deploy_tre_reusable.yml

---
name: Deploy Azure TRE Reusable

on:  # yamllint disable-line rule:truthy
  workflow_call:
    inputs:
      prRef:
        description: The git ref to checkout
        type: string
        required: false
      prHeadSha:
        description: >-
          For PR builds where GITHUB_REF isn't set to the PR (e.g. comment trigger),
          pass the PR's head SHA commit here
        type: string
        required: false
      ciGitRef:
        description: The git ref to use in annotations to associate a deployment with the code that triggered it
        type: string
        required: true
      e2eTestsCustomSelector:
        description: The pytest marker selector for the e2e tests to be run
        type: string
        default: ""
        required: false
      environmentName:
        description: The name of the Github Action's environment this will deploy into
        type: string
        required: true
      E2E_TESTS_NUMBER_PROCESSES:
        description: ""
        type: number
        required: false
      DEVCONTAINER_TAG:
        description: ""
        type: string
        required: true
    secrets:
      AAD_TENANT_ID:
        description: ""
        required: true
      ACR_NAME:
        description: ""
        required: true
      API_CLIENT_ID:
        description: ""
        required: true
      API_CLIENT_SECRET:
        description: ""
        required: true
      APPLICATION_ADMIN_CLIENT_ID:
        description: ""
        required: true
      APPLICATION_ADMIN_CLIENT_SECRET:
        description: ""
        required: true
      MGMT_RESOURCE_GROUP_NAME:
        description: ""
        required: true
      MS_TEAMS_WEBHOOK_URI:
        description: ""
        required: true
      MGMT_STORAGE_ACCOUNT_NAME:
        description: ""
        required: true
      SWAGGER_UI_CLIENT_ID:
        description: ""
        required: true
      TEST_APP_ID:
        description: ""
        required: true
      TEST_WORKSPACE_APP_ID:
        description: ""
        required: true
      TEST_WORKSPACE_APP_SECRET:
        description: ""
        required: true
      TEST_ACCOUNT_CLIENT_ID:
        description: ""
        required: true
      TEST_ACCOUNT_CLIENT_SECRET:
        description: ""
        required: true
      TRE_ID:
        description: ""
        required: true
      CI_CACHE_ACR_NAME:
        description: ""
        required: false
      AZURE_CREDENTIALS:
        description: ""
        required: true

# This will prevent multiple runs of this entire workflow.
# We should NOT cancel in progress runs as that can destabilize the environment.
concurrency: "deploy-${{ inputs.ciGitRef }}"

jobs:
  deploy_management:
    name: Deploy Management
    runs-on: ubuntu-latest
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Show inputs
        run: |
          echo "Inputs"
          echo "======"
          echo "prRef       : ${{ inputs.prRef }}"
          echo "prRHeadSha  : ${{ inputs.prHeadSha }}"
          echo "ciGitRef    : ${{ inputs.ciGitRef }}"
          echo "environment : ${{ inputs.environmentName }}"

