Deploy Cellenics infrastructure on AWS #506
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| name: Deploy Cellenics infrastructure on AWS | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| environment_name: | |
| type: string | |
| description: Select the environment name to run the actions on | |
| required: true | |
| default: all | |
| workflow_actions: | |
| type: choice | |
| description: Select actions to perform | |
| options: | |
| - create and configure cluster | |
| - configure cluster | |
| - deploy monitoring | |
| default: configure cluster | |
| environment_type: | |
| type: choice | |
| description: Select environment type | |
| options: | |
| - staging | |
| - production | |
| - staging and production | |
| default: staging | |
| # this ensures that only one CI pipeline with the same key | |
| # can run at once in order to prevent undefined states | |
| concurrency: cluster-update-mutex | |
| permissions: | |
| id-token: write | |
| contents: read | |
| # After load-config and check-secrets jobs are finished: | |
| # "create and configure cluster" workflow_actions option runs all jobs. | |
| # "configure cluster" workflow_actions option runs only configure-cluster job | |
| # "deploy monitoring" workflow_actions option runs only deploy-monitoring job | |
| jobs: | |
| load-config: | |
| uses: ./.github/workflows/load-config.yaml | |
| with: | |
| environment_name: ${{ github.event.inputs.environment_name }} | |
| environment_type: ${{ github.event.inputs.environment_type }} | |
| check-secrets: | |
| name: Check that sufficient secrets are specified for environment name | |
| runs-on: ubuntu-20.04 | |
| needs: load-config | |
| strategy: | |
| matrix: | |
| environment_name: ${{ fromJson(needs.load-config.outputs.environment_names) }} | |
| environment: ${{ matrix.environment_name }} | |
| steps: | |
| - id: check-secrets-for-environment | |
| name: Check if necessary secrets are installed. | |
| run: |- | |
| echo Checking if secrets are defined in the repository. | |
| if [ -z "${{ secrets.ACM_CERTIFICATE_ARN}}" ] | |
| then | |
| echo AWS certificate ARN is not defined. | |
| ERROR=true | |
| fi | |
| if [ -z "${{ secrets.AWS_ACCOUNT_ID }}" ] | |
| then | |
| echo AWS Account ID is not defined. | |
| ERROR=true | |
| fi | |
| if [ -z "${{ secrets.API_TOKEN_GITHUB }}" ] | |
| then | |
| echo GitHub deploy key access token is not defined. | |
| ERROR=true | |
| fi | |
| if [ -z "${{ secrets.PRIMARY_DOMAIN_NAME }}" ] | |
| then | |
| echo Secret PRIMARY_DOMAIN_NAME is not set in repository secrets. Make sure this secret exists in the repository secrets. | |
| ERROR=true | |
| fi | |
| if [ -z "${{ secrets.DOMAIN_NAME }}" ] | |
| then | |
| echo Secret DOMAIN_NAME is not set in repository secrets. Make sure this secret exists in the repository secrets. | |
| ERROR=true | |
| fi | |
| if [ -n "$ERROR" ] | |
| then | |
| echo | |
| echo This workflow requires some secrets to complete. | |
| echo Please make they are created by adding/rotating them manually. | |
| exit 1 | |
| fi | |
| create-eks-cluster: | |
| name: Create EKS cluster | |
| runs-on: ubuntu-20.04 | |
| needs: [check-secrets, load-config] | |
| if: github.event.inputs.workflow_actions == 'create and configure cluster' | |
| env: | |
| CLUSTER_ENV: ${{ matrix.environment.type }} | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| environment: ${{ fromJson(needs.load-config.outputs.deployment_matrix) }} | |
| environment: ${{ matrix.environment.name }} | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| - id: setup-aws | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-iac-role | |
| role-duration-seconds: 4800 | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: fill-metadata | |
| name: Add name and region to the eksctl file. | |
| run: |- | |
| export CLUSTER_NAME="biomage-$CLUSTER_ENV" | |
| yq -i ' | |
| .metadata.name = strenv(CLUSTER_NAME) | | |
| .metadata.region = strenv(AWS_REGION) | |
| ' infra/config/cluster/cluster-template.yaml | |
| # CELLENICS_VPC_ID is set if using custom cluster deployment. In this case, use the custom template file. | |
| # If not set, create an empty template file to let eksctl create a new cluster for the deployment. | |
| if [ ! -z "$CELLENICS_VPC_ID" ]; then | |
| export PRIVATE_SUBNET_1_ID=$(aws ec2 describe-subnets --filters "Name=vpc-id,Values=$CELLENICS_VPC_ID" "Name=map-public-ip-on-launch,Values=false" | jq -r '.Subnets[0].SubnetId') | |
| export PRIVATE_SUBNET_2_ID=$(aws ec2 describe-subnets --filters "Name=vpc-id,Values=$CELLENICS_VPC_ID" "Name=map-public-ip-on-launch,Values=false" | jq -r '.Subnets[1].SubnetId') | |
| export PUBLIC_SUBNET_1_ID=$(aws ec2 describe-subnets --filters "Name=vpc-id,Values=$CELLENICS_VPC_ID" "Name=map-public-ip-on-launch,Values=true" | jq -r '.Subnets[0].SubnetId') | |
