preprocess_manual.yaml

name: Preprocessing of specified datasets

on:
  workflow_dispatch:
    inputs:
      datasets:
        description: 'Datasets to preprocess, separated by space. Example: 0001 0002 0044'
        required: True
        type: string
      do_standardize:
        description: 'Whether to standardize compounds'
        type: boolean
        default: true
      do_classyfire:
        description: 'Whether to compute ClassyFire classes'
        type: boolean
        default: true

jobs:
  preprocess:
    name: Preprocess raw data
    # NOTE: on windows as computing of descriptors has a bug on linux right now
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} # needed for pulling R packages from github

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3
      with:
         lfs: true


    - name: List all files for selected datasets
      run: |
        for f in ${{ inputs.datasets }}; do
          ls -lh raw_data/$f || true
          ls -lh processed_data/$f || true
        done
      continue-on-error: true

    - name: Standardize compounds
      using: 'docker'
      image: 'Dockerfile'
      args:
        - Rscript scripts/R_ci/compounds_standardize.R
        - ${{ inputs.datasets }}
      if: ${{ inputs.do_standardize }}

    - name: Compounds classyfire classes
      using: 'docker'
      image: 'Dockerfile'
      args:
        - Rscript scripts/R_ci/compounds_classyfire.R
        - ${{ inputs.datasets }}
      if: ${{ inputs.do_classyfire }}

    - name: Commit preprocessing
      run: |
        git config --global user.email 'actions@github.com'
        git config --global user.name 'Github Actions'
        # Use LFS storage of main repository: no push access to fork LFS storage
        # TODO: change once repository is moved
        git add processed_data raw_data
        git commit -m "Preprocessing ${{ inputs.datasets }}" -m "Tasks:
          - standardize compounds: ${{ inputs.do_standardize }}
          - compute classyfire classes: ${{ inputs.do_classyfire }}
          - compute descriptors: ${{ inputs.do_descriptors }}
          - compute fingerprints: ${{ inputs.do_fingerprints }}
          - standardize metadata: ${{ inputs.do_metadata }}"
        git lfs push origin HEAD # first push LFS, otherwise failure because of lfs.url
        git push origin HEAD

    - name: Debug with tmate on failure
      if: ${{ failure() }}
      uses: mxschmitt/action-tmate@v3