      - name: Check required values
        id: check_required_values
        # since this is a resuable workflow, required=true secrets will always have a value but it can be empty.
        run: |
          if [ "${{ secrets.AAD_TENANT_ID }}" == '' ]; then
            echo "Missing secret: AAD_TENANT_ID" && exit 1
          fi
          if [ "${{ secrets.ACR_NAME }}" == '' ]; then
            echo "Missing secret: ACR_NAME" && exit 1
          fi
          if [ "${{ secrets.API_CLIENT_ID }}" == '' ]; then
            echo "Missing secret: API_CLIENT_ID" && exit 1
          fi
          if [ "${{ secrets.API_CLIENT_SECRET }}" == '' ]; then
            echo "Missing secret: API_CLIENT_SECRET" && exit 1
          fi
          if [ "${{ secrets.APPLICATION_ADMIN_CLIENT_ID }}" == '' ]; then
            echo "Missing secret: APPLICATION_ADMIN_CLIENT_ID" && exit 1
          fi
          if [ "${{ secrets.APPLICATION_ADMIN_CLIENT_SECRET }}" == '' ]; then
            echo "Missing secret: APPLICATION_ADMIN_CLIENT_SECRET" && exit 1
          fi
          if [ "${{ secrets.MGMT_RESOURCE_GROUP_NAME }}" == '' ]; then
            echo "Missing secret: MGMT_RESOURCE_GROUP_NAME" && exit 1
          fi
          if [ "${{ secrets.MGMT_STORAGE_ACCOUNT_NAME }}" == '' ]; then
            echo "Missing secret: MGMT_STORAGE_ACCOUNT_NAME" && exit 1
          fi
          if [ "${{ secrets.SWAGGER_UI_CLIENT_ID }}" == '' ]; then
            echo "Missing secret: SWAGGER_UI_CLIENT_ID" && exit 1
          fi
          if [ "${{ secrets.TEST_APP_ID }}" == '' ]; then
            echo "Missing secret: TEST_APP_ID" && exit 1
          fi
          if [ "${{ secrets.TEST_WORKSPACE_APP_ID }}" == '' ]; then
            echo "Missing secret: TEST_WORKSPACE_APP_ID" && exit 1
          fi
          if [ "${{ secrets.TEST_WORKSPACE_APP_SECRET }}" == '' ]; then
            echo "Missing secret: TEST_WORKSPACE_APP_SECRET" && exit 1
          fi
          if [ "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}" == '' ]; then
            echo "Missing secret: TEST_ACCOUNT_CLIENT_ID" && exit 1
          fi
          if [ "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}" == '' ]; then
            echo "Missing secret: TEST_ACCOUNT_CLIENT_SECRET" && exit 1
          fi
          if [ "${{ secrets.TRE_ID }}" == '' ]; then
            echo "Missing secret: TRE_ID" && exit 1
          fi
          if [ "${{ secrets.AZURE_CREDENTIALS }}" == '' ]; then
            echo "Missing secret: AZURE_CREDENTIALS" && exit 1
          fi

          if [ "${{ inputs.DEVCONTAINER_TAG }}" == '' ]; then
            echo "Missing input: DEVCONTAINER_TAG" && exit 1
          fi

          if [ "${{ vars.LOCATION }}" == '' ]; then
            echo "Missing variable: LOCATION" && exit 1
          fi

      - name: Report check status start
        if: inputs.prHeadSha != ''
        uses: LouisBrunner/checks-action@v1.6.0
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          sha: ${{ inputs.prHeadSha }}
          name: "Deploy PR / Run E2E Tests (Smoke)"
          status: "in_progress"
          details_url: "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"

      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Set up Docker BuildKit
        uses: docker/setup-buildx-action@v2

      - name: Azure Login
        uses: azure/login@v1
        with:
          creds: ${{ secrets.AZURE_CREDENTIALS }}
          environment: ${{ (vars.AZURE_ENVIRONMENT != '' && vars.AZURE_ENVIRONMENT) || 'AzureCloud' }}

      - name: ACR Login
        id: ci_cache_cr_login
        # will fail if this is a new env which is expected
        continue-on-error: true
        run: az acr login --name "${{ secrets.CI_CACHE_ACR_NAME }}"

      - name: Build new devcontainer
        env:
          DOCKER_BUILDKIT: 1
        run: |
          set -e

          USER_UID=$(id -u)
          USER_GID=$(id -g)
          acr_domain_suffix=$(az cloud show --query suffixes.acrLoginServerEndpoint --output tsv)
          CI_CACHE_ACR_URI=${{ secrets.CI_CACHE_ACR_NAME }}${acr_domain_suffix}
          echo "CI_CACHE_ACR_URI=$CI_CACHE_ACR_URI" >> "$GITHUB_ENV"

          docker_cache=()
          if [ "${{ steps.ci_cache_cr_login.outcome }}" = "success" ]; then
            docker_cache+=(--cache-from "$CI_CACHE_ACR_URI/tredev:${{ inputs.DEVCONTAINER_TAG }}")
            docker_cache+=(--cache-from "$CI_CACHE_ACR_URI/tredev:latest")
          fi

          docker build . "${docker_cache[@]}" \
            -t "tredev:${{ inputs.DEVCONTAINER_TAG }}" -f ".devcontainer/Dockerfile" \
            --build-arg BUILDKIT_INLINE_CACHE=1 --build-arg USER_UID="${USER_UID}" --build-arg USER_GID="${USER_GID}"

          docker image tag tredev:"${{ inputs.DEVCONTAINER_TAG }}" \
            "$CI_CACHE_ACR_URI/tredev:${{ inputs.DEVCONTAINER_TAG }}"

