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update dfamodules to v23.12.1 #200

update dfamodules to v23.12.1

update dfamodules to v23.12.1 #200

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
name: shiny-deploy
on:
# on push to branches labeled main and dev* or commits tagged as VYY.MM.n deploy
push:
branches:
- main
- dev*
tags:
- v[0-9]+.[0-9]+.[0-9]+
paths-ignore:
- '.github/ISSUE_TEMPLATE/**'
- '**/*.md'
- '**/.gitignore'
jobs:
shiny-deploy:
runs-on: ubuntu-latest
container: rocker/rstudio:4.1.2
env:
SCHEMATIC_URL_DEV: https://schematic-dev.api.sagebionetworks.org
SCHEMATIC_URL_STAGING: https://schematic-staging.api.sagebionetworks.org
SCHEMATIC_URL_PROD: https://schematic.api.sagebionetworks.org
# This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Install System Dependencies
run: |
sudo apt-get update
sudo apt-get install -y pip libcurl4-openssl-dev libpng-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff-dev libxml2-dev
# this action checks out the $GITHUB_WORKSPACE repository so that the workflow can access it
- uses: actions/checkout@v3
# this action sets up pandoc
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
r-version: 'renv'
# install packages
- name: Install rsconnect
run: |
install.packages("renv")
renv::upgrade(version = "0.17.3")
renv::install("[email protected]")
shell: Rscript {0}
# this action activates renv
- uses: r-lib/actions/setup-renv@v2
# deploy app using rsconnect
- name: Authorize and deploy app
run: |
renv::restore(packages = "renv")
refName <- Sys.getenv("GITHUB_REF_NAME")
repo <- Sys.getenv("GITHUB_REPOSITORY")
appName <- strsplit(repo, "/")[[1]][2]
# if tag is v*.*.*, deploy to prod
# if main to staging
# otherwise to test
if (grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) {
message("Deploying release version of app using schematic API production instance")
renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_PROD }}'"
} else if (refName == "main") {
appName <- paste(appName, "staging", sep = "-")
renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_STAGING }}'"
message("Deploying staging version of app using schematic API staging instance")
} else {
appName <- paste(appName, "testing", sep = "-")
renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_DEV }}'"
message("Deploying testing version of app using schematic API dev instance")
}
# write .Renviron
writeLines(renviron, ".Renviron")
# deploy
message(sprintf("Deploying to %s instance.", appName))
# assign secrets to variables
rsConnectUser <-"${{ secrets.RSCONNECT_USER }}"
rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}"
# create config file
config <- "client_id: ${{ secrets.OAUTH_CLIENT_ID }}"
config <- c(config, "client_secret: ${{ secrets.OAUTH_CLIENT_SECRET }}")
appUrl<- sprintf("https://%s.shinyapps.io/%s", rsConnectUser, appName)
config <- c(config, sprintf("app_url: %s", appUrl))
# write config file
configFileConn<-file("oauth_config.yml")
tryCatch(
writeLines(config, configFileConn),
finally=close(configFileConn)
)
# set account info
rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
# get app names. If app exists, configure then deploy. Otherwise
# deploy then configure.
apps <- rsconnect::applications()$name
if (appName %in% apps) {
rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose")
rsconnect::deployApp(appName = appName)
} else {
rsconnect::deployApp(appName = appName)
rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose")
}
shell: Rscript {0}