| export PUBLIC_SUBNET_2_ID=$(aws ec2 describe-subnets --filters "Name=vpc-id,Values=$CELLENICS_VPC_ID" "Name=map-public-ip-on-launch,Values=true" | jq -r '.Subnets[1].SubnetId') | |
| yq ' | |
| .vpc.id = strenv(CELLENICS_VPC_ID) | | |
| .vpc.subnets.private.private-1 = strenv(PRIVATE_SUBNET_1_ID) | | |
| .vpc.subnets.private.private-2 = strenv(PRIVATE_SUBNET_2_ID) | | |
| .vpc.subnets.public.public-1 = strenv(PUBLIC_SUBNET_1_ID) | | |
| .vpc.subnets.public.public-2 = strenv(PUBLIC_SUBNET_2_ID) | |
| ' infra/config/cluster/cluster-config-template.yaml > /tmp/cluster-config-values.yaml | |
| else | |
| touch /tmp/cluster-config-values.yaml | |
| fi | |
| yq eval-all '. as $item ireduce ({}; . *d $item)' infra/config/cluster/cluster-template.yaml /tmp/cluster-config-values.yaml > /tmp/cluster-$CLUSTER_ENV.yaml | |
| cat /tmp/cluster-$CLUSTER_ENV.yaml | |
| env: | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| CELLENICS_VPC_ID: ${{ secrets.CELLENICS_VPC_ID }} | |
| - id: install-eksctl | |
| name: Install eksctl | |
| run: |- | |
| curl --silent --location "https://github.com/weaveworks/eksctl/releases/latest/download/eksctl_$(uname -s)_amd64.tar.gz" | tar xz -C /tmp | |
| sudo mv /tmp/eksctl /usr/local/bin | |
| - id: create-clusters | |
| name: Attempt to create clusters from spec. | |
| # this job will always pass, irrespective of whether creation was successful or not. | |
| # this is because the cluster may already exist. we will check for this condition | |
| # on failure in the next step | |
| continue-on-error: true | |
| run: |- | |
| exec &> >(tee /tmp/eksctl-$CLUSTER_ENV.log) | |
| eksctl create cluster -f /tmp/cluster-$CLUSTER_ENV.yaml | |
| echo "outcome=created" >> $GITHUB_OUTPUT | |
| - id: check-for-failure | |
| name: Check for reason of failure if cluster creation failed. | |
| if: steps.create-clusters.outcome == 'failure' | |
| run: |- | |
| # Check if failure was caused by an already exists exception. | |
| # If not, the job should fail. | |
| ALREADY_EXISTS=$(grep AlreadyExistsException /tmp/eksctl-$CLUSTER_ENV.log | wc -l | xargs) | |
| if [ $ALREADY_EXISTS -ne 1 ] | |
| then | |
| echo Step failed for reason other than stack already existing. | |
| echo Job failing... | |
| echo "reason=error" >> $GITHUB_OUTPUT | |
| false | |
| fi | |
| echo Cluster already exists. | |
| echo "reason=already-exists" >> $GITHUB_OUTPUT | |
| - id: update-addons-for-cluster | |
| name: Attempt to create addons for cluster. | |
| continue-on-error: true | |
| run: |- | |
| exec &> >(tee /tmp/eksctl-$CLUSTER_ENV.log) | |
| eksctl create addon -f /tmp/cluster-$CLUSTER_ENV.yaml | |
| - id: update-nodegroup | |
| name: Attempt to update node groups for existing cluster. | |
| if: steps.create-clusters.outcome == 'failure' && steps.check-for-failure.outputs.reason == 'already-exists' | |
| run: |- | |
| eksctl create nodegroup --config-file=/tmp/cluster-$CLUSTER_ENV.yaml | |
| eksctl delete nodegroup --config-file /tmp/cluster-$CLUSTER_ENV.yaml --only-missing --approve | |
| # note: iam service accounts should really be created from within the helm chart as seen here: | |
| # https://docs.aws.amazon.com/eks/latest/userguide/specify-service-account-role.html | |
| - id: update-serviceaccounts | |
| name: Attempt to update IAM service accounts for existing cluster. | |
| if: steps.create-clusters.outcome == 'failure' && steps.check-for-failure.outputs.reason == 'already-exists' | |
| run: |- | |
| eksctl utils associate-iam-oidc-provider --config-file=/tmp/cluster-$CLUSTER_ENV.yaml --approve | |
| eksctl create iamserviceaccount --config-file=/tmp/cluster-$CLUSTER_ENV.yaml | |
| eksctl delete iamserviceaccount --config-file=/tmp/cluster-$CLUSTER_ENV.yaml --only-missing --approve | |
| configure-cluster: | |
| name: Configure Kubernetes resources on the EKS cluster | |
| runs-on: ubuntu-20.04 | |
| needs: [check-secrets, create-eks-cluster, load-config] | |
| if: always() && (github.event.inputs.workflow_actions == 'create and configure cluster' || github.event.inputs.workflow_actions == 'configure cluster') && (needs.check-secrets.result == 'success') && (needs.create-eks-cluster.result == 'success' || needs.create-eks-cluster.result == 'skipped') | |
| env: | |
| CLUSTER_ENV: ${{ matrix.environment.type }} | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| environment: ${{ fromJson(needs.load-config.outputs.deployment_matrix) }} | |
| environment: ${{ matrix.environment.name }} | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| - id: setup-aws | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-iac-role | |
| role-duration-seconds: 4800 | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: add-kubeconfig | |
