Preprocessing of specified datasets #29
Workflow file for this run
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| 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 | |
| do_descriptors: | |
| description: 'Whether to compute descriptors' | |
| type: boolean | |
| default: true | |
| do_fingerprints: | |
| description: 'Whether to compute fingerprints' | |
| type: boolean | |
| default: true | |
| do_metadata: | |
| description: 'Whether to standardize metadata' | |
| 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: windows-2019 | |
| 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 | |
| shell: bash {0} | |
| 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: Pyton dependencies | |
| run: pip install -r scripts/Python/requirements.txt | |
| # needed for every task | |
| - name: Set java version | |
| run: echo ("JAVA_HOME=" + $Env:JAVA_HOME_13_X64) >> $env:GITHUB_ENV | |
| # needed for every task | |
| - name: Set RENV_PATHS_ROOT | |
| shell: bash | |
| run: | | |
| echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV | |
| # needed for every task | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| # needed for every task | |
| - name: Restore Renv package cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-renv- | |
| # needed for every task | |
| - name: Install and activate renv | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("renv") | |
| renv::restore() | |
| # needed for every task | |
| - name: Standardize compounds | |
| run: Rscript scripts/R_ci/compounds_standardize.R ${{ inputs.datasets }} | |
| if: ${{ inputs.do_standardize }} | |
| - name: Compounds classyfire classes | |
| run: Rscript scripts/R_ci/compounds_classyfire.R ${{ inputs.datasets }} | |
| if: ${{ inputs.do_classyfire }} | |
| - name: Compounds descriptors | |
| run: Rscript scripts/R_ci/compounds_descriptors.R ${{ inputs.datasets }} | |
| if: ${{ inputs.do_descriptors }} | |
| - name: Compounds fingerprints | |
| run: Rscript scripts/R_ci/compounds_fingerprints.R ${{ inputs.datasets }} | |
| if: ${{ inputs.do_fingerprints }} | |
| - name: Metadata standardization | |
| run: Rscript scripts/R_ci/metadata_standardize.R ${{ inputs.datasets }} | |
| if: ${{ inputs.do_metadata }} | |
| - name: Generate dataset reports | |
| run: Rscript scripts/R_ci/compounds_overview.R ${{ inputs.datasets }} | |
| - name: Verify that required files are present | |
| run: Rscript scripts/R_ci/files_complete.R ${{ inputs.datasets }} | |
| - name: Update overview table of all datasets | |
| run: python3 scripts/Python/datasets_overview.py | |
| continue-on-error: true | |
| - name: Commit preprocessing | |
| run: | | |
| git config --global user.email '[email protected]' | |
| 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 |