uses a mount, you can see the changes by starting and stopping the container without rebuilding it.

Running tests locally

Run pytest within a development container:

docker exec {container_name} pytest --cov-report term-missing --cov

Preparing the production image

1. On your machine, build the image

   docker compose -f docker-compose.yaml build
   

2. Publish the image to Docker Hub

   docker tag hubmap-pancreas-data-explorer-dash-app jlabyer/hubmap-pancreas-data-explorer:{tag}
   docker push jlabyer/hubmap-pancreas-data-explorer:{tag}
   

3. On the production server, pull the newly published image from Docker Hub

   docker pull jlabyer/hubmap-pancreas-data-explorer:{tag}
   

4. Run the image and test it

   docker run -p 127.0.0.1:8050:8050 jlabyer/hubmap-pancreas-data-explorer:{tag}
   

5. Clean up old images

   docker system prune -a --volumes
   

Preparing assets for display on the website

See the documentation folder for more information about how to prepare optical clearing files and 3d model files for display on the website.