| name: Add k8s config file for existing cluster. | |
| run: |- | |
| aws eks update-kubeconfig --name biomage-$CLUSTER_ENV | |
| - id: deploy-metrics-server | |
| name: Deploy k8s metrics server | |
| run: |- | |
| kubectl apply -f https://github.com/kubernetes-sigs/metrics-server/releases/latest/download/components.yaml | |
| - id: install-helm | |
| name: Install Helm | |
| run: |- | |
| sudo snap install helm --classic | |
| - id: install-eksctl | |
| name: Install eksctl | |
| run: |- | |
| curl --silent --location "https://github.com/weaveworks/eksctl/releases/latest/download/eksctl_$(uname -s)_amd64.tar.gz" | tar xz -C /tmp | |
| sudo mv /tmp/eksctl /usr/local/bin | |
| - id: deploy-load-balancer-role | |
| name: Deploy permissions for AWS load balancer controller | |
| run: |- | |
| curl -o iam-policy.json https://raw.githubusercontent.com/kubernetes-sigs/aws-load-balancer-controller/v2.7.2/docs/install/iam_policy.json | |
| aws iam create-policy \ | |
| --policy-name AWSLoadBalancerControllerIAMPolicy-$CLUSTER_ENV \ | |
| --policy-document file://iam-policy.json || true | |
| eksctl create iamserviceaccount \ | |
| --cluster=biomage-$CLUSTER_ENV \ | |
| --namespace=kube-system \ | |
| --name=aws-load-balancer-controller \ | |
| --attach-policy-arn=arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:policy/AWSLoadBalancerControllerIAMPolicy-$CLUSTER_ENV \ | |
| --role-name eksctl-$CLUSTER_ENV-load-balancer-controller-role \ | |
| --override-existing-serviceaccounts \ | |
| --approve | |
| # we need to retry this due to an active issue with the AWS Load Balancer Controller | |
| # where there are intermittent failures that are only fixable by retrying | |
| # see issue at https://github.com/kubernetes-sigs/aws-load-balancer-controller/issues/2071 | |
| - id: install-lbc | |
| name: Deploy AWS Load Balancer Controller | |
| uses: nick-invision/retry@v2 | |
| with: | |
| timeout_seconds: 600 | |
| max_attempts: 20 | |
| retry_on: error | |
| on_retry_command: sleep $(shuf -i 5-15 -n 1) | |
| command: |- | |
| helm repo add eks https://aws.github.io/eks-charts | |
| wget https://raw.githubusercontent.com/aws/eks-charts/master/stable/aws-load-balancer-controller/crds/crds.yaml | |
| kubectl apply -f crds.yaml | |
| helm repo update | |
| helm upgrade aws-load-balancer-controller eks/aws-load-balancer-controller \ | |
| --namespace kube-system \ | |
| --set serviceAccount.create=false \ | |
| --set serviceAccount.name=aws-load-balancer-controller \ | |
| --set clusterName=biomage-$CLUSTER_ENV \ | |
| --install --wait | |
| - id: platform-public-facing | |
| name: Get config for whether platform should be public facing | |
| uses: mikefarah/yq@master | |
| with: | |
| cmd: yq '.[env(ENVIRONMENT_NAME)].publicFacing' 'infra/config/github-environments-config.yaml' | |
| env: | |
| ENVIRONMENT_NAME: ${{ matrix.environment.name }} | |
| - id: install-elb-503-subscription-endpoint | |
| name: Install ELB 503 subscription endpoint | |
| run: |- | |
| echo "value of publicFacing: $PUBLIC_FACING" | |
| # Check that publicFacing is set to true or false | |
| if [ "$PUBLIC_FACING" != "true" ] && [ "$PUBLIC_FACING" != "false" ]; then | |
| echo "value of publicFacing in infra/config/github-environments-config.yaml is not set to true or false" | |
| exit 1 | |
| fi | |
| # this is needed so SNS does not stop trying to subscribe to not-yet-deployed | |
| # API staging environments because their endpoints are not yet available. | |
| helm upgrade aws-elb-503-subscription-endpoint infra/aws-elb-503-subscription-endpoint \ | |
| --namespace default \ | |
| --set clusterEnv=$CLUSTER_ENV \ | |
| --set acmCertificate="$ACM_CERTIFICATE_ARN" \ | |
| --set-string publicFacing="$PUBLIC_FACING" \ | |
| --install --wait | |
| env: | |
| PUBLIC_FACING: ${{ steps.platform-public-facing.outputs.result }} | |
| ACM_CERTIFICATE_ARN: ${{ steps.setup-domain.outputs.acm-certificate-arn }} | |
| - id: deploy-env-loadbalancer | |
| name: Deploy AWS Application Load Balancer for environment | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},PublicFacing=${{ steps.platform-public-facing.outputs.result }}" | |
| name: "biomage-k8s-alb-${{ matrix.environment.type }}" | |
| template: 'infra/cf-loadbalancer.yaml' | |
| no-fail-on-empty-changeset: "1" | |
| # For HMS ACM_CERTIFICATE_ARN_STAGING exists, having different domains for staging and prod | |
| # so we need to check if it exists, otherwise set it to ACM_CERTIFICATE_ARN | |
| # same applies for PRIMARY_DOMAIN_NAME_STAGING | |
| - id: setup-domain | |
| name: Compile environment-specific domain name | |
| run: |- | |
| if [ "${{ matrix.environment.type }}" = "production" ]; then | |
