🚀 Model Inference Run 🤖 eos2re5: ADMETlab models for evaluation of drug candidates 📅 2025-01-28 #252
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| name: Model Inference Run | |
| on: | |
| issues: | |
| types: [ "opened" ] | |
| jobs: | |
| predict-model: | |
| if: github.event.issue.labels[0].name == 'model-inference-run' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Issue Forms Body Parser | |
| id: parse | |
| uses: zentered/issue-forms-body-parser@v2.0.0 | |
| - name: Update Issue title | |
| run: | | |
| gh repo clone ersilia-os/ersilia-self-service | |
| MODEL_NAME=$(echo '${{ steps.parse.outputs.data }}' | jq -r '.model.text' | awk -F' - ' '{print $1}') | |
| MODEL_ID=$(echo '${{ steps.parse.outputs.data }}' | jq -r '.model.text' | awk -F' - ' '{print $2}') | |
| CURRENT_DATE=$(date +'%Y-%m-%d') | |
| cd ersilia-self-service | |
| gh issue edit ${{ github.event.issue.number }} --title "🚀 Model Inference Run 🤖 $MODEL_ID: $MODEL_NAME 📅 $CURRENT_DATE" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: ersilia-os/ersilia | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install Ersilia | |
| run: | | |
| python -m pip install git+https://github.com/ersilia-os/bentoml-ersilia.git | |
| python -m pip install -e . | |
| - name: Test help command | |
| run: | | |
| ersilia --help | |
| ersilia --version | |
| - name: Model Inference Run | |
| id: model-inference-run | |
| continue-on-error: true | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID_SPLUNK }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_SPLUNK }} | |
| run: | | |
| MODEL_ID=$(echo '${{ steps.parse.outputs.data }}' | jq -r '.model.text' | awk -F' - ' '{print $2}') | |
| ersilia -v fetch $MODEL_ID --from_dockerhub | |
| ersilia -v serve $MODEL_ID --track | |
| echo "smiles" > input.csv | |
| echo '${{ steps.parse.outputs.data }}' | jq -r '.molecules.text' >> input.csv | |
| echo "Predicting output for input.csv file using model $MODEL_ID" | |
| ersilia -v run -i "input.csv" -o "output.csv" | |
| ersilia -v close | |
| - name: Upload output to GitHub | |
| id: upload-artifact | |
| if: steps.model-inference-run.outcome == 'success' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Model Inference Run | |
| path: output.csv | |
| retention-days: 30 | |
| - name: Add success comment | |
| id: success-comment | |
| if: steps.model-inference-run.outcome == 'success' | |
| run: gh issue comment "$NUMBER" --body "$BODY" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GH_REPO: ${{ github.repository }} | |
| NUMBER: ${{ github.event.issue.number }} | |
| BODY: > | |
| Greetings @${{ github.event.issue.user.login }}! | |
| We have successfully completed your model inference run. You can download your results [here](${{ steps.upload-artifact.outputs.artifact-url }}) | |
| Please note that these results will only be available for 30 days after which they will be removed and this issue closed. | |
| - name: Add failure comment | |
| id: failure-comment | |
| if: steps.model-inference-run.outcome == 'failure' | |
| run: gh issue comment "$NUMBER" --body "$BODY" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GH_REPO: ${{ github.repository }} | |
| NUMBER: ${{ github.event.issue.number }} | |
| BODY: > | |
| Greetings @${{ github.event.issue.user.login }}! | |
| We encountered an error while running this model. Rest assured that we are working on resolving this issue. We will update you as soon as we have more information. | |
| If you need further assistance, please feel free to reach out to us. |