upload-model-to-s3.yml

name: Upload model to S3
on:
  workflow_dispatch:
  
  workflow_run:
    workflows: ["Model test on push"]
    types:
      - completed
  
jobs:
  upload_model_to_s3:
    if: ${{ github.repository != 'ersilia-os/eos-template' && github.event.workflow_run.conclusion == 'success' }}
    runs-on: ubuntu-latest
    steps:
      - name: Checkout persist credentials
        uses: actions/checkout@master
        with:
          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
          lfs: 'true'
            
      - name: Add conda to system path
        run: echo $CONDA/bin >> $GITHUB_PATH
      
      - name: Source conda
        run: source $CONDA/etc/profile.d/conda.sh

      - name: Set Python to 3.10.10
        run:
         conda install -y python=3.10.10 
      
      - name: Install dependencies
        run: |
          source activate
          conda init
          conda install git-lfs -c conda-forge
          git-lfs install
          conda install gh -c conda-forge
          
      - name: Install ersilia
        run: |
          source activate
          python --version
          echo "After conda init"
          conda init
          python -m pip install git+https://github.com/ersilia-os/ersilia.git
                  
      - name: Check metadata file
        id: checkMetadata
        continue-on-error: true
        run: |
          if [[ ! -f metadata.yml ]]; then
            echo "metadata.yml file not found"
            exit 1
          fi

      - name: Update Metadata JSON file with DockerHub info
        if: steps.checkMetadata.outcome == 'failure'
        id: UpdateMetadataJSON
        run: |
          python3 -c "
          import json
          with open('metadata.json', 'r') as f:
             data = json.load(f)
          data['S3'] = 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/{0}.zip'.format(data['Identifier'])
          with open('metadata.json', 'w') as f:
             json.dump(data, f, indent=4)
          "

      - name: Update Metadata YAML file with DockerHub info
        if: steps.checkMetadata.outcome == 'success'
        id: UpdateMetadataYAML
        run: |
          python3 -c "
          import yaml
          with open('metadata.yml', 'r') as f:
             data = yaml.safe_load(f)
          data['S3'] = 'https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/{0}.zip'.format(data['Identifier'])
          with open('metadata.yml', 'w') as f:
             yaml.dump(data, f, default_flow_style=False, sort_keys=False)
          "
          
      - name: Commit and push changes done to the Metadata JSON file
        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
        with:
          author_name: "ersilia-bot"
          author_email: "ersilia-bot@users.noreply.github.com"
          message: "updating metadata [skip ci]"
          repository: "ersilia-os/${{ github.event.repository.name }}"
          github_token: ${{ secrets.GITHUB_TOKEN }}
          amend: true
          force: true

      - name: Update metadata to AirTable
        id: update-metadata-to-airtable
        env:
          USER_NAME: ${{ github.repository_owner }}
          BRANCH: "main"
          REPO_NAME: ${{ github.event.repository.name }}
          AIRTABLE_API_KEY: ${{ secrets.AIRTABLE_API_KEY }}
        run: |
          source activate
          echo "Updating metadata to AirTable looking at owner: $USER_NAME"
          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_metadata_to_airtable.py
          python3 update_metadata_to_airtable.py $USER_NAME $REPO_NAME $BRANCH $AIRTABLE_API_KEY
          rm update_metadata_to_airtable.py
  
      - name: Update README file
        id: update-readme-file
        env:
          MODEL_ID: ${{ github.event.repository.name }}
        run: |
          source activate
          echo "Updating README file with AirTable metadata for model: $MODEL_ID"
          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/update_readme_from_airtable.py
          python3 update_readme_from_airtable.py $MODEL_ID .
          rm update_readme_from_airtable.py
          less README.md

      - name: Commit and push changes done to the README file
        uses: actions-js/push@156f2b10c3aa000c44dbe75ea7018f32ae999772 # pin@v1.4
        with:
          author_name: "ersilia-bot"
          author_email: "ersilia-bot@users.noreply.github.com"
          message: "updating readme [skip ci]"
          repository: "ersilia-os/${{ github.event.repository.name }}"
          github_token: ${{ secrets.GITHUB_TOKEN }}
          amend: true
          force: true

      - name: Upload model to S3
        id: upload-model-to-s3
        env:
          REPO_NAME: ${{ github.event.repository.name }}
          AWS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        run: |
          source activate
          echo "Uploading model to S3 bucket"
          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/.github/scripts/upload_model_to_s3.py
          python3 upload_model_to_s3.py $REPO_NAME $AWS_ACCESS_KEY $AWS_SECRET_ACCESS_KEY .
          rm upload_model_to_s3.py