      - name: Deploy management
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make bootstrap mgmt-deploy"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          ACR_NAME: ${{ secrets.ACR_NAME }}
          TERRAFORM_STATE_CONTAINER_NAME: ${{ vars.TERRAFORM_STATE_CONTAINER_NAME }}
          MGMT_RESOURCE_GROUP_NAME: ${{ secrets.MGMT_RESOURCE_GROUP_NAME }}
          MGMT_STORAGE_ACCOUNT_NAME: ${{ secrets.MGMT_STORAGE_ACCOUNT_NAME }}

      - name: ACR Login
        # failure in the first attempt indicates a new ACR, so we need to try again after it's been created
        if: steps.ci_cache_cr_login.outcome != 'success'
        run: |
          # shellcheck disable=SC2034,SC2015,SC2125
          for i in {1..3}; do
            az acr login --name "${{ secrets.CI_CACHE_ACR_NAME }}" && ec=0 && break || ec=\$? && sleep 10
          done
          # shellcheck disable=SC2242
          (exit \$ec)

      - name: Push cached devcontainer
        run: docker image push ${{ env.CI_CACHE_ACR_URI }}/tredev:${{ inputs.DEVCONTAINER_TAG }}

  build_core_images:
    # used to build images used by core infrastructure
    name: Build Core Docker Images
    runs-on: ubuntu-latest
    needs: [deploy_management]
    environment: ${{ inputs.environmentName }}
    strategy:
      fail-fast: true
      matrix:
        target: [build-and-push-api, build-and-push-resource-processor, build-and-push-airlock-processor]

    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Docker build
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make ${{ matrix.target }}"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          ACR_NAME: ${{ secrets.ACR_NAME }}

  start_tre:
    name: Start TRE
    runs-on: ubuntu-latest
    needs: [deploy_management]
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Start TRE
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make tre-start"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          TRE_ID: ${{ secrets.TRE_ID }}

  deploy_tre:
    name: Deploy TRE
    runs-on: ubuntu-latest
    needs: [build_core_images, start_tre]
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Deploy TRE Core
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "TF_VAR_ci_git_ref=${{ inputs.ciGitRef }} TF_LOG=${{ vars.TF_LOG }} make deploy-core"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          ACR_NAME: ${{ secrets.ACR_NAME }}
          TERRAFORM_STATE_CONTAINER_NAME: ${{ vars.TERRAFORM_STATE_CONTAINER_NAME }}
          MGMT_RESOURCE_GROUP_NAME: ${{ secrets.MGMT_RESOURCE_GROUP_NAME }}
          MGMT_STORAGE_ACCOUNT_NAME: ${{ secrets.MGMT_STORAGE_ACCOUNT_NAME }}
          CORE_ADDRESS_SPACE: ${{ vars.CORE_ADDRESS_SPACE }}
          TRE_ADDRESS_SPACE: ${{ vars.TRE_ADDRESS_SPACE }}
          ENABLE_SWAGGER: ${{ vars.ENABLE_SWAGGER }}
          SWAGGER_UI_CLIENT_ID: "${{ secrets.SWAGGER_UI_CLIENT_ID }}"
          API_CLIENT_SECRET: "${{ secrets.API_CLIENT_SECRET }}"
          APPLICATION_ADMIN_CLIENT_ID: "${{ secrets.APPLICATION_ADMIN_CLIENT_ID }}"
          APPLICATION_ADMIN_CLIENT_SECRET: "${{ secrets.APPLICATION_ADMIN_CLIENT_SECRET }}"
          STATEFUL_RESOURCES_LOCKED: "${{ github.ref == 'refs/heads/main' && inputs.prRef == '' && true || false }}"
          CORE_APP_SERVICE_PLAN_SKU: ${{ vars.CORE_APP_SERVICE_PLAN_SKU }}
          RESOURCE_PROCESSOR_NUMBER_PROCESSES_PER_INSTANCE: ${{ vars.RESOURCE_PROCESSOR_NUMBER_PROCESSES_PER_INSTANCE }}
          RP_BUNDLE_VALUES: ${{ vars.RP_BUNDLE_VALUES }}

