Reload data on a demo server #9
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| 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 | |
| END | |
| ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts | |
| - name: Setup and Reload | |
| run: | | |
| xid=`date +"%Y-%m-%dT%H-%M-%S"` | |
| cat <<'EOF' > cleanup_apollo.$xid.sh | |
| set -e | |
| set -u | |
| set -o pipefail | |
| set -x | |
| # Download data | |
| demoDataDir=${{ '${HOME}' }}/reload_demo_data/demoData | |
| rm -rf $demoDataDir | |
| mkdir -p $demoDataDir | |
| cd $demoDataDir | |
| wormbase='https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species' | |
| curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa.gz | |
| curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa.gz | |
| curl -O -s -L $wormbase/schistosoma_haematobium/TD2_PRJEB44434/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3.gz | |
| curl -O -s -L $wormbase/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3.gz | |
| gunzip *.gz | |
| # Setup docker | |
| if [ "${{ inputs.environment }}" = "staging" ]; then | |
| env=devel | |
| elif [ "${{ inputs.environment }}" = "prod" ]; then | |
| env=latest | |
| else | |
| echo "Invalid environment: ${{ inputs.environment }}" >&2 | |
| fi | |
| docker pull ghcr.io/gmod/apollo-cli:${env} | |
| cfgDir=${{ '${HOME}' }}/reload_demo_data/config | |
| mkdir -p $cfgDir | |
| touch $cfgDir/config.yml | |
| function apollo () { | |
| docker run --network host -v $cfgDir:/root/.config/apollo-cli -v $demoDataDir:/data ghcr.io/gmod/apollo-cli:${env} "$@" | |
| } | |
| cfg="--config-file /root/.config/apollo-cli/config.yml --profile auto" | |
| # Configure Apollo | |
| apollo config $cfg address http://localhost/apollo | |
| apollo config $cfg accessType root | |
| apollo config $cfg rootCredentials.username ${{ secrets.ROOT_USER_NAME }} | |
| apollo config $cfg rootCredentials.password ${{ secrets.ROOT_USER_PASSWORD }} | |
| apollo login $cfg | |
| # Cleanup & import | |
| asm=`apollo assembly get $cfg | jq -r '.[] | ._id'` | |
| apollo assembly delete $cfg -v -a $asm | |
| apollo assembly add-fasta $cfg -i /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.genomic.fa -a schistosoma_haematobium -f | |
| apollo assembly add-fasta $cfg -i /data/schistosoma_mansoni.PRJEA36577.WBPS19.genomic.fa -a schistosoma_mansoni -f | |
| apollo feature import $cfg -i /data/schistosoma_haematobium.TD2_PRJEB44434.WBPS19.annotations.gff3 -a schistosoma_haematobium -d | |
| apollo feature import $cfg -i /data/schistosoma_mansoni.PRJEA36577.WBPS19.annotations.gff3 -a schistosoma_mansoni -d | |
| echo `date +"%Y-%m-%dT%H-%M-%S"` 'OK' | |
| EOF | |
| logDir=reload_demo_data/logs | |
| ssh "${{ inputs.environment }}" -f "mkdir -p ${logDir}" | |
| rsync -av cleanup_apollo.$xid.sh "${{ inputs.environment }}":${logDir}/logs/ | |
| ssh "${{ inputs.environment }}" -f "bash ${logDir}/cleanup_apollo.$xid.sh > ${logDir}/cleanup_apollo.$xid.out 2> ${logDir}/cleanup_apollo.$xid.err" |