reload_demo_data.yml

name: Reload data on a demo server

on:
  workflow_call:
    inputs:
      environment:
        description: Environment in which to reload data
        type: string
        required: true
  workflow_dispatch:
    inputs:
      environment:
        description: Environment in which to reload data
        type: environment
        required: true

jobs:
  reload:
    name: Clean up ${{ inputs.environment }} demo server
    runs-on: ubuntu-latest
    environment: ${{ inputs.environment }}
    steps:
      - name: Check out
        uses: actions/checkout@v4
      - name: Configure AWS credentials
        uses: aws-actions/configure-aws-credentials@v4
        with:
          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          aws-region: us-east-1
      - name: Get instance address
        id: ec2-describe-instances
        run: |
          INSTANCE_ADDRESS=$(aws ec2 describe-instances \
            --instance-ids ${{ vars.INSTANCE_ID }} \
            --query "Reservations[*].Instances[*].[PublicDnsName]" \
            --output text)
          echo "INSTANCE_ADDRESS=$INSTANCE_ADDRESS" >> "$GITHUB_OUTPUT"
      - name: Set up SSH
        run: |
          mkdir --parents ~/.ssh
          echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/staging
          chmod 600 ~/.ssh/staging
          cat >>~/.ssh/config <<END
          Host staging
            HostName ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }}
            User ec2-user
            IdentityFile ~/.ssh/staging
            ServerAliveInterval 60
            ServerAliveCountMax 10
          END
          ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts
      - name: Create Docker context
        run: |
          docker context create staging \
            --docker host=ssh://staging \
            --description "Staging server"
      - name: Load data
        run: |
          docker pull ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }}
          function apollo() {
            docker \
              --context staging \
              run \
              --rm \
              --interactive \
              --add-host host.docker.internal=host-gateway \
              --volume /home/ec2-user/.config/apollo-cli:/root/.config/apollo-cli \
              --volume /home/ec2-user/data:/data \
              --env APOLLO_PROFILE=auto \
              ghcr.io/gmod/apollo-cli:${{ vars.DOCKER_TAG }} \
              "$@"
          }

          set -x
          apollo config address http://host.docker.internal/apollo
          apollo config accessType root
          apollo config rootCredentials.username ${{ secrets.ROOT_USER_NAME }}
          apollo config rootCredentials.password ${{ secrets.ROOT_USER_PASSWORD }}
          apollo login --force

          apollo jbrowse set-config /data/config.json

          apollo assembly get | apollo assembly delete --verbose --assembly -
          apollo file get | apollo file delete

          apollo assembly \
            add-from-fasta \
            /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz \
            --fai /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.fai \
            --gzi /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz.gzi \
            --assembly 'Schistosoma haematobium'

          apollo assembly \
            add-from-fasta \
            /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz \
            --fai /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.fai \
            --gzi /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz.gzi \
            --assembly 'Schistosoma mansoni'

          apollo feature \
            import \
            /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.genes.gff3 \
            --assembly 'Schistosoma haematobium'

          apollo feature \
            import \
            /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.genes.gff3 \
            --assembly 'Schistosoma mansoni'