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Robert Chu
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Updates terraform and deployment.
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‎.github/workflows/publish-docker-images.yml‎

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‎.github/workflows/publish.yml‎

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name: Publish docker images
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on:
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push:
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branches:
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- main
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release:
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types: [published]
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jobs:
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publish-pypi:
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name: Publish script-runner to pypi
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runs-on: ubuntu-latest
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steps:
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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publish-docker:
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name: Publish script-runner to dockerhub
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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- name: Prepare
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id: prep
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run: |
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PYTHON_IMAGE_TAG=alpine
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DOCKER_IMAGE=labflow/script-runner
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VERSION=latest
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if [[ $GITHUB_REF == refs/tags/* ]]; then
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VERSION=${GITHUB_REF#refs/tags/}
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elif [[ $GITHUB_REF == refs/heads/* ]]; then
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VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
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elif [[ $GITHUB_REF == refs/pull/* ]]; then
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VERSION=pr-${{ github.event.number }}
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fi
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TAGS="${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-latest,${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-${VERSION}"
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if [ "${{ github.event_name }}" = "push" ]; then
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TAGS="$TAGS,${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-sha-${GITHUB_SHA::8}"
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fi
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echo ::set-output name=version::${VERSION}
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echo ::set-output name=tags::${TAGS}
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echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
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echo ::set-output name=hashtag::"sha-${GITHUB_SHA::8}"
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echo ::set-output name=pyversion::"${PYTHON_IMAGE_TAG}"
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v1
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- name: Cache Docker layers
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uses: actions/cache@v2.1.4
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with:
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path: /tmp/.buildx-cache
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key: ${{ runner.os }}-buildx-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-buildx-
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- name: Login to DockerHub
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if: github.event_name != 'pull_request'
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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- name: Push to Docker Hub
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uses: docker/build-push-action@v2
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with:
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context: ./docker
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file: ./Dockerfile
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builder: ${{ steps.buildx.outputs.name }}
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.prep.outputs.tags }}
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cache-from: type=local,src=/tmp/.buildx-cache
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cache-to: type=local,dest=/tmp/.buildx-cache
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labels: |
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org.opencontainers.image.source=${{ github.event.repository.clone_url }}
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org.opencontainers.image.created=${{ steps.prep.outputs.created }}
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org.opencontainers.image.revision=${{ github.sha }}
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build-args: |
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SCRIPT_RUNNER_VERSION=${{ steps.prep.outputs.version }}
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PYTHON_IMAGE_TAG=${{ steps.prep.outputs.pyversion }}
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deploy-aws-example:
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name: Deploy swabseq-analysis-example to AWS
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runs-on: ubuntu-latest
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steps:
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- name: Configure AWS credentials
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uses: aws-actions/configure-aws-credentials@v1
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with:
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aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
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aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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aws-region: us-west-1
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- name: Setup Terraform tfvars
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uses: nowactions/envsubst@v1
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working-directory: ./examples/aws
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with:
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input: ./example.tfvars
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output: ./terraform.tfvars
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env:
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DNS_SUBDOMAIN: ${{secrets.DNS_SUBDOMAIN}}
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DNS_ZONE_ID: ${{secrets.DNS_ZONE_ID}}
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- name: Setup Terraform
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working-directory: ./examples/aws
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uses: hashicorp/setup-terraform@v1
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# - name: Terraform Format
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# id: fmt
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# run: terraform fmt -check
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- name: Terraform Init
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id: init
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working-directory: ./examples/aws
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run: terraform init
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- name: Terraform Plan
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id: plan
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working-directory: ./examples/aws
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if: github.event_name == 'pull_request'
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run: terraform plan -no-color
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continue-on-error: true
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- uses: actions/github-script@v3
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working-directory: ./examples/aws
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if: github.event_name == 'pull_request'
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env:
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PLAN: "terraform\n${{ steps.plan.outputs.stdout }}"
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |
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const output = `#### Terraform Format and Style 🖌\`${{ steps.fmt.outcome }}\`
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#### Terraform Initialization ⚙️\`${{ steps.init.outcome }}\`
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#### Terraform Plan 📖\`${{ steps.plan.outcome }}\`
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<details><summary>Show Plan</summary>
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\`\`\`${process.env.PLAN}\`\`\`
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</details>
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*Pusher: @${{ github.actor }}, Action: \`${{ github.event_name }}\`*`;
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await github.issues.createComment({
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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body: output
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})
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- name: Terraform Plan Status
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if: steps.plan.outcome == 'failure'
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run: exit 1
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- name: Terraform Apply
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working-directory: ./examples/aws
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if: (github.event_name == 'release') || (github.event_name == 'push' && github.ref == 'refs/heads/main')
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run: terraform apply -auto-approve
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deploy-azure-example:
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name: Deploy swabseq-analysis-example to Azure
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runs-on: ubuntu-latest
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steps:
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- name: Configure Azure credentials
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uses: azure/login@v1
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with:
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creds: ${{ secrets.AZURE_CREDENTIALS }}
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- name: Setup Terraform tfvars
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uses: nowactions/envsubst@v1
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working-directory: ./examples/azure
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with:
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input: ./example.tfvars
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output: ./terraform.tfvars
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env:
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DNS_SUBDOMAIN: ${{secrets.DNS_SUBDOMAIN}}
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DNS_ZONE_NAME: ${{secrets.DNS_ZONE_NAME}}
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- name: Setup Terraform
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working-directory: ./examples/azure
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uses: hashicorp/setup-terraform@v1
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# - name: Terraform Format
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# id: fmt
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# run: terraform fmt -check
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- name: Terraform Init
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id: init
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working-directory: ./examples/azure
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run: terraform init
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- name: Terraform Plan
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id: plan
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working-directory: ./examples/azure
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if: github.event_name == 'pull_request'
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run: terraform plan -no-color
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continue-on-error: true
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- uses: actions/github-script@v3
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working-directory: ./examples/azure
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if: github.event_name == 'pull_request'
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env:
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PLAN: "terraform\n${{ steps.plan.outputs.stdout }}"
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |
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const output = `#### Terraform Format and Style 🖌\`${{ steps.fmt.outcome }}\`
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#### Terraform Initialization ⚙️\`${{ steps.init.outcome }}\`
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#### Terraform Plan 📖\`${{ steps.plan.outcome }}\`
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<details><summary>Show Plan</summary>
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\`\`\`${process.env.PLAN}\`\`\`
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</details>
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*Pusher: @${{ github.actor }}, Action: \`${{ github.event_name }}\`*`;
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await github.issues.createComment({
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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body: output
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})
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- name: Terraform Plan Status
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if: steps.plan.outcome == 'failure'
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run: exit 1
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- name: Terraform Apply
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working-directory: ./examples/azure
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if: (github.event_name == 'release') || (github.event_name == 'push' && github.ref == 'refs/heads/main')
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run: terraform apply -auto-approve
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‎terraform/aws/example.tfvars‎

