deploy_stable.yaml

---
name: Deploy Stable Apps 🚀

on:
  push:
    branches:
      - main
  workflow_dispatch:
  schedule:
    - cron: "12 3 * * *"

concurrency:
  group: publish-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  SHINYAPPSIO_ACCOUNT: genentech
  APP_PREFIX: NEST
  APP_SUFFIX: stable
  GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
  BRANCH: main

jobs:
  deploy:
    defaults:
      run:
        shell: bash
    name: Publish 🗞
    runs-on: ubuntu-latest
    container:
      image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest
    if: >
      !contains(github.event.commits[0].message, '[skip deploy]')
    strategy:
      fail-fast: false
      matrix:
        directory:
          [
            "RNA-seq",
            "basic-teal",
            "efficacy",
            "exploratory",
            "longitudinal",
            "early-dev",
            "patient-profile",
            "python",
            "safety",
          ]
    steps:
      - name: Checkout repo 🛎
        uses: actions/checkout@v3

      - name: Check if cypress test exists
        id: find-cypress
        run: |
          if [ -d ${{ matrix.directory }}/tests/cypress ]; then
            echo "has-cypress-tests=true" >> $GITHUB_OUTPUT
          else
            echo "Skipping frontend tests because cypress directory does not exist."
            echo "has-cypress-tests=false" >> $GITHUB_OUTPUT
          fi

      - name: Setup system dependencies for cypress and python app
        run: >
          apt-get update && apt-get install --yes
          libgtk2.0-0 libgbm-dev libnotify-dev libgconf-2-4 xvfb python3.10-venv

      - name: Setup Node
        uses: actions/setup-node@v3
        if: steps.find-cypress.outputs.has-cypress-tests == 'true'
        with:
          node-version: 16

      - name: Restore renv from cache
        uses: actions/cache@v3
        env:
          CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ env.APP_SUFFIX }}
        with:
          path: ${{ matrix.directory }}/renv/library
          key: ${{ env.CACHE_KEY }}-${{ hashFiles(format('{0}/renv.lock', matrix.directory)) }}
          restore-keys: ${{ env.CACHE_KEY }}-

      - name: Update renv.lock file with updated GitHub packages
        shell: Rscript {0}
        run: |
          setwd("${{ matrix.directory }}")
          lockfile <- renv::lockfile_read()
          for (package in lockfile$Packages) {
              if (package$Source == "GitHub") {
                  renv::record(paste0(package$RemoteUsername, "/", package$Package, "@*release"))
              }
          }

      - name: Install R packages using renv and update the renv snapshot
        shell: Rscript {0}
        working-directory: ${{ matrix.directory }}
        run: |
          options(renv.config.cache.symlinks = FALSE)
          lockfile_pkgs <- renv::lockfile_read()$Package
          github_pkgs <- names(lockfile_pkgs)[sapply(lockfile_pkgs, function(x) x$Source == "GitHub")]
          renv::restore(clean = TRUE)
          renv::update(exclude = github_pkgs)
          renv::snapshot()

      - name: Print the new renv.lock file for ${{ matrix.directory }}
        working-directory: ${{ matrix.directory }}
        run: cat renv.lock

      - name: Front end test to check if the app works fine
        if: steps.find-cypress.outputs.has-cypress-tests == 'true'
        continue-on-error: true
        uses: cypress-io/github-action@v6
        with:
          build: npm install cypress --save-dev
          working-directory: ${{ matrix.directory }}/tests
          start: npm run run-app
          wait-on: "http://localhost:3333"
          wait-on-timeout: 500

      - name: Install deploy R package dependencies
        shell: Rscript {0}
        working-directory: ${{ matrix.directory }}
        run: |
          install.packages(c("BiocManager", "rsconnect"))

      - name: Deploy 🖨 ${{ matrix.directory }} 🎨
        shell: Rscript {0}
        working-directory: ${{ matrix.directory }}
        run: |
          rsconnect::setAccountInfo(
            name = "${{ env.SHINYAPPSIO_ACCOUNT }}",
            token = "${{ secrets.SHINYAPPSIO_TOKEN }}",
            secret = "${{ secrets.SHINYAPPSIO_SECRET }}",
            server = "shinyapps.io"
          )
          rsconnect::deployApp(
            appFiles = c("app.R"),
            appName = rsconnect::generateAppName("${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.APP_SUFFIX }}"),
            appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ env.APP_SUFFIX }}",
            account = "${{ env.SHINYAPPSIO_ACCOUNT }}",
            upload = TRUE,
            logLevel = "normal",
            lint = FALSE,
            forceUpdate = TRUE
          )

      - name: Commit updated renv.lock file
        continue-on-error: true
        run: |
          git config --global user.email "action@github.com"
          git config --global user.name "GitHub Action"
          git config --global --add safe.directory /__w/teal.gallery/teal.gallery
          git fetch
          git stash
          git checkout ${{ env.BRANCH_NAME }}
          git pull
          git stash apply
          git add ${{ matrix.directory }}/renv.lock
          git add ${{ matrix.directory }}/renv/activate.R
          if [ -n "$(git diff --staged)" ]; then
            git commit -m "[skip deploy] Update renv.lock file for ${{ matrix.directory }} app"
            git push origin ${{ env.BRANCH_NAME }}
          else
            echo "renv.lock was not modified. Nothing to commit.";
          fi