rstats-base-plumber

R/plumber template for OpenFaaS with of-watchdog

Sends and receives JSON using plumber and of-watchdog.

This template uses the rocker/r-base:latest image.

Making a new function

Use the faas-cli and pull R templates

faas-cli template pull https://github.com/analythium/openfaas-rstats-templates

Create a new function

faas-cli new --lang rstats-base-plumber r-base-plumber-hello --prefix=dockeruser

Customizing your function

Now we have a r-base-plumber-hello.yml file and function folder ./r-base-plumber-hello. Files in the function folder will get copied to the /home/app directory of the image. Read more about the YAML configuration. Customize the ./r-base-plumber-hello/handler.R file as needed:

• load required packages using library(),
• put your data in the folder and load it relative to the function folder (e.g. data.RData) or use the full path (e.g. /home/app/data.csv),
• define the output given the input of the handle function, the output must be JSON parsable,
• add packages/remotes/system requirements and optionally metadata to the DESCRIPTION file.

Build, push, and deploy

The up command includes build (build an image into the local Docker library) push (push that image to a remote container registry), and deploy (deploy your function into a cluster):

faas-cli up -f r-base-plumber-hello.yml

Testing

Test the local Docker image forwarding to port 4000

docker run -p 4000:8080 dockeruser/r-base-plumber-hello

Curl should return ["Hello Friend!"]:

curl http://localhost:4000/ -d '["Friend"]'
# ["Hello Friend!"]

The log looks like this:

2020/12/13 06:03:04 Started logging stderr from function.
2020/12/13 06:03:04 Started logging stdout from function.
2020/12/13 06:03:04 OperationalMode: http
2020/12/13 06:03:04 Timeouts: read: 10s, write: 10s hard: 10s.
2020/12/13 06:03:04 Listening on port: 8080
2020/12/13 06:03:04 Writing lock-file to: /tmp/.lock
2020/12/13 06:03:04 Metrics listening on port: 8081
Forking - Rscript [index.R]
2020/12/13 06:03:05 stderr: Running plumber API at http://0.0.0.0:5000
2020/12/13 06:03:05 stderr: Running swagger Docs at http://127.0.0.1:5000/__docs__/
2020/12/13 06:03:19 POST / - 200 OK - ContentLength: 17

Use the OpenFaaS UI or curl (should give ["Hello Friend!"]). Replace localhost with IP address if testing on remote location:

curl http://localhost:8080/function/<function-name> -d '["Friend"]'
# ["Hello Friend!"]

Example: PCA

Create a new function:

faas-cli new --lang rstats-base-plumber r-base-pca --prefix=dockeruser

Change handler.R:

suppressMessages(library(vegan))
handle <- function(req) {
  x <- jsonlite::fromJSON(paste(req$postBody))
  scores(rda(x), 1:2)$sites
}

Edit DESCRIPTION:

Package: OpenFaaStR
Version: 0.0.1
Imports:
  vegan
Remotes:
SystemRequirements:
VersionedPackages:

Build the image: faas-cli build -f r-base-pca.yml and test with docker run -p 4000:8080 dockeruser/r-base-pca and

curl http://localhost:4000/ -H \
  "Content-Type: application/json" -d \
  '[[-1,3,16],[10,-10,9],[-5,10,-14],[14,3,-12]]'
# [[2.9545,3.042],[2.7754,-2.5023],[-3.4647,2.7223],[-2.2652,-3.262]]