add spatial #1442
Workflow file for this run
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| name: Deploy changed CloudFormation templates | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| environment_name: | |
| type: string | |
| description: Select the environment name to run the actions on | |
| required: true | |
| default: all | |
| environment_type: | |
| type: choice | |
| description: Select environment type | |
| options: | |
| - staging | |
| - production | |
| - staging and production | |
| default: staging | |
| push: | |
| branches: | |
| - master | |
| paths: | |
| - 'cf/**.yaml' | |
| - 'cf/**.yml' | |
| pull_request: | |
| branches: | |
| - master | |
| paths: | |
| - 'cf/**.yaml' | |
| - 'cf/**.yml' | |
| permissions: | |
| id-token: write | |
| contents: read | |
| 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 secrets | |
| needs: load-config | |
| runs-on: ubuntu-20.04 | |
| if: github.ref == 'refs/heads/master' || github.event_name == 'workflow_dispatch' | |
| strategy: | |
| matrix: | |
| environment_name: ${{fromJson(needs.load-config.outputs.environment_names)}} | |
| environment: ${{ matrix.environment_name }} | |
| steps: | |
| - id: check-secrets | |
| name: Check if necessary secrets are installed. | |
| run: |- | |
| if [ -z "${{ secrets.AWS_ACCOUNT_ID }}" ] | |
| then | |
| echo "This workflow requires AWS_ACCOUNT_ID defined in this repository secrets to complete." | |
| echo "The secrets can be set/rotated by running 'rotate-ci' from 'cellenics-utils'." | |
| ERROR=true | |
| fi | |
| if [ ! -z "$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 | |
| get-modified-templates: | |
| name: Fetch paths to modified CloudFormation templates | |
| runs-on: ubuntu-20.04 | |
| needs: load-config | |
| outputs: | |
| files: ${{ steps.exclude-services.outputs.files }} | |
| num-files: ${{ steps.exclude-services.outputs.num-files }} | |
| steps: | |
| - id: checkout | |
| name: Check out current branch source code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - id: validate-workflow-dispatch | |
| if: github.event_name == 'workflow_dispatch' && github.ref == 'refs/heads/master' | |
| name: Validate workflow dispatch | |
| run: |- | |
| echo Deploying the master branch via workflow_dispatch is not supported. | |
| echo To deploy master branch, raise a PR with changes to the CF files | |
| echo that needs to be deployed and merge the PR. | |
| exit 1 | |
| - id: get-changed-files-on-pr-merge | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| name: Get changed files on PR merge to master | |
| uses: lots0logs/[email protected] | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - id: get-changed-files-on-branch | |
| if: github.ref != 'refs/heads/master' | |
| name: Get changed files on branch | |
| run: | | |
| echo "[]" > empty.json | |
| # Get name of changed files | |
| CHANGED_FILES=$(git diff --name-only --diff-filter=ACMRT remotes/origin/master ${{ github.sha }}) | |
| # If there are no changed files, create an empty array | |
| # else concatenate into an array | |
| if [ -z "$CHANGED_FILES" ]; then | |
| echo "[]" > ${HOME}/files.json | |
| else | |
| echo "$CHANGED_FILES" | xargs -I 'value' jq --arg filename "value" '. |= . + [$filename]' empty.json | jq -s 'add' > ${HOME}/files.json | |
| fi | |
| echo "All changed files" | |
| cat ${HOME}/files.json | |
| - id: check-number-of-cf-files | |
| name: Check CloudFormation templates | |
| run: |- | |
| # Select those that are CF templates (path starts with `cf/`) | |
| jq '[.[] | select(match("^cf/"))]' ${HOME}/files.json > ${HOME}/changed_cf_files.json | |