| PRIMARY_DOMAIN_NAME="${{ secrets.PRIMARY_DOMAIN_NAME }}" | |
| DOMAIN_NAME="${{ secrets.DOMAIN_NAME }}" | |
| ACM_CERTIFICATE_ARN="${{ secrets.ACM_CERTIFICATE_ARN }}" | |
| fi | |
| if [ "${{ matrix.environment.type }}" = "staging" ]; then | |
| PRIMARY_DOMAIN_NAME="${{ secrets.PRIMARY_DOMAIN_NAME_STAGING }}" | |
| if [ -z "$PRIMARY_DOMAIN_NAME" ]; then | |
| PRIMARY_DOMAIN_NAME="${{ secrets.PRIMARY_DOMAIN_NAME }}" | |
| fi | |
| DOMAIN_NAME="${{ secrets.DOMAIN_NAME_STAGING }}" | |
| ACM_CERTIFICATE_ARN="${{ secrets.ACM_CERTIFICATE_ARN_STAGING }}" | |
| if [ -z "$ACM_CERTIFICATE_ARN" ]; then | |
| ACM_CERTIFICATE_ARN="${{ secrets.ACM_CERTIFICATE_ARN }}" | |
| fi | |
| fi | |
| echo "primary-domain-name=$PRIMARY_DOMAIN_NAME" >> $GITHUB_OUTPUT | |
| echo "domain-name=$DOMAIN_NAME" >> $GITHUB_OUTPUT | |
| echo "acm-certificate-arn=$ACM_CERTIFICATE_ARN" >> $GITHUB_OUTPUT | |
| # This step should be run only once per deployment. The associated Route 53 records to be created | |
| # e.g. DOMAIN_NAME and *.DOMAIN_NAME should be deleted before running this comment, otherwise this step fails. | |
| # Refer to the new deployment runbook to learn more. | |
| # - id: deploy-route53 | |
| # name: Deploy Route 53 DNS records to ELB | |
| # uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| # with: | |
| # parameter-overrides: "Environment=${{ matrix.environment.type }},DNSName=${{ steps.deploy-env-loadbalancer.outputs.DNSName }},HostedZoneId=${{ steps.deploy-env-loadbalancer.outputs.CanonicalHostedZoneID }},PrimaryDomainName=${{ steps.setup-domain.outputs.primary-domain-name }},DomainName=${{ steps.setup-domain.outputs.domain-name }}" | |
| # name: "biomage-alb-route53-${{ matrix.environment.type }}" | |
| # template: 'infra/cf-route53.yaml' | |
| # no-fail-on-empty-changeset: "1" | |
| - id: deploy-xray-daemon | |
| name: Deploy AWS X-Ray daemon | |
| run: |- | |
| helm upgrade "aws-xray-daemon" infra/aws-xray-daemon \ | |
| --namespace default \ | |
| --set iamRole=arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:role/xray-daemon-role-$CLUSTER_ENV \ | |
| --install --wait | |
| - id: install-ebs-csi-driver | |
| name: Install AWS EBS Container Storage Interface (CSI) drivers | |
| run: |- | |
| helm upgrade \ | |
| aws-ebs-csi-driver https://github.com/kubernetes-sigs/aws-ebs-csi-driver/releases/download/helm-chart-aws-ebs-csi-driver-2.17.2/aws-ebs-csi-driver-2.17.2.tgz \ | |
| --namespace kube-system \ | |
| --set enableVolumeScheduling=true \ | |
| --set enableVolumeResizing=true \ | |
| --set enableVolumeSnapshot=true \ | |
| --install --wait | |
| - id: deploy-read-only-group | |
| name: Deploy read-only permission definition for cluster | |
| run: |- | |
| helm upgrade "biomage-read-only-group" infra/biomage-read-only-group \ | |
| --install --wait | |
| - id: deploy-state-machine-role | |
| name: Deploy AWS Step Function (state machine) roles | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }}" | |
| name: "biomage-state-machine-role-${{ matrix.environment.type }}" | |
| template: 'infra/cf-state-machine-role.yaml' | |
| capabilities: 'CAPABILITY_IAM,CAPABILITY_NAMED_IAM' | |
| no-fail-on-empty-changeset: "1" | |
| - id: remove-identitymappings | |
| name: Remove all previous identity mappings for IAM users | |
| run: |- | |
| eksctl get iamidentitymapping --cluster=biomage-$CLUSTER_ENV --output=json | \ | |
| jq -r '.[] | select(.userarn != null) | .userarn' > /tmp/users_to_remove | |
| while IFS= read -r user | |
| do | |
| echo "Remove rights of $user" | |
| eksctl delete iamidentitymapping \ | |
| --cluster=biomage-$CLUSTER_ENV \ | |
| --arn $user \ | |
| --all | |
| done < "/tmp/users_to_remove" | |
| # see https://eksctl.io/usage/iam-identity-mappings/ | |
| # Grant login rights to ci-iac-role | |
| - id: add-ci-iac-oidc-cluster-role | |
| name: Allow the OIDC role to log in to our cluster. | |
| run: |- | |
| eksctl create iamidentitymapping \ | |
| --cluster=biomage-$CLUSTER_ENV \ | |
| --arn arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:role/ci-iac-role \ | |
| --group system:masters \ | |
| --username ci-iac-role | |
| # SSO access to cluster is only added if accessing AWS and cluster using SSO | |
| - id: allow-sso-roles-to-access-cluster | |
| env: | |
| SSO_ROLE: ${{ secrets.SSO_ROLE }} | |
| if: ${{ env.SSO_ROLE != '' }} | |
| name: Allow SSO role to log into the cluster | |
| run: |- | |
| eksctl create iamidentitymapping \ | |
| --cluster biomage-$CLUSTER_ENV \ | |
| --arn arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:role/${{ env.SSO_ROLE }} \ | |
| --username sso-cluster-admin \ | |
| --no-duplicate-arns \ | |
| --group system:masters | |
| - id: add-state-machine-cluster-role | |
| name: Grant rights to the state machine IAM role. | |
