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site_deploy.yml
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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: '7.6.0'
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/[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: ${{ github.event.inputs.server_only != 'true' }}
# run: |
# cd docker/swarm
# echo "${{ secrets.GITHUB_TOKEN }}" | sudo docker login ghcr.io -u ${{ github.actor }} --password-stdin
# 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: build
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/[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: 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: ${{ github.event.inputs.server_only != 'true' }}
run: |
set -ux
mvn clean install -DskipTests
# - name: deploy installers and web help to vcell.org
# run: |
# set -ux
# cd docker/swarm
# ssh -t vcell@${VCELL_MANAGER_NODE} sudo docker login -u ${{ github.actor }} -p "${{ secrets.GITHUB_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 vcell \
# --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 $VCELL_CONFIG_FILE_NAME | grep VCELL_SITE_CAMEL | cut -d"=" -f2`
# ssh vcell@${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: Deploy Web Help
run: |
set -ux
webhelp_local_dir="../../vcell-client/target/classes/vcellDoc"
ssh_user="vcell"
webhelp_deploy_dir="${VCELL_WEBHELP_REMOTE_DIR}"
manager_node="${VCELL_MANAGER_NODE}"
if [[ -z "${webhelp_deploy_dir}" || -z "${manager_node}" ]]; then
echo "Error: VCELL_WEBHELP_REMOTE_DIR or manager_node is not set."
exit 1
fi
if ! rsync -a -vvv "${webhelp_local_dir}/topics" "$ssh_user@$manager_node:${webhelp_deploy_dir}";
then
echo "failed to copy html files in topic directory to webhelp deploy directory";
exit 1;
fi
if ! scp "${webhelp_local_dir}/VCellHelpTOC.html" "$ssh_user@$manager_node:${webhelp_deploy_dir}/index.html";
then
echo "failed to index.html to webhelp deploy directory";
exit 1;
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
with:
limit-access-to-actor: true
# if: ${{ failure() }}