CD-sites #325
Workflow file for this run
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| # 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: '7.5.0' | |
| vcell_build: | |
| description: 'build number' | |
| required: true | |
| default: '148' | |
| vcell_site: | |
| description: 'rel or alpha or test (note rel is Swarm, alpha and test are Kubernetes)' | |
| 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@v3 | |
| 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/[email protected] | |
| 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@v2 | |
| - 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@v3 | |
| with: | |
| ref: ${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }} | |
| - name: retrieve installers and variables | |
| uses: actions/download-artifact@v2 | |
| - 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/[email protected] | |
| 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: install singularity | |
| uses: eWaterCycle/setup-singularity@v6 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: retrieve batch and opt singularity images | |
| run: | | |
| set -ux | |
| cd docker/swarm | |
| export BATCH_SINGULARITY_FILENAME=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_BATCH_SINGULARITY_FILENAME | cut -d"=" -f2` | |
| export OPT_SINGULARITY_FILENAME=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_OPT_SINGULARITY_FILENAME | cut -d"=" -f2` | |
| cd ../build/singularity-vm | |
| singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io | |
| singularity pull $BATCH_SINGULARITY_FILENAME oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }} | |
| singularity pull $OPT_SINGULARITY_FILENAME oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }} | |
| - name: setup java 17 with maven cache (for documentation build) | |
| uses: actions/setup-java@v3 | |
| 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 singularity to kubernetes site and web help to vcell.org | |
| if: ${{ github.event.inputs.vcell_site != 'rel' }} | |
| 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, the singularity images, and the web help (kubernetes cluster deployments are separate) | |
| ./deploy-action-kubernetes.sh \ | |
| --ssh-user ${{ secrets.CD_FULL_USER }} \ | |
| --install-singularity \ | |
| --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 | |
| else | |
| # build and install only the singularity images (kubernetes cluster deployments are separate) | |
| ./deploy-action-kubernetes.sh \ | |
| --ssh-user ${{ secrets.CD_FULL_USER }} \ | |
| --install-singularity \ | |
| ${VCELL_MANAGER_NODE} \ | |
| ./${VCELL_CONFIG_FILE_NAME} | |
| 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') | |
| if: ${{ github.event.inputs.vcell_site != 'rel' }} | |
| run: | | |
| git_sha=$(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: deploy to swarm site | |
| if: ${{ github.event.inputs.vcell_site == 'rel' }} | |
| 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, singularity images, and docker swarm configuration | |
| ./deploy-action-swarm.sh \ | |
| --ssh-user ${{ secrets.CD_FULL_USER }} \ | |
| --install-singularity \ | |
| --build-installers \ | |
| --installer-deploy-dir $VCELL_INSTALLER_REMOTE_DIR \ | |
| ${VCELL_MANAGER_NODE} \ | |
| ./${VCELL_CONFIG_FILE_NAME} \ | |
| ${VCELL_DEPLOY_REMOTE_DIR}/config/${VCELL_CONFIG_FILE_NAME} \ | |
| ./docker-compose.yml \ | |
| ${VCELL_DEPLOY_REMOTE_DIR}/config/docker-compose_${VCELL_TAG}.yml \ | |
| vcell${VCELL_SITE} | |
| 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 | |
| else | |
| # build and install only the singularity images and docker swarm configuration | |
| ./deploy-action-swarm.sh \ | |
| --ssh-user ${{ secrets.CD_FULL_USER }} \ | |
| --install-singularity \ | |
| ${VCELL_MANAGER_NODE} \ | |
| ./${VCELL_CONFIG_FILE_NAME} \ | |
| ${VCELL_DEPLOY_REMOTE_DIR}/config/${VCELL_CONFIG_FILE_NAME} \ | |
| ./docker-compose.yml \ | |
| ${VCELL_DEPLOY_REMOTE_DIR}/config/docker-compose_${VCELL_TAG}.yml \ | |
| vcell${VCELL_SITE} | |
| fi | |
| - name: Setup tmate session 3 | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} | |