| run: |- | |
| eksctl create iamidentitymapping \ | |
| --cluster=biomage-$CLUSTER_ENV \ | |
| --arn arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:role/state-machine-role-$CLUSTER_ENV \ | |
| --group state-machine-runner-group \ | |
| --username state-machine-runner | |
| # NOTE: after updating this step, make sure you apply the updates in other relevant Github Actions workflows | |
| - id: update-identitymapping-admin | |
| name: Add cluster admin rights to everyone on the admin list. | |
| run: |- | |
| echo "Setting cluster admin rights for ${{matrix.environment.name}} in ${{matrix.environment.type}} environment" | |
| ADMINS="${{ join(matrix.environment.admins, ' ') }}" | |
| echo $ADMINS | |
| for user in $ADMINS; do | |
| echo "Adding cluster admin rights to $user" | |
| eksctl create iamidentitymapping \ | |
| --cluster=biomage-$CLUSTER_ENV \ | |
| --arn arn:aws:iam::${{ steps.setup-aws.outputs.aws-account-id }}:user/$user \ | |
| --group system:masters \ | |
| --username $user | |
| done | |
| ### | |
| ### INSTALL AND CONFIGURE FLUX V2 ### | |
| ### | |
| - id: using-self-signed-certificate | |
| name: Get config for whether deployment is using self-signed certificate | |
| uses: mikefarah/yq@master | |
| with: | |
| cmd: yq '.[env(ENVIRONMENT_NAME)].selfSignedCertificate' 'infra/config/github-environments-config.yaml' | |
| env: | |
| ENVIRONMENT_NAME: ${{ matrix.environment.name }} | |
| - id: fill-account-specific-metadata | |
| name: Fill in account specific metadata in ConfigMap | |
| run: |- | |
| yq -i ' | |
| .myAccount.domainName = strenv(DOMAIN_NAME) | | |
| .myAccount.region = strenv(AWS_REGION) | | |
| .myAccount.accountId = strenv(AWS_ACCOUNT_ID) | | |
| .myAccount.publicFacing = strenv(PUBLIC_FACING) | | |
| .myAccount.acmCertificate = strenv(ACM_CERTIFICATE_ARN) | | |
| .myAccount.selfSignedCertificate = strenv(SELF_SIGNED_CERTIFICATE) | |
| ' infra/config/account-config.yaml | |
| if [[ -n "${{ secrets.DATADOG_API_KEY }}" ]] | |
| then | |
| export DATADOG_API_KEY="${{ secrets.DATADOG_API_KEY }}" | |
| export DATADOG_APP_KEY="${{ secrets.DATADOG_APP_KEY }}" | |
| yq -i ' | |
| .myAccount.datadogAppKey = strenv(DATADOG_APP_KEY) | | |
| .myAccount.datadogApiKey = strenv(DATADOG_API_KEY) | |
| ' infra/config/account-config.yaml | |
| fi | |
| cat infra/config/account-config.yaml | |
| env: | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| AWS_ACCOUNT_ID: ${{ steps.setup-aws.outputs.aws-account-id }} | |
| DOMAIN_NAME: ${{ steps.setup-domain.outputs.domain-name }} | |
| ACM_CERTIFICATE_ARN: ${{ steps.setup-domain.outputs.acm-certificate-arn }} | |
| PUBLIC_FACING: ${{ steps.platform-public-facing.outputs.result }} | |
| SELF_SIGNED_CERTIFICATE: ${{ steps.using-self-signed-certificate.outputs.result }} | |
| - id: create-flux-namespace | |
| name: Attempt to create flux namespace | |
| continue-on-error: true | |
| run: |- | |
| kubectl create namespace flux-system | |
| - id: create-account-information-configmap | |
| name: Create a configmap containing AWS account specific details | |
| continue-on-error: false | |
| run: |- | |
| kubectl create configmap account-config --from-file=infra/config/account-config.yaml -n flux-system -o yaml --dry-run | kubectl apply -f - | |
| - id: install-flux-v2 | |
| name: Install flux CLI version 2.1.0 | |
| run: |- | |
| curl -s https://fluxcd.io/install.sh | sudo FLUX_VERSION=2.1.2 bash | |
| - id: delete-old-flux-github-deploy-key | |
| name: Attempt to delete previous github flux deploy key | |
| continue-on-error: true | |
| run: |- | |
| kubectl -n flux-system delete secret flux-system | |
| - id: install-flux | |
| name: Install Flux to EKS cluster | |
| run: |- | |
| # Refer to https://github.com/fluxcd/flux2/releases | |
| FLUX_VERSION=v2.1.2 | |
| FLUX_REPO=releases | |
| FLUX_PATH=deployments/$ENVIRONMENT_NAME-$CLUSTER_ENV | |
| REPO_FULL_PATH=$GITHUB_REPOSITORY_OWNER/$FLUX_REPO | |
| echo "flux-full-repo=$(echo $REPO_FULL_PATH)" >> $GITHUB_ENV | |
| echo "flux-path=$(echo $FLUX_PATH)" >> $GITHUB_ENV | |
| args=( | |
| --version $FLUX_VERSION | |
| --owner $GITHUB_REPOSITORY_OWNER | |
| --repository $FLUX_REPO | |
| --branch master | |
| --path $FLUX_PATH | |
| --timeout 40s | |
| –-interval 2m | |
| --components-extra=image-reflector-controller,image-automation-controller | |
| --namespace flux-system | |
| --cluster arn:aws:eks:$AWS_REGION:$AWS_ACCOUNT_ID:cluster/biomage-$CLUSTER_ENV | |
| --context arn:aws:eks:$AWS_REGION:$AWS_ACCOUNT_ID:cluster/biomage-$CLUSTER_ENV | |
| ) | |
| if [ "${{ matrix.environment.type }}" = "staging" ] | |
| then | |
| echo Flux will be deployed in staging with read and write permissions | |
| args+=(--read-write-key) | |
