Create Hub Ingest Endpoint #27
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| name: Create Hub Ingest Endpoint | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| username: | |
| description: 'Username for the endpoint' | |
| required: true | |
| type: string | |
| size: | |
| description: 'Storage size (e.g., 50Gi)' | |
| required: true | |
| type: string | |
| env: | |
| BIOC_HUBSINGEST_PATH: "${{ github.workspace }}" | |
| jobs: | |
| create-endpoint: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: amazon/aws-cli:latest | |
| env: | |
| BIOC_HUBSINGEST_PATH: "/hubsingest" | |
| steps: | |
| - name: Install required packages | |
| run: | | |
| yum update -y && yum install -y curl tar gzip | |
| - name: save kubeconfig | |
| shell: bash | |
| run: mkdir -p ~/.kube && echo "${{ secrets.KUBECONFIG }}" > ~/.kube/config | |
| - name: Install Kubectl | |
| run: | | |
| curl -LO "https://storage.googleapis.com/kubernetes-release/release/v1.24.4/bin/linux/amd64/kubectl" && \ | |
| chmod +x ./kubectl && \ | |
| mv ./kubectl /usr/local/bin/kubectl && \ | |
| kubectl version | |
| - name: Set up environment | |
| run: | | |
| USERNAME_LOWER=$(echo "${{ inputs.username }}" | tr '[:upper:]' '[:lower:]') | |
| USERNAME_UPPER=$(echo "${{ inputs.username }}" | tr '[:lower:]' '[:upper:]') | |
| echo "SECRET_NAME=S3KEY_${USERNAME_UPPER}" >> $GITHUB_ENV | |
| echo "USERNAME=${USERNAME_LOWER}" >> $GITHUB_ENV | |
| - name: Create endpoint then test | |
| run: | | |
| mkdir -p $BIOC_HUBSINGEST_PATH | |
| cd $BIOC_HUBSINGEST_PATH | |
| curl -O https://raw.githubusercontent.com/Bioconductor/hubsingest/devel/install_hubsingest.sh | |
| bash install_hubsingest.sh | |
| export PATH="$PATH:$BIOC_HUBSINGEST_PATH" | |
| hubsingest create_endpoint "${{ env.USERNAME }}" "${{ inputs.size }}" ${{ secrets[env.SECRET_NAME] }} | |
| kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready pod -l app=versitygw --timeout=300s | |
| kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready certificate ${{ env.USERNAME }}-hubsingest-bioconductor-org-key --timeout=600s || bash scripts/reset_endpoint_ssl.sh "${{ env.USERNAME }}" && kubectl wait -n "${{ env.USERNAME }}-ns" --for=condition=ready certificate ${{ env.USERNAME }}-hubsingest-bioconductor-org-key --timeout=600s | |
| sleep 30 | |
| hubsingest test_endpoint "${{ env.USERNAME }}" |