| - id: exclude-services | |
| name: Exclude services | |
| run: |- | |
| echo "Excluding services: $EXCLUDED_SERVICES" | |
| # Select files that are not in excluded_services | |
| jq --argjson excluded_services "$EXCLUDED_SERVICES" 'map(select(. as $in | $excluded_services | any(. == $in) | not))' ${HOME}/changed_cf_files.json > ${HOME}/filtered_cf_files.json | |
| # Set as output the minified JSON. | |
| echo "Filtered CF files" | |
| cat ${HOME}/filtered_cf_files.json | |
| echo "num-files=$(jq '. | length' ${HOME}/filtered_cf_files.json)" >> $GITHUB_OUTPUT | |
| echo "files=$(jq -c . < ${HOME}/filtered_cf_files.json)" >> $GITHUB_OUTPUT | |
| env: | |
| EXCLUDED_SERVICES: ${{ needs.load-config.outputs.excluded_services }} | |
| lint-templates: | |
| name: Lint template files | |
| runs-on: ubuntu-20.04 | |
| needs: get-modified-templates | |
| if: needs.get-modified-templates.outputs.num-files > 0 | |
| strategy: | |
| matrix: | |
| template: ${{fromJson(needs.get-modified-templates.outputs.files)}} | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| - id: lint | |
| name: Lint template | |
| uses: scottbrenner/[email protected] | |
| with: | |
| args: ${{ matrix.template }} | |
| deploy-templates: | |
| name: Deploy changed CloudFormation template | |
| runs-on: ubuntu-20.04 | |
| needs: [load-config, check-secrets, get-modified-templates, lint-templates] | |
| if: github.ref == 'refs/heads/master' || github.event_name == 'workflow_dispatch' | |
| outputs: | |
| deploy-rds: ${{ steps.set-name.outputs.deploy-rds }} | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| environment: ${{fromJson(needs.load-config.outputs.deployment_matrix)}} | |
| template: ${{fromJson(needs.get-modified-templates.outputs.files)}} | |
| environment: ${{ matrix.environment.name }} | |
| env: | |
| CLUSTER_ENV: ${{ matrix.environment.type }} | |
| TEMPLATES_WITH_EXTRA_PARAMS: ("cf/sns.yaml" "cf/ses.yaml" "cf/post-register-lambda.yaml", "cf/canaries.yaml", "cf/cognito-case-insensitive.yaml", "cf/batch-job-definition.yaml") | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| # - name: Get parameters | |
| # id: get-params | |
| # run: echo "::set-output name=params::$(./get-params-for-template.sh ${{ matrix.template }})" | |
| # shell: bash | |
| - id: set-up-creds | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-iac-role | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: set-name | |
| name: Set name of the CloudFormation stack | |
| run: |- | |
| echo "Ref is $GITHUB_REF" | |
| BASE_NAME=$(basename $FILE_NAME | sed "s/\..*//") | |
| STACK_NAME=biomage-$BASE_NAME-$CLUSTER_ENV | |
| echo "stack-name=$STACK_NAME" >> $GITHUB_OUTPUT | |
| if [ "$BASE_NAME" == 'rds' ]; then | |
| echo "deploy-rds=true" >> $GITHUB_OUTPUT | |
| fi | |
| env: | |
| FILE_NAME: ${{ matrix.template }} | |
| - 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 }} | |
| ## TODO - GET THE "parameter-overrides" dynamically, to use one deploy action for all templates | |
| - id: deploy-template | |
| name: Deploy CloudFormation template | |
| if: ${{ !contains(matrix.template, 'irsa-') && !contains(env.TEMPLATES_WITH_EXTRA_PARAMS, matrix.template) }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-canaries-template | |
| name: Deploy CloudFormation PostRegisterLambda template | |
| if: ${{ matrix.template == 'cf/canaries.yaml' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},SupportEmail=${{ needs.load-config.outputs.support_email }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-batch-job-definition-template | |
| name: Deploy CloudFormation PostRegisterLambda template | |