| elif [ "${{ matrix.environment.type }}" = "production" ] | |
| then | |
| echo Flux will be deployed in production with read-only permissions | |
| fi | |
| flux bootstrap github "${args[@]}" | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.API_TOKEN_GITHUB }} | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| AWS_ACCOUNT_ID: ${{ steps.setup-aws.outputs.aws-account-id }} | |
| ENVIRONMENT_NAME: ${{ matrix.environment.name }} | |
| - id: fill-in-sync-yaml | |
| name: Create the sync.yaml file that contains the Kustomization to sync the cluster | |
| run: |- | |
| export SPEC_PATH="./$CLUSTER_ENV" | |
| yq -i ' | |
| .spec.path = strenv(SPEC_PATH) | |
| ' infra/flux/sync.yaml | |
| cat infra/flux/sync.yaml | |
| - id: push-sync-yaml | |
| name: Push the sync.yaml file that was filled in during the previous step | |
| uses: dmnemec/copy_file_to_another_repo_action@v1.0.4 | |
| env: | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| with: | |
| source_file: infra/flux/sync.yaml | |
| destination_repo: ${{ env.flux-full-repo }} | |
| destination_folder: ${{ env.flux-path }} | |
| user_email: ci@biomage.net | |
| user_name: 'Biomage CI/CD' | |
| - id: fill-kustomization-template | |
| name: Fill in Kustomization template | |
| run: |- | |
| cat infra/flux/kustomization-template.yaml \ | |
| | sed "s/AWS_ACCOUNT_ID/$AWS_ACCOUNT_ID/g" \ | |
| | sed "s/CLUSTER_ENV/$CLUSTER_ENV/g" \ | |
| > infra/flux/kustomization.yaml | |
| cat infra/flux/kustomization.yaml | |
| env: | |
| AWS_ACCOUNT_ID: ${{ steps.setup-aws.outputs.aws-account-id }} | |
| - id: push-kustomization-yaml | |
| name: Push the kustomization.yaml file to apply our custom config | |
| uses: dmnemec/copy_file_to_another_repo_action@v1.0.4 | |
| env: | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| with: | |
| source_file: infra/flux/kustomization.yaml | |
| destination_repo: ${{ env.flux-full-repo }} | |
| destination_folder: ${{ env.flux-path }}/flux-system | |
| user_email: ci@biomage.net | |
| user_name: 'Biomage CI/CD' | |
| - id: install-kubernetes-reflector | |
| name: Install kubernetes reflector | |
| run: |- | |
| helm repo add emberstack https://emberstack.github.io/helm-charts | |
| helm repo update | |
| helm upgrade --install reflector emberstack/reflector --namespace flux-system | |
| - id: add-account-config-configmap-annotations | |
| name: Add annotations to account-config configmap | |
| run: |- | |
| kubectl annotate configmap account-config \ | |
| --overwrite \ | |
| --namespace flux-system \ | |
| reflector.v1.k8s.emberstack.com/reflection-allowed="true" \ | |
| reflector.v1.k8s.emberstack.com/reflection-allowed-namespaces="ui-.*,api-.*,pipeline-.*,worker-.*" \ | |
| reflector.v1.k8s.emberstack.com/reflection-auto-enabled="true" | |
| ### | |
| ### END OF INSTALL AND CONFIGURE FLUX V2 ### | |
| ### | |
| deploy-monitoring: | |
| name: Setup logging and monitoring | |
| runs-on: ubuntu-20.04 | |
| needs: [check-secrets, create-eks-cluster, configure-cluster, load-config] | |
| if: always() && (needs.check-secrets.result == 'success') && (github.event.inputs.workflow_actions == 'deploy monitoring') | |
| env: | |
| CLUSTER_ENV: ${{ matrix.environment.type }} | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| strategy: | |
| matrix: | |
| environment: ${{ fromJson(needs.load-config.outputs.deployment_matrix)}} | |
| environment: ${{ matrix.environment.name }} | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| - id: setup-aws | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-iac-role | |
| role-duration-seconds: 3600 | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: add-kubeconfig | |
| name: Add k8s config file for existing cluster. | |
| run: |- | |
| aws eks update-kubeconfig --name biomage-$CLUSTER_ENV | |
| - id: install-eksctl | |
| name: Install eksctl | |
| run: |- | |
| curl --silent --location "https://github.com/weaveworks/eksctl/releases/latest/download/eksctl_$(uname -s)_amd64.tar.gz" | tar xz -C /tmp | |
| sudo mv /tmp/eksctl /usr/local/bin | |
| - id: setup-cluster-cloudwatch-logging-policy | |
| name: Setup permissions required for cluster to log to Cloudwatch | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }}" | |
| name: "cluster-cloudwatch-logging-policy-${{ matrix.environment.type }}" | |
| template: 'infra/cluster-logging/cf-cluster-log-cloudwatch-policy.yaml' | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM" | |
| # Setting up log forwarding for pods hosted in EC2 nodes | |
| - id: create-fluent-bit-namespace | |
| name: Create namespace for node FluentBit deployment | |
| run: kubectl apply -f infra/cluster-logging/node-fluentbit-namespace.yaml | |
| - id: create-service-account-for-node-fluent-bit | |