      - name: API Healthcheck
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make api-healthcheck"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}

  publish_bundles:
    name: Publish Bundles
    runs-on: ubuntu-latest
    needs: [deploy_management]
    strategy:
      matrix:
        include:
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/base"}
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/unrestricted"}
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/airlock-import-review"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/guacamole"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/azureml"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/innereye"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/gitea"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/mlflow"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/mysql"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/health-services"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/databricks"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/ohdsi"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-windowsvm"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-linuxvm"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-export-reviewvm"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-import-reviewvm"}
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Publish bundle
        uses: ./.github/actions/devcontainer_run_command
        with:
          # Although porter publish will build automatically, our makefile build target includes logic that should run
          COMMAND: >-
            for i in {1..3}; do make bundle-build bundle-publish DIR=${{ matrix.BUNDLE_DIR }}
            && ec=0 && break || ec=\$? && sleep 30; done; (exit \$ec)
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          ACR_NAME: ${{ secrets.ACR_NAME }}

  publish_shared_bundles:
    name: Publish Shared Bundles
    runs-on: ubuntu-latest
    needs: [deploy_management]
    strategy:
      matrix:
        include:
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/firewall/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/gitea/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/admin-vm/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/airlock_notifier/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/certs/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/cyclecloud/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/sonatype-nexus-vm/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/databricks-auth/"}
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Publish bundle
        uses: ./.github/actions/devcontainer_run_command
        with:
          # Although porter publish will build automatically, our makefile build target includes logic that should run
          COMMAND: >-
            for i in {1..3}; do make bundle-build bundle-publish DIR=${{ matrix.BUNDLE_DIR }}
            && ec=0 && break || ec=\$? && sleep 30; done; (exit \$ec)
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          ACR_NAME: ${{ secrets.ACR_NAME }}

  register_shared_bundles:
    name: Register Shared Bundles
    runs-on: ubuntu-latest
    needs: [publish_shared_bundles, deploy_tre]
    strategy:
      matrix:
        include:
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/firewall"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/gitea"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/admin-vm/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/airlock_notifier/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/certs/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/cyclecloud/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/sonatype-nexus-vm/"}
          - {BUNDLE_TYPE: "shared_service",
             BUNDLE_DIR: "./templates/shared_services/databricks-auth/"}
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}
      - name: Register bundle
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: >-
            for i in {1..3}; do make bundle-register DIR=${{ matrix.BUNDLE_DIR }}
            && ec=0 && break || ec=\$? && sleep 10; done; (exit \$ec)
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          ACR_NAME: ${{ secrets.ACR_NAME }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          BUNDLE_TYPE: ${{ matrix.BUNDLE_TYPE }}

  register_bundles:
    name: Register Bundles
    runs-on: ubuntu-latest
    needs: [publish_bundles, deploy_tre]
    strategy:
      matrix:
        include:
          # bundles type can be inferred from the bundle dir (but this is more explicit)
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/base"}
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/unrestricted"}
          - {BUNDLE_TYPE: "workspace",
             BUNDLE_DIR: "./templates/workspaces/airlock-import-review"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/guacamole"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/azureml"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/innereye"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/gitea"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/mlflow"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/mysql"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/health-services"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/databricks"}
          - {BUNDLE_TYPE: "workspace_service",
             BUNDLE_DIR: "./templates/workspace_services/ohdsi"}