| if: ${{ matrix.template == 'cf/batch-job-definition.yaml' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: >- | |
| Environment=${{ matrix.environment.type }}, | |
| ImageAccountId=${{ needs.load-config.outputs.image_account_id }}, | |
| ImageAccountRegion=${{ needs.load-config.outputs.image_account_region }} | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-cognito-case-insensitive | |
| name: Deploy CloudFormation cognito-case-insensitive template | |
| if: ${{ matrix.template == 'cf/cognito-case-insensitive.yaml' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: >- | |
| Environment=${{ matrix.environment.type }}, | |
| ReplyEmail=${{ needs.load-config.outputs.reply_email }}, | |
| UserPoolDomainName=${{ needs.load-config.outputs.user_pool_domain_name }} | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-post-register-lambda-template | |
| name: Deploy CloudFormation PostRegisterLambda template | |
| if: ${{ matrix.template == 'cf/post-register-lambda.yaml' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},UsingSelfSignedCert=${{ steps.using-self-signed-certificate.outputs.result }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-sns-template | |
| name: Deploy CloudFormation SNS template | |
| if: ${{ matrix.template == 'cf/sns.yaml' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},UsingSelfSignedCert=${{ steps.using-self-signed-certificate.outputs.result }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM,CAPABILITY_AUTO_EXPAND" | |
| - id: deploy-ses-template | |
| name: Deploy CloudFormation SES template | |
| if: ${{ matrix.template == 'cf/ses.yaml' && needs.load-config.outputs.should_deploy_ses == 'true' }} | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},DomainName=${{ secrets.DOMAIN_NAME }},PrimaryDomainName=${{ secrets.PRIMARY_DOMAIN_NAME }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| # The following steps are only necessary for IAM Service Account roles. | |
| - id: get-oidc | |
| if: ${{ contains(matrix.template, 'irsa-') }} | |
| name: Get OIDC provider information for IRSA role | |
| run: |- | |
| OIDC_PROVIDER=$(aws eks describe-cluster --name "biomage-$CLUSTER_ENV" --query "cluster.identity.oidc.issuer" --output text | sed -e "s/^https:\/\///") | |
| echo "oidc-provider=$OIDC_PROVIDER" >> $GITHUB_OUTPUT | |
| - id: deploy-irsa-template | |
| if: ${{ contains(matrix.template, 'irsa-') }} | |
| name: Deploy IRSA CloudFormation template | |
| uses: aws-actions/aws-cloudformation-github-deploy@v1 | |
| with: | |
| parameter-overrides: "Environment=${{ matrix.environment.type }},OIDCProvider=${{ steps.get-oidc.outputs.oidc-provider }}" | |
| name: ${{ steps.set-name.outputs.stack-name }} | |
| template: ${{ matrix.template }} | |
| no-fail-on-empty-changeset: "1" | |
| capabilities: "CAPABILITY_IAM,CAPABILITY_NAMED_IAM" | |
| setup-rds-roles: | |
| name: Setup RDS roles for default resources | |
| runs-on: ubuntu-20.04 | |
| needs: [check-secrets, deploy-templates, load-config] | |
| if: ${{ needs.deploy-templates.outputs.deploy-rds == 'true' }} | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| environment: ${{ fromJson(needs.load-config.outputs.deployment_matrix) }} | |
| environment: ${{ matrix.environment.name }} | |
| env: | |
| CLUSTER_ENV: ${{ matrix.environment.type }} | |
| steps: | |
| - id: set-up-creds | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-iac-role | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| # This step is needed to change the environment name (e.g. staging) into its uppercase form. | |
| # This is required because the action that is used in get-rds-secrets store the secret in environment variables, | |