| name: Create service account for node FluentBit | |
| env: | |
| LOGGING_POLICY_ARN: ${{ steps.setup-cluster-cloudwatch-logging-policy.outputs.PolicyARN }} | |
| run: |- | |
| eksctl create iamserviceaccount \ | |
| --name fluent-bit \ | |
| --namespace node-logging \ | |
| --cluster biomage-$CLUSTER_ENV \ | |
| --role-name irsa-fluent-bit-$CLUSTER_ENV \ | |
| --attach-policy-arn $LOGGING_POLICY_ARN \ | |
| --override-existing-serviceaccounts \ | |
| --approve | |
| - id: deploy-node-fluent-bit | |
| name: Deploy FluentBit for EC2 nodes | |
| env: | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| run: | | |
| # FluentBit configuration is determined in infra/cluster-logging/node-fluentbit-config.yaml, specifically under [INPUT] > Path | |
| # We do not want to log everything for costs/security concerns | |
| yq -i "(.. | select(type == \"!!str\")) |= sub(\"CI_CLUSTER_ENV\", \"$CLUSTER_ENV\")" infra/cluster-logging/node-fluentbit-config.yaml | |
| yq -i "(.. | select(type == \"!!str\")) |= sub(\"CI_AWS_REGION\", \"$AWS_REGION\")" infra/cluster-logging/node-fluentbit-config.yaml | |
| kubectl apply -f infra/cluster-logging/node-fluentbit-config.yaml | |
| # Setting up log forwarding for pods hosted on Fargate nodes | |
| - id: attach-pod-execution-role-name | |
| name: Attach logging policy to pod execution role | |
| env: | |
| LOGGING_POLICY_ARN: ${{ steps.setup-cluster-cloudwatch-logging-policy.outputs.PolicyARN }} | |
| run: |- | |
| # Pods launched in the same cluster has the same pod execution role, as pod execution role scope is cluster-wide. | |
| # See https://eksctl.io/usage/fargate-support/#creating-a-cluster-with-fargate-support | |
| # Getting fargate-profile of pipeline or worker in the same cluster gets the same pod execution role. | |
| POD_EXEC_ROLE_NAME=$(aws eks describe-fargate-profile \ | |
| --cluster-name biomage-$CLUSTER_ENV \ | |
| --fargate-profile-name pipeline-default | jq -r '.fargateProfile.podExecutionRoleArn' | awk -F"/" '{print (NF>1)? $NF : ""}' ) | |
| aws iam attach-role-policy --role-name $POD_EXEC_ROLE_NAME --policy-arn $LOGGING_POLICY_ARN | |
| - id: deploy-fargate-fluent-bit | |
| name: Deploy FluentBit config for Fargate pods | |
| env: | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| run: |- | |
| # FluentBit configuration is determined in infra/cluster-logging/fargate-fluentbit-config.yaml | |
| yq -i "(.. | select(type == \"!!str\")) |= sub(\"CI_CLUSTER_ENV\", \"$CLUSTER_ENV\")" infra/cluster-logging/fargate-fluentbit-config.yaml | |
| yq -i "(.. | select(type == \"!!str\")) |= sub(\"CI_AWS_REGION\", \"$AWS_REGION\")" infra/cluster-logging/fargate-fluentbit-config.yaml | |
| kubectl apply -f infra/cluster-logging/fargate-fluentbit-config.yaml | |
| # Setting up Datadog to watch pod metrics for pods hosted on EC2 and Fargate nodes | |
| - id: setup-datadog-cluster-agent | |
| name: Setup Datadog cluster agent | |
| run: |- | |
| if [[ -n "${{ secrets.DATADOG_API_KEY }}" ]]; | |
| then | |
| helm repo add datadog https://helm.datadoghq.com | |
| helm repo update | |
| helm upgrade datadog-agent datadog/datadog \ | |
| -f infra/datadog/cluster-agent-values.yaml \ | |
| --set datadog.apiKey=$DATADOG_API_KEY \ | |
| --set datadog.clusterName=biomage-$CLUSTER_ENV \ | |
| --install | |
| else | |
| echo "Datadog api key missing, skipping datadog setup" | |
| fi | |
| - id: setup-datadog-sidecar-permissions | |
| name: Setup Datadog sidecar permissions | |
| run: |- | |
| if [[ -n "${{ secrets.DATADOG_API_KEY }}" ]]; | |
| then | |
| kubectl apply -f infra/datadog/datadog-sidecar-rbac.yaml | |
| fi | |
| - id: login-ecr | |
| name: Login to Amazon ECR | |
| uses: aws-actions/amazon-ecr-login@v1 | |
| - id: create-falcon-ecr-registries | |
| name: Create an ECR repositories for the Falcon Sensor (if needed) | |
| # This will fail if the registry already exists, which is fine. If there is some other | |
| # error, the `push` step will fail instead. | |
| continue-on-error: true | |
| run: |- | |
| if [[ -n "${{ secrets.FALCON_CID }}" ]]; | |
| then | |
| aws ecr create-repository --repository-name falcon-container/falcon-sensor --image-tag-mutability MUTABLE | |
| aws ecr create-repository --repository-name falcon-sensor/falcon-sensor --image-tag-mutability MUTABLE | |
| else | |
| echo "CrowdStrike CID missing, not creating falcon sensor repos" | |
| fi | |
| - id: create-falcon-namespace | |
| name: Attempt to create falcon namespace | |
| continue-on-error: true | |
| run: |- | |
| if [[ -n "${{ secrets.FALCON_CID }}" ]]; | |
| then | |
| kubectl create namespace falcon-system | |
| else | |
| echo "CrowdStrike CID missing, not creating falcon namespace" | |
| fi | |
| - id: setup-falcon-sensor | |
| name: Setup Falcon Sensor | |
