deploy.yml

---
name: Deploy Apps 🚀

on:
  push:
    branches:
      - main
      - dev
      - deploy
    paths:
      - RNA-seq/**
      - basic-teal/**
      - efficacy/**
      - exploratory/**
      - longitudinal/**
      - early-dev/**
      - patient-profile/**
      - python/**
      - safety/**
  workflow_dispatch:
  schedule:
    - cron: "12 3 * * *"

env:
  SHINYAPPSIO_ACCOUNT: genentech
  APP_PREFIX: NEST
  GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}

jobs:
  deploy:
    permissions:
      contents: write
    defaults:
      run:
        shell: bash
    name: Publish 🗞
    runs-on: ubuntu-latest
    container:
      image: ghcr.io/insightsengineering/rstudio:2024.03.05
    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
        channel:
          - stable
          - dev
    steps:
      - name: Set channel related constants
        run: |
          echo "BRANCH_NAME=dev" >> $GITHUB_ENV
          if [ "${{ matrix.channel }}" == "stable" ]; then
            echo "BRANCH_NAME=main" >> $GITHUB_ENV
          fi

      - name: Setup job token 🔑
        id: github-token
        run: |
          if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
            echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
            echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
          else
            echo "Using REPO_GITHUB_TOKEN."
            echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
          fi
        shell: bash

      - name: Checkout repo 🛎
        uses: actions/checkout@v4
        with:
          ref: "${{ env.BRANCH_NAME }}"
          token: "${{ steps.github-token.outputs.token }}"

      - name: Add safe directory in git config
        run: |
          git config --global --add safe.directory $(pwd)

      - name: Check if Cypress tests exist
        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: Install additional system dependencies
        run: |
          apt-get update
          apt-get install --yes \
            libgtk2.0-0 \
            libgbm-dev \
            libnotify-dev \
            libgconf-2-4 \
            xvfb
          if [ " ${{ matrix.directory }}" == "python" ]
          then {
            apt-get install --yes python3.10-venv
          }
          fi

      - name: Setup Node
        uses: actions/setup-node@v4
        if: steps.find-cypress.outputs.has-cypress-tests == 'true'
        with:
          node-version: 20

      - name: Restore renv from cache
        uses: actions/cache@v4
        env:
          CACHE_KEY: renv-${{ runner.arch }}-${{ runner.os }}-${{ matrix.directory }}-${{ matrix.channel }}
        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("${{ matrix.directory }}")
          lockfile <- renv::lockfile_read()
          pkg_name_structure <- ifelse("${{ matrix.channel }}" == "stable", "%s/%s@*release", "%s/%s")
          unreleased_packages <- c(
            "osprey", "hermes", "goshawk", "teal.osprey", "teal.logger",
            "teal.modules.hermes", "teal.goshawk", "nestcolor"
          )
          for (package in lockfile$Packages) {
              if (package$Source == "GitHub") {
                print(package$Package)
                  if (package$Package %in% unreleased_packages) {
                    print(paste0("Recording ", package$Package, " from main"))
                    renv::record(sprintf("%s/%s", package$RemoteUsername, package$Package))
                  } else {
                    print(paste0("Recording ", package$Package, " from stable"))
                    renv::record(sprintf(pkg_name_structure, package$RemoteUsername, package$Package))
                  }
              }
          }

      - 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'
        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 deployment-related 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 }}_${{ matrix.channel }}"),
            appTitle = "${{ env.APP_PREFIX }}_${{ matrix.directory }}_${{ matrix.channel }}",
            account = "${{ env.SHINYAPPSIO_ACCOUNT }}",
            upload = TRUE,
            logLevel = "normal",
            lint = FALSE,
            forceUpdate = TRUE
          )

      - name: Commit and push changes 📌
        run: |
          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
          git config --global user.name "github-actions"
          git config --global --add safe.directory /__w/teal.gallery/teal.gallery
          git fetch
          git stash
          git checkout ${{ env.BRANCH_NAME }}
          git pull
          if [ -n "$(git stash list)" ]; then
            git stash apply
          else
            echo "No stash entries found."
          fi
          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