    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}
      - name: Register bundle
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: >-
            for i in {1..3}; do make bundle-register DIR=${{ matrix.BUNDLE_DIR }}
            && ec=0 && break || ec=\$? && sleep 10; done; (exit \$ec)
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          ACR_NAME: ${{ secrets.ACR_NAME }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          BUNDLE_TYPE: ${{ matrix.BUNDLE_TYPE }}

  register_user_resource_bundles:
    name: Register User Resource Bundles
    runs-on: ubuntu-latest
    # user resource bundles need to wait for their parent resource to be registered.
    needs: [register_bundles, publish_bundles, deploy_tre]
    strategy:
      matrix:
        include:
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-windowsvm",
             WORKSPACE_SERVICE_NAME: "tre-service-guacamole"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-linuxvm",
             WORKSPACE_SERVICE_NAME: "tre-service-guacamole"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-export-reviewvm",
             WORKSPACE_SERVICE_NAME: "tre-service-guacamole"}
          - {BUNDLE_TYPE: "user_resource",
             BUNDLE_DIR: "./templates/workspace_services/guacamole/user_resources/guacamole-azure-import-reviewvm",
             WORKSPACE_SERVICE_NAME: "tre-service-guacamole"}
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}
      - name: Register bundle
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: >-
            for i in {1..3}; do make bundle-register DIR=${{ matrix.BUNDLE_DIR }}
            && ec=0 && break || ec=\$? && sleep 10; done; (exit \$ec)
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          ACR_NAME: ${{ secrets.ACR_NAME }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          BUNDLE_TYPE: ${{ matrix.BUNDLE_TYPE }}
          WORKSPACE_SERVICE_NAME: ${{ matrix.WORKSPACE_SERVICE_NAME }}

  deploy_shared_services:
    name: Deploy shared services
    runs-on: ubuntu-latest
    needs: [register_shared_bundles, deploy_tre]
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Deploy firewall
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make deploy-shared-service DIR=./templates/shared_services/firewall/ BUNDLE_TYPE=shared_service"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}

      - name: State Store Migrations
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make db-migrate"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          TERRAFORM_STATE_CONTAINER_NAME: ${{ vars.TERRAFORM_STATE_CONTAINER_NAME }}
          MGMT_RESOURCE_GROUP_NAME: ${{ secrets.MGMT_RESOURCE_GROUP_NAME }}
          MGMT_STORAGE_ACCOUNT_NAME: ${{ secrets.MGMT_STORAGE_ACCOUNT_NAME }}

  deploy_ui:
    name: Deploy UI
    runs-on: ubuntu-latest
    needs: [deploy_tre]
    environment: ${{ inputs.environmentName }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}
      - name: Deploy UI
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make build-and-deploy-ui"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          LOCATION: ${{ vars.LOCATION }}
          TERRAFORM_STATE_CONTAINER_NAME: ${{ vars.TERRAFORM_STATE_CONTAINER_NAME }}
          MGMT_RESOURCE_GROUP_NAME: ${{ secrets.MGMT_RESOURCE_GROUP_NAME }}
          MGMT_STORAGE_ACCOUNT_NAME: ${{ secrets.MGMT_STORAGE_ACCOUNT_NAME }}
          SWAGGER_UI_CLIENT_ID: "${{ secrets.SWAGGER_UI_CLIENT_ID }}"

  e2e_tests_smoke:
    name: "Run E2E Tests (Smoke)"
    runs-on: ubuntu-latest
    environment: ${{ inputs.environmentName }}
    needs: [deploy_shared_services, register_bundles, deploy_ui]
    timeout-minutes: 10
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Run E2E Tests (Smoke)
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make test-e2e-smoke"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          LOCATION: ${{ vars.LOCATION }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_WORKSPACE_APP_ID: "${{ secrets.TEST_WORKSPACE_APP_ID }}"
          TEST_WORKSPACE_APP_SECRET: "${{ secrets.TEST_WORKSPACE_APP_SECRET }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          IS_API_SECURED: false
          WORKSPACE_APP_SERVICE_PLAN_SKU: ${{ vars.WORKSPACE_APP_SERVICE_PLAN_SKU }}

      - name: Upload Test Results
        if: always()
        uses: actions/upload-artifact@v3
        with:
          name: E2E Test (Smoke) Results
          path: "./e2e_tests/pytest_e2e_smoke.xml"

  e2e_tests_custom:
    name: "Run E2E Tests"
    if: ${{ inputs.e2eTestsCustomSelector != '' }}
    runs-on: ubuntu-latest
    environment: ${{ inputs.environmentName }}
    needs: [deploy_shared_services, register_bundles, register_user_resource_bundles]
    timeout-minutes: 300
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        with:
          persist-credentials: false
          # if the following values are missing (i.e. not triggered via comment workflow)
          # then the default checkout will apply
          ref: ${{ inputs.prRef }}