| run: |- | |
| if [[ -n "${{ secrets.FALCON_CID }}" ]]; | |
| then | |
| # configure the API client ID and password | |
| export FALCON_CLIENT_ID="${{ secrets.FALCON_CLIENT_ID }}" | |
| export FALCON_CLIENT_SECRET="${{ secrets.FALCON_CLIENT_SECRET }}" | |
| # confgure CID | |
| export FALCON_CID="${{ secrets.FALCON_CID }}" | |
| # URL of falcon-container-sensor-pull.sh | |
| PULL_SCRIPT_URL="https://raw.githubusercontent.com/CrowdStrike/falcon-scripts/main/bash/containers/falcon-container-sensor-pull/falcon-container-sensor-pull.sh" | |
| # Download the pull script from GitHub and save it to the current directory | |
| # --silent - Supresses standard/error output | |
| # --remote-name - Keeps the original filename when saving | |
| # --location - Follow redirects | |
| curl --silent --remote-name --location "$PULL_SCRIPT_URL" | |
| # make script executable | |
| chmod +x falcon-container-sensor-pull.sh | |
| # download latest version of the Falcon Container (for fargate) and copy it to ECS | |
| ./falcon-container-sensor-pull.sh \ | |
| --client-id ${FALCON_CLIENT_ID} \ | |
| --client-secret ${FALCON_CLIENT_SECRET} \ | |
| --type falcon-container \ | |
| --copy "${ECR_REGISTRY}/falcon-container" | |
| # download latest version of the Falcon Node Sensor (for EC2) and copy it to ECS | |
| ./falcon-container-sensor-pull.sh \ | |
| --client-id ${FALCON_CLIENT_ID} \ | |
| --client-secret ${FALCON_CLIENT_SECRET} \ | |
| --type falcon-sensor \ | |
| --copy "${ECR_REGISTRY}/falcon-sensor" | |
| # functions to get image names for helm | |
| get_image_path() { | |
| local container_type=$1 | |
| ./falcon-container-sensor-pull.sh \ | |
| --client-id ${FALCON_CLIENT_ID} \ | |
| --client-secret ${FALCON_CLIENT_SECRET} \ | |
| --type ${container_type} \ | |
| --get-image-path | |
| } | |
| get_image_name() { | |
| local container_type=$1 | |
| local image_path=$(get_image_path "$container_type") | |
| # Extract the image name using awk | |
| local image_name=$(echo "$image_path" | awk -F':' '{print $2}') | |
| echo "$image_name" | |
| } | |
| FALCON_CONTAINER_IMAGE_TAG=$(get_image_name "falcon-container") | |
| FALCON_SENSOR_IMAGE_TAG=$(get_image_name "falcon-sensor") | |
| # install container sensor (for fargate) into a customized namespace | |
| helm repo add crowdstrike https://crowdstrike.github.io/falcon-helm | |
| helm repo update | |
| helm upgrade --install falcon-container-helm crowdstrike/falcon-sensor \ | |
| -n falcon-container-system --create-namespace \ | |
| --set node.enabled=false \ | |
| --set container.enabled=true \ | |
| --set falcon.cid="$FALCON_CID" \ | |
| --set container.image.repository="${ECR_REGISTRY}/falcon-container/falcon-sensor" \ | |
| --set container.image.tag="$FALCON_CONTAINER_IMAGE_TAG" | |
| # install node sensor (for ec2) with different release name (falcon-sensor-helm) | |
| helm upgrade --install falcon-sensor-helm crowdstrike/falcon-sensor \ | |
| -n falcon-sensor-system --create-namespace \ | |
| --set falcon.cid="$FALCON_CID" \ | |
| --set node.image.repository="${ECR_REGISTRY}/falcon-sensor/falcon-sensor" \ | |
| --set node.image.tag="$FALCON_SENSOR_IMAGE_TAG" | |
| # install KPA (kubernetes protection agent) | |
| helm upgrade --install kpagent crowdstrike/cs-k8s-protection-agent \ | |
| -n falcon-kubernetes-protection --create-namespace \ | |
| --set image.repository="registry.crowdstrike.com/kubernetes_protection/kpagent" \ | |
| --set image.tag="0.2117.0" \ | |
| --set crowdstrikeConfig.clientID="$FALCON_CLIENT_ID" \ | |
| --set crowdstrikeConfig.clientSecret="$FALCON_CLIENT_SECRET" \ | |
| --set crowdstrikeConfig.clusterName="arn:aws:eks:${AWS_REGION}:${AWS_ACCOUNT_ID}:cluster/biomage-${CLUSTER_ENV}" \ | |
| --set crowdstrikeConfig.env="${{ secrets.FALCON_REGION }}" \ | |
| --set crowdstrikeConfig.cid="${{ secrets.FALCON_CCID }}" \ | |
| --set crowdstrikeConfig.dockerAPIToken="${{ secrets.FALCON_DOCKER_API_TOKEN }}" | |
| else | |
| echo "CrowdStrike CID missing, skipping falcon sensor setup" | |
| fi | |
| env: | |
| ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }} | |
| AWS_REGION: ${{ secrets.AWS_REGION }} | |
| AWS_ACCOUNT_ID: ${{ secrets.AWS_ACCOUNT_ID }} | |
| report-if-failed: | |
| name: Report if workflow failed | |
| runs-on: ubuntu-20.04 | |
| needs: [load-config, check-secrets, create-eks-cluster, configure-cluster, deploy-monitoring] | |
| if: failure() && github.ref == 'refs/heads/master' | |
| steps: | |
| - id: send-to-slack | |
| name: Send failure notification to Slack on failure | |
| env: | |
| SLACK_BOT_TOKEN: ${{ secrets.WORKFLOW_STATUS_BOT_TOKEN }} | |
| uses: voxmedia/github-action-slack-notify-build@v1 | |
| with: | |
| channel: workflow-failures | |
| status: FAILED | |
| color: danger |