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xiaoyao00nhoktenz
xiaoyao00
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nhoktenz
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Qa (#6)
* create dev branch and modify deploy to automatically deploy * Trigger deployment * update docker build push actions * update aws_account_id variable * add AWS_ACCOUNT_ID in env * add inputs.tier * update deploy script * update the role name * update role as github-actions-cicd * update cache mode and move env block * add timeout, change to inline cache, modify cicd role * update cache image name * separate data import workflow * update videos url (#5) * update videos url * update url link for video --------- Co-authored-by: Thuong Nguyen <6723699+nhoktenz@users.noreply.github.com>
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‎.github/workflows/data-import.yml‎

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name: Data Import to AWS ECS
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on:
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workflow_dispatch:
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inputs:
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tier:
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description: 'Deployment tier'
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required: true
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type: choice
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options:
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- dev
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- qa
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- stage
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- prod
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jobs:
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data-import:
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timeout-minutes: 60
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runs-on: ubuntu-latest
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environment: ${{ inputs.tier }}
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env:
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APP: icdgenie
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AWS_REGION: us-east-1
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AWS_ACCOUNT_ID: ${{ secrets.AWS_ACCOUNT_ID }}
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DATA_IMPORT_CONTAINER_PORT: 9000
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permissions:
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id-token: write
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contents: read
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steps:
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- name: Checkout code
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uses: actions/checkout@v5
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- name: Configure AWS credentials
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uses: aws-actions/configure-aws-credentials@v5.1.0
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with:
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role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT_ID }}:role/power-user-github-actions-cicd
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aws-region: ${{ env.AWS_REGION }}
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- name: Setup environment variables
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run: |
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echo "TIER=${{ inputs.tier }}" >> $GITHUB_ENV
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echo "TIER_UPPER=$(echo ${{ inputs.tier }} | tr '[:lower:]' '[:upper:]')" >> $GITHUB_ENV
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echo "DATETIME=$(date +%Y%m%d%H%M%S)" >> $GITHUB_ENV
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echo "APP_GIT_TAG=${GITHUB_SHA::7}" >> $GITHUB_ENV
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echo "PARAMETER_PATH=/analysistools/${{ inputs.tier }}/${{ env.APP }}" >> $GITHUB_ENV
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if [[ "${{ inputs.tier }}" == "prod" || "${{ inputs.tier }}" == "stage" ]]; then
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echo "IMAGE_TIER=release" >> $GITHUB_ENV
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else
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echo "IMAGE_TIER=development" >> $GITHUB_ENV
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fi
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- name: Set Docker registry and repository
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run: |
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echo "DOCKER_REGISTRY=${{ env.AWS_ACCOUNT_ID }}.dkr.ecr.${{ env.AWS_REGION }}.amazonaws.com" >> $GITHUB_ENV
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echo "IMAGE_REPOSITORY=${{ env.AWS_ACCOUNT_ID }}.dkr.ecr.${{ env.AWS_REGION }}.amazonaws.com/${{ env.APP }}" >> $GITHUB_ENV
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- name: Set data import image tags
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run: |
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echo "DATA_IMPORT_IMAGE=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-data-import-${{ env.APP_GIT_TAG }}-${{ env.DATETIME }}" >> $GITHUB_ENV
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echo "DATA_IMPORT_IMAGE_LATEST=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-data-import-latest" >> $GITHUB_ENV
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- name: Retrieve AWS SSM parameters
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run: |
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PARAMS=$(aws ssm get-parameters-by-path --path ${{ env.PARAMETER_PATH }} --output json)
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echo "SUBNET_IDS=$(echo $PARAMS | jq -r '.Parameters[] | select(.Name=="${{ env.PARAMETER_PATH }}/subnet_ids") | .Value')" >> $GITHUB_ENV
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echo "SECURITY_GROUP_IDS=$(echo $PARAMS | jq -r '.Parameters[] | select(.Name=="${{ env.PARAMETER_PATH }}/security_group_ids") | .Value')" >> $GITHUB_ENV
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echo "ECS_CLUSTER=$(echo $PARAMS | jq -r '.Parameters[] | select(.Name=="${{ env.PARAMETER_PATH }}/ecs_cluster") | .Value')" >> $GITHUB_ENV
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echo "ECS_DATA_IMPORT_TASK=$(echo $PARAMS | jq -r '.Parameters[] | select(.Name=="${{ env.PARAMETER_PATH }}/ecs_data_import_task") | .Value')" >> $GITHUB_ENV
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- name: Login to Amazon ECR
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run: aws ecr get-login-password | docker login --username AWS --password-stdin ${{ env.DOCKER_REGISTRY }}
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Build and push data import image
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uses: docker/build-push-action@v5
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with:
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context: .
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file: docker/data-import.dockerfile
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push: true
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tags: |
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${{ env.DATA_IMPORT_IMAGE }}
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${{ env.DATA_IMPORT_IMAGE_LATEST }}
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cache-from: type=registry,ref=${{ env.DATA_IMPORT_IMAGE_LATEST }}
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cache-to: type=inline
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- name: Prepare data-import task definition
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run: |
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mkdir -p ecs-tasks
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envsubst < .github/aws/data-import.yml > ecs-tasks/data-import.yml
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- name: Register data import task definition
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run: aws ecs register-task-definition --cli-input-yaml file://ecs-tasks/data-import.yml
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- name: Run data import task
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run: |
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aws ecs run-task \
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--cluster ${{ env.ECS_CLUSTER }} \
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--count 1 \
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--launch-type FARGATE \
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--network-configuration "awsvpcConfiguration={subnets=[${{ env.SUBNET_IDS }}],securityGroups=[${{ env.SECURITY_GROUP_IDS }}]}" \
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--task-definition ${{ env.ECS_DATA_IMPORT_TASK }}