| # with uppercase letters (see action ref). Therefore, we need the uppercased form of the environment | |
| # Which is output in .outputs.uppercase of this step. | |
| - id: setup-rds-env | |
| name: Uppercase environment name | |
| uses: ASzc/change-string-case-action@v2 | |
| with: | |
| string: ${{ matrix.environment.type }} | |
| - id: get-rds-secrets | |
| name: Export RDS secrets into environment variables | |
| uses: abhilash1in/[email protected] | |
| with: | |
| secrets: aurora-${{ matrix.environment.type }} | |
| parse-json: true | |
| - id: check-rds-secrets | |
| name: Check RDS secrets are fetched | |
| run: |- | |
| # These checks if the RDS username and passwords are set | |
| if [ -z $AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_USERNAME ]; then | |
| echo "RDS username not provided" | |
| exit 1 | |
| fi | |
| if [ -z $AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_PASSWORD ]; then | |
| echo "RDS password not provided" | |
| exit 1 | |
| fi | |
| - id: setup-rds-roles | |
| name: Setup RDS roles for default RDS instances | |
| run: |- | |
| INSTANCE_ID=$(aws ec2 describe-instances \ | |
| --filters "Name=tag:Name,Values=rds-${CLUSTER_ENV}-ssm-agent" \ | |
| --output text \ | |
| --query 'Reservations[*].Instances[*].InstanceId') | |
| if [ -z $INSTANCE_ID ]; then | |
| echo "Can not connect to RDS agent: No instances found for $CLUSTER_ENV" | |
| exit 1 | |
| fi | |
| CLUSTER_NAME=aurora-cluster-${CLUSTER_ENV}-default | |
| RDSHOST=$(aws rds describe-db-cluster-endpoints \ | |
| --region $REGION \ | |
| --db-cluster-identifier $CLUSTER_NAME \ | |
| --filter Name=db-cluster-endpoint-type,Values='writer' \ | |
| --query 'DBClusterEndpoints[0].Endpoint' \ | |
| --output text) | |
| if [ -z $RDSHOST ]; then | |
| echo "Failed getting RDS host with name $CLUSTER_NAME" | |
| exit 1 | |
| fi | |
| ENSURE_PSQL_INSTALLED_COMMAND="sudo yum -y install postgresql" | |
| aws ssm send-command --instance-ids "$INSTANCE_ID" \ | |
| --document-name AWS-RunShellScript \ | |
| --parameters "commands='$ENSURE_PSQL_INSTALLED_COMMAND'" | |
| SETUP_ROLES_CMD=" | |
| PGPASSWORD=\'${AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_PASSWORD}\' psql \ | |
| --host=${RDSHOST} \ | |
| --port=5432 \ | |
| --username=${AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_USERNAME} \ | |
| --dbname=aurora_db <<EOF | |
| CREATE ROLE api_role WITH LOGIN; | |
| CREATE ROLE dev_role WITH LOGIN; | |
| GRANT USAGE ON SCHEMA public TO api_role; | |
| GRANT USAGE, SELECT ON ALL SEQUENCES IN SCHEMA public to api_role; | |
| GRANT dev_role TO ${AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_USERNAME}; | |
| ALTER DEFAULT PRIVILEGES FOR USER dev_role IN SCHEMA public GRANT SELECT, INSERT, UPDATE, DELETE ON TABLES TO api_role; | |
| ALTER DEFAULT PRIVILEGES FOR USER dev_role IN SCHEMA public GRANT USAGE, SELECT ON SEQUENCES TO api_role; | |
| REVOKE dev_role FROM ${AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_USERNAME}; | |
| GRANT rds_iam TO api_role; | |
| GRANT rds_iam, ${AURORA_${{ steps.setup-rds-env.outputs.uppercase }}_USERNAME} TO dev_role; | |
| EOF" | |
| aws ssm send-command --instance-ids "$INSTANCE_ID" \ | |
| --document-name AWS-RunShellScript \ | |
| --parameters "commands='$SETUP_ROLES_CMD'" | |
| env: | |
| REGION: ${{ secrets.AWS_REGION }} | |
| report-if-failed: | |
| name: Report if workflow failed | |
| runs-on: ubuntu-20.04 | |
| needs: [check-secrets, lint-templates, deploy-templates, setup-rds-roles] | |
| 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 |