shinyapps_deploy.yml

name: shiny-deploy

on:
  pull_request:
    branches:
      - main

jobs:
  shiny-deploy:
    runs-on: ubuntu-latest
    container: rocker/rstudio:4.1.2
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      DCA_SCHEMATIC_API_TYPE: rest
      DCA_API_HOST: "https://schematic-dev.api.sagebionetworks.org"
    steps:
      - name: Install System Dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev libpng-dev libxml2-dev
          
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-pandoc@v2
          
      - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        name: Install python
        run: |
          sudo apt-get install -y pip python3.8-venv
          
      - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        name: Set up virtual environment
        # When shinyapps.io supports python 3.9+ split this into two steps
        # to install schematic from pypi or github
        shell: bash
        run: |
          python3 -m venv .venv
          chmod 755 .venv/bin/activate
          source .venv/bin/activate

      - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        name: Install schematicpy
        shell: bash
        run: |
          source .venv/bin/activate
          pip install schematicpy==23.1.1 
          
# https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
# For the future, look at poetry install
# - uses: actions/checkout@v3
# - name: Install poetry
#   run: pipx install poetry
# - uses: actions/setup-python@v4
#   with:
#     python-version: '3.9'
#     cache: 'poetry'
# - run: poetry install
# - run: poetry run pytest
#           

      - name: Set Configurations for Schematic
      # write out configuration files using github secrets
        if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        shell: bash
        run: |
          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > .synapseConfig

      - name: Save service account credentials for Schematic
        if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        id: create-json
        uses: jsdaniell/create-json@1.1.2
        with:
          name: 'schematic_service_account_creds.json'
          json: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}
          
      - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        name: Set Configurations for Data Model
        shell: bash
        run: |
          source .venv/bin/activate
          # download the data models and create config.json
          python3 .github/config_schema.py \
            -c schematic_config.yml \
            --service_repo 'Sage-Bionetworks/schematic' \
            --overwrite
          
      - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }}
        name: zip virtual env
        shell: bash
        # ShinyApps has a limit of 7000 files, far exceeded by the many Python dependencies
        # that this app' has.  As a workaround we zip the virtual environment and later
        # unzip it in 'global.R'
        run: |
          zip -rm .venv.zip .venv
          
      - uses: r-lib/actions/setup-renv@v2
          
      - name: shinyapps.io R pkg hack
        # Delete files that makes shinyapps.io treat this like a golem app
        shell: bash
        run: |
          cp R/* functions/
          rm -r R/ DESCRIPTION NAMESPACE
          
      - name: Write R environmental variables
        shell: bash
        run: |
          echo 'DCA_CLIENT_ID="${{ secrets.OAUTH_CLIENT_ID }}"' >> .Renviron
          echo 'DCA_CLIENT_SECRET="${{ secrets.OAUTH_CLIENT_SECRET }}"' >> .Renviron
          
          echo 'DCA_SCHEMATIC_API_TYPE="${{ env.DCA_SCHEMATIC_API_TYPE }}"' >> .Renviron
          echo 'DCA_API_HOST="${{ env.DCA_API_HOST }}"' >> .Renviron

          echo 'DCA_SYNAPSE_PROJECT_API=TRUE' >> .Renviron
          echo 'DCA_DCC_CONFIG="https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/shinyapps-io/dcc_config.csv"' >> .Renviron
          
          echo 'GITHUB_PAT="${{ secrets.GITHUB_TOKEN }}"' >> .Renviron

      - name: Authorize and deploy app
        shell: Rscript {0}
        run: |
          renv::restore()
          install.packages("rsconnect")
          
          repo <- Sys.getenv("GITHUB_REPOSITORY")
          appName <- strsplit(repo, "/")[[1]][2]
          refName <- Sys.getenv("GITHUB_REF_NAME")
          
          # 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")
          } else if (refName %in% c("main")) {
            appName <- paste(appName, "staging", sep = "-")
            message("Deploying staging version of app")
          } else {
            appName <- paste(appName, "testing1", sep = "-")
            message("Deploying testing version of app")
          }
          message(sprintf("Deploying to %s instance.", appName))
          
          rsConnectUser <- "${{ secrets.RSCONNECT_USER }}"
          rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
          rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}"
          rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
          
          # Set app URL for OAuth
          appUrl <- sprintf("https://%s.shinyapps.io/%s", rsConnectUser, appName)
          renviron <- readLines(".Renviron")
          renviron <- c(renviron, sprintf("DCA_APP_URL=%s", appUrl))
          writeLines(renviron, ".Renviron") 
          
          # 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")
          }