README.md

ImmuneSpaceAPI

This package holds all API endpoints for use within ImmuneSpace internally by reports or front-end elements. The inst/api/main.R script defines all the endpoints used by plumber::plumb() that is started when a docker container is created from an image defined by the inst/Dockerfile. The endpoint functions are simple wrappers for private functions in the /R directory. Since these higher level private functions depend on file inputs often, the unit tests are focused on the analysis and data munging functionality.

Local Development

To do local development, the file-loading function loadLocalFile() that pulls in .rds artifacts for munging is found in utils.R. It looks for a localPath environmental variable specifying the local path to use. If this is not found, then it assumes the location is the server and will use the /app directory specified during the docker run command. So, it is recommended to put localPath in your .Renviron file.

mkdir /share/resources
scp rsT:'/share/resources/*.rds' /share/resources

cd /labkey/git
git clone https://github.com/RGLab/ImmuneSpaceAPI.git
cd ImmuneSpaceAPI
git checkout dev
docker build -t immunespaceapi .
docker run -p 1169:8000 -v /share/resources:/app immunespaceapi

Server Deployment

After changes are made locally, push changes to the respective branch on GitHub. GitHub Actions will build and push the image to Docker Hub and GitHub Packages.

Pull the latest image on the wsT/wsP machine and start a new container with a command that includes an "always" restart policy:

# on wsT
ssh wsT
s
docker pull rglab/immunespaceapi:dev
docker run -d --restart always -p 1169:8000 -v /share/resources:/app rglab/immunespaceapi:dev

# on wsP
ssh wsP
s
docker pull rglab/immunespaceapi:latest
docker run -d --restart always -p 1169:8000 -v /share/resources:/app rglab/immunespaceapi:latest

Proxy Note

• In order to ensure that the API is accessible via the web, an ImmuneSpace administrator must set the path within LabKey.
• Click "gear symbol" > Site > Admin Console > PROXY SERVLETS
  • https://www.immunespace.org/proxy/proxyAdmin.view
  • https://test.immunespace.org/proxy/proxyAdmin.view
  • http://localhost:8080/proxy/proxyAdmin.view
• Fill out and add proxy
  • Proxy Name: plumber
  • Target URI: http://localhost:1169

Extending

• Add endpoint in the inst/api/main.R
• Add functions in /R with the format <ModuleName>_<endpointName>.R

Resources

• https://github.com/rstudio/plumber/blob/master/Dockerfile
• https://www.rplumber.io/articles/hosting.html#docker-basic-