‎.github/workflows/icdgenie-deploy.yml‎

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- qa
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- stage
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- prod
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import_data:
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description: 'Execute data import'
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type: boolean
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default: false
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jobs:
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deploy:
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timeout-minutes: 60
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runs-on: ubuntu-latest
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environment: ${{ inputs.tier }}
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env:
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FRONTEND_APP_PATH: /
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ECS_CPU_UNITS: 1 vCPU
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ECS_MEMORY_UNITS: 2 GB
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ECS_DATA_IMPORT_CPU_UNITS: 2 vCPU
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ECS_DATA_IMPORT_MEMORY_UNITS: 4 GB
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permissions:
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id-token: write
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contents: read
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- name: Configure AWS credentials
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uses: aws-actions/configure-aws-credentials@v5.1.0
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with:
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role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT_ID }}:role/github-actions-cicd
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role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT_ID }}:role/power-user-github-actions-cicd
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aws-region: ${{ env.AWS_REGION }}
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- name: Setup environment variables
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run: |
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echo "FRONTEND_IMAGE=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-frontend-${{ env.APP_GIT_TAG }}-${{ env.DATETIME }}" >> $GITHUB_ENV
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echo "BACKEND_IMAGE=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-backend-${{ env.APP_GIT_TAG }}-${{ env.DATETIME }}" >> $GITHUB_ENV
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echo "DATA_IMPORT_IMAGE=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-data-import-${{ env.APP_GIT_TAG }}-${{ env.DATETIME }}" >> $GITHUB_ENV
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echo "FRONTEND_IMAGE_LATEST=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-frontend-latest" >> $GITHUB_ENV
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echo "BACKEND_IMAGE_LATEST=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-backend-latest" >> $GITHUB_ENV
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echo "DATA_IMPORT_IMAGE_LATEST=${{ env.IMAGE_REPOSITORY }}:${{ env.IMAGE_TIER }}-data-import-latest" >> $GITHUB_ENV
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- name: Retrieve AWS SSM parameters
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run: |
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tags: |
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${{ env.BACKEND_IMAGE }}
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${{ env.BACKEND_IMAGE_LATEST }}
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cache-from: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:backend-cache
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cache-to: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:backend-cache,mode=max
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- name: Build and push data import image
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uses: docker/build-push-action@v5
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with:
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context: .
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file: docker/data-import.dockerfile
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push: true
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tags: |
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${{ env.DATA_IMPORT_IMAGE }}
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${{ env.DATA_IMPORT_IMAGE_LATEST }}
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cache-from: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:data-import-cache
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cache-to: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:data-import-cache,mode=max
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cache-from: type=registry,ref=${{ env.BACKEND_IMAGE_LATEST }}
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cache-to: type=inline
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- name: Build and push frontend image
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uses: docker/build-push-action@v5
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tags: |
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${{ env.FRONTEND_IMAGE }}
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${{ env.FRONTEND_IMAGE_LATEST }}
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cache-from: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:frontend-cache
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cache-to: type=registry,ref=${{ env.IMAGE_REPOSITORY }}:frontend-cache,mode=max
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cache-from: type=registry,ref=${{ env.FRONTEND_IMAGE_LATEST }}
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cache-to: type=inline
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- name: Prepare task definitions
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run: |
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mkdir -p ecs-tasks
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envsubst < .github/aws/web.yml > ecs-tasks/web.yml
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envsubst < .github/aws/data-import.yml > ecs-tasks/data-import.yml
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- name: Register web task definition
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run: aws ecs register-task-definition --cli-input-yaml file://ecs-tasks/web.yml
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- name: Register data import task definition
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run: aws ecs register-task-definition --cli-input-yaml file://ecs-tasks/data-import.yml
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- name: Update ECS service
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run: |
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aws ecs update-service \
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--task-definition ${{ env.ECS_WEB_TASK }} \
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--desired-count 1 \
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--force-new-deployment
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- name: Run data import task
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if: inputs.import_data == true
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run: |
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aws ecs run-task \
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--cluster ${{ env.ECS_CLUSTER }} \
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--count 1 \
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--launch-type FARGATE \
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--network-configuration "awsvpcConfiguration={subnets=[${{ env.SUBNET_IDS }}],securityGroups=[${{ env.SECURITY_GROUP_IDS }}]}" \
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--task-definition ${{ env.ECS_DATA_IMPORT_TASK }}

‎client/src/modules/about/getting-started.js‎

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title="formatting"
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width="80%"
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height="400vw"
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src="https://nci.rev.vbrick.com/embed?id=5008d4e6-38c4-431f-96f7-e999f284f3b4"
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src="https://cbiit.github.io/nci-webtools-dceg-icdgenie/22-1202-Checking_ICD_O_3_ICD_10_Codes.mp4"
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allowFullScreen
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></iframe>
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<h3 style={{ fontWeight: "bold" }}>Using the Tool</h3>
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title="batch"
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width="80%"
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height="400vw"
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src="https://nci.rev.vbrick.com/embed?id=6f9e1353-f6bf-4725-bd4e-2b03509e18a5"
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src="https://cbiit.github.io/nci-webtools-dceg-icdgenie/22-1201-How_to_Use_ICDgenie_s_Batch_Query_Tool.mp4"
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allowFullScreen
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></iframe>
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</Container>

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