site_deploy.yml

# This workflow will deploy the VCell full application (server +- client) to alpha or release

name: CD-sites

# Controls when the workflow will run
on:
  workflow_dispatch:
    inputs:
      vcell_version:
        description: 'version.major.minor' 
        required: true
        default: '7.6.0'
      vcell_build:
        description: 'build number'
        required: true
        default: '18'
      vcell_site:
        description: 'rel or alpha or test'
        required: true
        default: 'alpha'
      server_only:
        description: 'Deploy only the server components?'
        required: true
        default: 'false'
jobs:
  build:
    name: Build client installers
    runs-on: ubuntu-20.04
    steps:
    - name: checkout tag
      uses: actions/checkout@v4
      with:
        ref: ${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
    - name: setup global environment variables
      run: |
        echo "VCELL_VERSION=${{ github.event.inputs.vcell_version }}" >> $GITHUB_ENV
        echo "VCELL_BUILD=${{ github.event.inputs.vcell_build }}" >> $GITHUB_ENV
        echo "VCELL_SITE=${{ github.event.inputs.vcell_site }}" >> $GITHUB_ENV
        echo "VCELL_TAG=`git rev-parse --short HEAD`" >> $GITHUB_ENV
        echo "VCELL_REPO_NAMESPACE=ghcr.io/virtualcell" >> $GITHUB_ENV
        echo "VCELL_DEPLOY_REMOTE_DIR=/share/apps/vcell3/deployed_github" >> $GITHUB_ENV
        echo "VCELL_WEBHELP_REMOTE_DIR=/share/apps/vcell3/apache_webroot/htdocs/webstart/VCell_Tutorials/VCell_Help" >> $GITHUB_ENV
        if [ "${{ github.event.inputs.vcell_site }}" == "rel" ]; then\
        	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
        	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Rel"" >> $GITHUB_ENV;\
        else if [ "${{ github.event.inputs.vcell_site }}" == "alpha" ]; then\
         	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
        	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Alpha"" >> $GITHUB_ENV;\
        else if [ "${{ github.event.inputs.vcell_site }}" == "test" ]; then\
         	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
        	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Test"" >> $GITHUB_ENV;\
        else echo "Unknown site name ${{ github.event.inputs.vcell_site }}"; exit 1; fi; fi; fi
    - name: setup ssh-agent
      uses: webfactory/ssh-agent@v0.8.0
      with:
        ssh-private-key: ${{ secrets.VC_KEY }}
    - name: get installer secrets
      run: |
        ssh-keyscan $VCELL_MANAGER_NODE >> ~/.ssh/known_hosts
        sudo mkdir /usr/local/deploy
        sudo chmod 777 /usr/local/deploy
        cd /usr/local/deploy
        scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/deploy_dir_2023_07_30.tar .
        cd ..
        sudo tar -xvf deploy/deploy_dir_2023_07_30.tar
        sudo chmod 777 -R deploy
    - name: setup config
      run: |
        cd docker/swarm
        export VCELL_CONFIG_FILE_NAME="server_${VCELL_SITE}_${VCELL_VERSION}_${VCELL_BUILD}_${VCELL_TAG}.config"
        echo "VCELL_CONFIG_FILE_NAME=$VCELL_CONFIG_FILE_NAME" >> $GITHUB_ENV
        echo "| $VCELL_SITE | $VCELL_REPO_NAMESPACE | $VCELL_TAG | $VCELL_VERSION | $VCELL_BUILD | $VCELL_CONFIG_FILE_NAME |"
        ./serverconfig-uch.sh $VCELL_SITE $VCELL_REPO_NAMESPACE $VCELL_TAG $VCELL_VERSION $VCELL_BUILD $VCELL_CONFIG_FILE_NAME
        env | grep VCELL > variables
    - name: send home config file and variables
      run: |
        scp docker/build/admin/vcell-su.sh ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/config
        scp docker/swarm/$VCELL_CONFIG_FILE_NAME ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}
        scp docker/swarm/variables ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/variables_$VCELL_TAG
    - name: upload variables
      uses: actions/upload-artifact@v3
      with:
        name: variables
        path: docker/swarm/variables
        retention-days: 1
    - name: build client installers
      if: ${{ github.event.inputs.server_only != 'true' }}
      run: |
        cd docker/swarm
        sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
        sudo docker pull $VCELL_REPO_NAMESPACE/vcell-clientgen:$VCELL_TAG
        ./generate_installers.sh ./${VCELL_CONFIG_FILE_NAME}
    - name: upload generated installers
      if: ${{ github.event.inputs.server_only != 'true' }}
      uses: actions/upload-artifact@v3
      with:
        name: installers
        path: docker/swarm/generated_installers
        retention-days: 1
    - name: Setup tmate session
      if: ${{ failure() }}
      uses: mxschmitt/action-tmate@v3
      