      - name: Run E2E Tests
        uses: ./.github/actions/devcontainer_run_command
        with:
          COMMAND: "make test-e2e-custom SELECTOR='${{ inputs.e2eTestsCustomSelector }}'"
          DEVCONTAINER_TAG: ${{ inputs.DEVCONTAINER_TAG }}
          CI_CACHE_ACR_NAME: ${{ secrets.CI_CACHE_ACR_NAME}}
          AZURE_CREDENTIALS: ${{ secrets.AZURE_CREDENTIALS }}
          AZURE_ENVIRONMENT: ${{ vars.AZURE_ENVIRONMENT }}
          LOCATION: ${{ vars.LOCATION }}
          API_CLIENT_ID: "${{ secrets.API_CLIENT_ID }}"
          AAD_TENANT_ID: "${{ secrets.AAD_TENANT_ID }}"
          TEST_APP_ID: "${{ secrets.TEST_APP_ID }}"
          TEST_WORKSPACE_APP_ID: "${{ secrets.TEST_WORKSPACE_APP_ID }}"
          TEST_WORKSPACE_APP_SECRET: "${{ secrets.TEST_WORKSPACE_APP_SECRET }}"
          TEST_ACCOUNT_CLIENT_ID: "${{ secrets.TEST_ACCOUNT_CLIENT_ID }}"
          TEST_ACCOUNT_CLIENT_SECRET: "${{ secrets.TEST_ACCOUNT_CLIENT_SECRET }}"
          TRE_ID: ${{ secrets.TRE_ID }}
          IS_API_SECURED: false
          WORKSPACE_APP_SERVICE_PLAN_SKU: ${{ vars.WORKSPACE_APP_SERVICE_PLAN_SKU }}
          E2E_TESTS_NUMBER_PROCESSES: ${{ inputs.E2E_TESTS_NUMBER_PROCESSES }}

      - name: Upload Test Results
        if: always()
        uses: actions/upload-artifact@v3
        with:
          name: E2E Test Results
          path: "./e2e_tests/pytest_e2e_custom.xml"

  summary:
    name: Summary
    needs: [e2e_tests_smoke, e2e_tests_custom]
    runs-on: ubuntu-latest
    if: always()
    environment: ${{ inputs.environmentName }}
    steps:
      - uses: technote-space/workflow-conclusion-action@v3

      # For PR builds triggered from comment builds, the GITHUB_REF is set to main
      # so the checks aren't automatically associated with the PR
      # If prHeadSha is specified then explicity mark the checks for that SHA
      - name: Report check status
        if: inputs.prHeadSha != ''
        uses: LouisBrunner/checks-action@v1.6.0
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          # the name must be identical to the one received by the real job
          sha: ${{ inputs.prHeadSha }}
          name: "Deploy PR / Run E2E Tests (Smoke)"
          status: "completed"
          conclusion: ${{ env.WORKFLOW_CONCLUSION }}
          details_url: "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"

      - name: Notify teams channel
        env:
          MS_TEAMS_WEBHOOK_URI: ${{ secrets.MS_TEAMS_WEBHOOK_URI }}
        # notify only if failure
        if: |
          env.WORKFLOW_CONCLUSION == 'failure' &&
          env.MS_TEAMS_WEBHOOK_URI != '' &&
          (github.ref == 'refs/heads/main' && inputs.prRef == '')
        uses: sachinkundu/ms-teams-notification@1.4
        with:
          github-token: ${{ github.token }}
          ms-teams-webhook-uri: ${{ secrets.MS_TEAMS_WEBHOOK_URI }}
          notification-summary: "Failed to deploy from main"
          notification-color: dc3545
          timezone: Europe/Zurich

      - name: Download Artifacts
        uses: actions/download-artifact@v3
        with:
          path: artifacts

      - name: Publish E2E Test Results
        uses: EnricoMi/publish-unit-test-result-action@v2
        with:
          junit_files: "artifacts/**/*.xml"
          check_name: "E2E Test Results"