update dfamodules: schematic api move token to auth header #189
Workflow file for this run
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| # 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 $GITHUB_WORKSPACE repository so that the workflow can access it | |
| - uses: actions/checkout@v3 | |
| # this action sets up pandoc | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| r-version: 'renv' | |
| # install packages | |
| - name: Install rsconnect | |
| run: | | |
| install.packages("renv") | |
| renv::upgrade(version = "0.17.3") | |
| renv::install("rsconnect@0.8.29") | |
| shell: Rscript {0} | |
| # this action activates renv | |
| - uses: r-lib/actions/setup-renv@v2 | |
| # deploy app using rsconnect | |
| - name: Authorize and deploy app | |
| run: | | |
| renv::restore(packages = "renv") | |
| refName <- Sys.getenv("GITHUB_REF_NAME") | |
| repo <- Sys.getenv("GITHUB_REPOSITORY") | |
| appName <- strsplit(repo, "/")[[1]][2] | |
| # if tag is v*.*.*, deploy to prod | |
| # if main to staging | |
| # otherwise to test | |
| if (grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) { | |
| message("Deploying release version of app using schematic API production instance") | |
| renviron <- "DFA_SCHEMATIC_API_URL = '${{ 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} |