  notarize:
    name: Notarize the MacOS client
    runs-on: macos-latest
    needs: build
    steps:
    - name: download generated installers
      if: ${{ github.event.inputs.server_only != 'true' }}
      uses: actions/download-artifact@v3
    - name: notarize mac installer
      if: ${{ github.event.inputs.server_only != 'true' }}
      run: |
        set -x
        set +e
        cd installers
        export MAC_INSTALLER=`ls *dmg`
        xcrun notarytool submit --output-format normal --no-progress --no-wait --team-id "${{ secrets.MACTEAMID }}" --apple-id "${{ secrets.MACID }}" --password "${{ secrets.MACPW }}" $MAC_INSTALLER > submit_output
        echo "output returned by notarytool submit:"
        cat submit_output
        cat submit_output | grep "id:" | cut -d ':' -f2 > UUID
        for minutes in {1..5}
        do
          sleep 60
          xcrun notarytool info --output-format normal --no-progress --team-id "${{ secrets.MACTEAMID }}" --apple-id "${{ secrets.MACID }}" --password "${{ secrets.MACPW }}" `cat UUID` > info_output
          echo "output returned by notarytool info:"
          cat info_output
          grep -q Accepted info_output
          if [[ $? == 0 ]]; then
            echo "notarized succesfully"
            break
          else
            echo "wait another minute and check again"
          fi
        done
        grep -q Accepted info_output
        if [[ $? == 0 ]]; then
          xcrun stapler staple $MAC_INSTALLER
        else
          echo "notarization did not succeed in 5 minutes, giving up"
          exit 1
        fi
    - name: update generated installers
      if: ${{ github.event.inputs.server_only != 'true' }}
      uses: actions/upload-artifact@v3
      with:
        name: installers
        path: installers
        retention-days: 1
    - name: Setup tmate session
      uses: mxschmitt/action-tmate@v3
      if: ${{ failure() }}
        
  deploy:
    name: Deploy to site
    runs-on: ubuntu-20.04
    needs: notarize
    steps:
    - name: checkout tag
      uses: actions/checkout@v4
      with:
        ref: ${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
    - name: retrieve installers and variables
      uses: actions/download-artifact@v3
    - name: setenv
      run: |
        for line in $(cat variables/variables); do echo $line >> $GITHUB_ENV; done
    - name: stage installers
      if: ${{ github.event.inputs.server_only != 'true' }}
      run: |
        cd installers
        mkdir ../docker/swarm/generated_installers
        mv * ../docker/swarm/generated_installers
    - name: setup ssh-agent
      uses: webfactory/ssh-agent@v0.8.0
      with:
        ssh-private-key: ${{ secrets.VC_KEY }}
    - name: retrieve config file
      run: |
        set -ux
        ssh-keyscan $VCELL_MANAGER_NODE >> ~/.ssh/known_hosts
        cd docker/swarm
        scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/${VCELL_CONFIG_FILE_NAME} .
    - name: setup java 17 with maven cache (for documentation build)
      uses: actions/setup-java@v4
      with:
        distribution: 'temurin'
        java-version: '17'
        cache: 'maven'
    - name: build documentation for web help
      if: ${{ github.event.inputs.server_only != 'true' }}
      run: |
        set -ux
        mvn clean install -DskipTests
    - name: deploy installers and web help to vcell.org
      run: |
        set -ux
        cd docker/swarm
        ssh -t ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
        if ${{ github.event.inputs.server_only != 'true' }}; then
          # build and install the client installers, and the web help (kubernetes cluster deployments are separate)
          ./deploy-action-kubernetes.sh \
              --ssh-user ${{ secrets.CD_FULL_USER }} \
              --build-installers \
              --installer-deploy-dir $VCELL_INSTALLER_REMOTE_DIR \
              --webhelp-local-dir ../../vcell-client/target/classes/vcellDoc \
              --webhelp-deploy-dir $VCELL_WEBHELP_REMOTE_DIR \
              ${VCELL_MANAGER_NODE} \
              ./${VCELL_CONFIG_FILE_NAME}
          export VCELL_SITE_CAMEL=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_SITE_CAMEL | cut -d"=" -f2`
          ssh ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} \
            installer_deploy_dir=$VCELL_INSTALLER_REMOTE_DIR vcell_siteCamel=$VCELL_SITE_CAMEL vcell_version=$VCELL_VERSION vcell_build=$VCELL_BUILD \
            'bash -s' < link-installers.sh
        fi
    - name: Capitalize first character of site name
      id: capitalize
      run: |
        SITE="${{ github.event.inputs.vcell_site }}"
        SITE_CAPITALIZED="$(tr '[:lower:]' '[:upper:]' <<< ${SITE:0:1})${SITE:1}"
        VCELL_SWVERSION="${SITE_CAPITALIZED}_Version_${{ github.event.inputs.vcell_version }}_build_${{ github.event.inputs.vcell_build}}"
        KUSTOMIZE_OVERLAY='not-specified'
        if [ "${{ github.event.inputs.vcell_site }}" == "rel" ]; then KUSTOMIZE_OVERLAY="prod"; fi
        if [ "${{ github.event.inputs.vcell_site }}" == "alpha" ]; then KUSTOMIZE_OVERLAY="dev"; fi
        if [ "${{ github.event.inputs.vcell_site }}" == "test" ]; then KUSTOMIZE_OVERLAY="stage"; fi
        CONTAINER_IMAGE_TAG="${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build}}"
        echo "VCELL_SWVERSION=${VCELL_SWVERSION}" >> $GITHUB_ENV
        echo "KUSTOMIZE_OVERLAY=${KUSTOMIZE_OVERLAY}" >> $GITHUB_ENV
        echo "CONTAINER_IMAGE_TAG=${CONTAINER_IMAGE_TAG}" >> $GITHUB_ENV
    - name: Call webhook to deploy to kubernetes cluster (overlay 'prod', 'dev' or 'stage')
      run: |
        git_sha=$(git rev-parse --short "$GITHUB_SHA")
        echo '{"ref": "main","inputs":{"overlay": "'${KUSTOMIZE_OVERLAY}'","tag":"'${CONTAINER_IMAGE_TAG}'","swversion": "'${VCELL_SWVERSION}'"}}' >body
        curl -X POST 'https://api.github.com/repos/virtualcell/vcell-fluxcd/actions/workflows/deploy.yaml/dispatches' \
          -H 'Authorization: Bearer ${{ secrets.ACTION_TOKEN }}' \
          -H 'Content-Type: application/json' \
          --data "@body"
    - name: Setup tmate session 3
      uses: mxschmitt/action-tmate@v3
      if: ${{ failure() }}