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dns_name = "${DNS_NAME}"
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dns_zone_id = "${DNS_ZONE_ID}"
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dns_subdomain = "${DNS_SUBDOMAIN}"
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dns_zone_id = "${DNS_ZONE_ID}"
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auth0_domain = "${AUTH0_DOMAIN}"
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auth0_audience = "${AUTH0_AUDIENCE}"
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auth0_client_id = "${AUTH0_CLIENT_ID}"
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image_tag = "${IMAGE_TAG}"
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image_tag = "sha-d59d449a"

‎terraform/aws/main.tf‎

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stack_name = var.stack_name
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auth0_domain = var.auth0_domain
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auth0_audience = var.auth0_audience
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auth0_client_id = var.auth0_client_id
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auth_provider = "none"
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ecs_task_execution_role_arn = aws_iam_role.labflow_role.arn
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ecs_task_execution_role_name = aws_iam_role.labflow_role.name
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image = "labflow/swabseq-analysis-server-example"
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image_tag = var.image_tag
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dns_name = var.dns_name
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dns_zone_id = var.dns_zone_id
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dns_subdomain = var.dns_subdomain
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dns_zone_id = var.dns_zone_id
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}

‎terraform/aws/variables.tf‎

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default = "swabseq-analysis-example"
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}
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variable "dns_name" {
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variable "dns_subdomain" {
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type = string
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}
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variable "dns_zone_id" {
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type = string
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}
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variable "auth0_domain" {
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type = string
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}
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variable "auth0_audience" {
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type = string
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}
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variable "auth0_client_id" {
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type = string
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}
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variable "image_tag" {
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type = string
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default = "latest"

‎terraform/azure/example.tfvars‎

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dns_subdomain = "${DNS_SUBDOMAIN}"
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dns_domain = "${DNS_DOMAIN}"
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dns_zone_name = "${DNS_ZONE_NAME}"
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auth0_domain = "${AUTH0_DOMAIN}"
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auth0_audience = "${AUTH0_AUDIENCE}"
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auth0_client_id = "${AUTH0_CLIENT_ID}"
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image_tag = "${IMAGE_TAG}"
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image_tag = "sha-d59d449a"

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