Inspect Model #1045
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| name: Inspect model | |
| on: | |
| workflow_dispatch: #add input here | |
| inputs: | |
| model_id: | |
| description: Model ID | |
| required: false | |
| type: string | |
| schedule: | |
| - cron: '0 */4 * * *' | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| jobs: | |
| publications-and-repositories: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # [email protected] | |
| - name: Add conda to system path | |
| run: echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Source conda | |
| run: source $CONDA/etc/profile.d/conda.sh | |
| - name: Set Python to 3.10 | |
| run: | |
| conda install -y python=3.10 | |
| - name: Install dependencies | |
| run: | | |
| source activate | |
| conda init | |
| conda install git-lfs -c conda-forge | |
| git-lfs install | |
| conda install gh -c conda-forge | |
| - name: Install dependencies | |
| run: | | |
| source activate | |
| git clone https://github.com/ersilia-os/ersilia.git | |
| - name: Install ersilia | |
| run: | | |
| source activate | |
| python --version | |
| echo "After conda init" | |
| conda init | |
| cd ersilia | |
| python -m pip install -e . | |
| - name: Inspect model | |
| run: | | |
| if [ -n "${{ github.event.inputs.model_id }}" ]; then | |
| echo "Using input model ID: ${{ github.event.inputs.model_id }}" | |
| export MODEL_ID="${{ github.event.inputs.model_id }}" | |
| else | |
| echo "Getting next model from Python script: " | |
| export MODEL_ID=$(python3 pickRepo.py) | |
| # Find the element in the JSON array with the matching "name" field and update its "time" field to the current datetime | |
| jq --arg repo_name "$MODEL_ID" \ | |
| --arg current_time "$(date -u +'%Y-%m-%dT%H:%M:%SZ')" \ | |
| 'map(if .repository_name == $repo_name then .most_recent_date_checked = $current_time else . end)' \ | |
| repo_info.json > temp_repo_info.json | |
| mv temp_repo_info.json repo_info.json | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "Julia Poulson" | |
| git add repo_info.json | |
| git commit -m "Edited the JSON file" | |
| git push | |
| fi | |
| REPO_OWNER="ersilia-os" | |
| REPO_NAME="ersilia-maintenance" | |
| # check if model exists | |
| echo "Sample model id selected: $MODEL_ID" | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.is_github_url_available')" = true ]; then | |
| echo "Model Found" | |
| else | |
| echo "Model not found" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID does not exist 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID does not have an associated repository in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that the repository exists and is accessible. <br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.is_github_url_available_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| exit | |
| fi | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.metadata_complete')" = true ]; then | |
| echo "Metadata Complete" | |
| else | |
| echo "Metadata Incomplete" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID does not have complete metadata 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID does not have valid metadata in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that the metadata.json file is filled out with the correct fields.<br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.metadata_complete_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| fi | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.folder_structure_complete')" = true ]; then | |
| echo "Folder Structure Complete" | |
| else | |
| echo "Folder Structure Incomplete" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID does not have complete folder structure 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID does not have a valid folder structure in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that the repository contains the correct folders.<br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.folder_structure_complete_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| fi | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.docker_check')" = true ]; then | |
| echo "Docker Complete" | |
| else | |
| echo "Docker Incomplete" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID does not have complete Dockerfile 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID does not have a complete Dockerfile in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that the Docker file contains specified versions for installs and ends with proper functionality. <br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.docker_check_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| fi | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.extra_files_check')" = true ]; then | |
| echo "No Extra Files/Folders Found" | |
| else | |
| echo "Extra Files/Folders Found" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID has extra files/folders 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID has unexpected files/folders found in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that all files/folders in the root directory are valid. <br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.extra_files_check_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| fi | |
| if [ "$(ersilia inspect $MODEL_ID | jq '.computational_performance_tracking')" = true ]; then | |
| echo "Model Ran. Computational Perfomance: " | |
| echo "$(ersilia inspect $MODEL_ID | jq '.computational_performance_tracking_details')" | |
| else | |
| echo "Model did not Run Properly" | |
| ISSUE_TITLE="🚨 Model $MODEL_ID did not run properly 🚨" | |
| ISSUE_BODY="Hi! 👋 The model $MODEL_ID did not run properly in the [ersilia-os](https://github.com/ersilia-os) organization profile. 🙏 Please ensure that the model can be served.<br><br>Detailed eror message: $(ersilia inspect $MODEL_ID | jq '.computational_performance_tracking_details') <br><br>The failed action is found at ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # Check if issue already exists | |
| if gh issue list --repo $REPO_OWNER/$REPO_NAME --search "$ISSUE_TITLE in:title" | grep -q "$ISSUE_TITLE"; then | |
| echo "Issue already exists for $MODEL_ID" | |
| else | |
| # Create new issue | |
| gh issue create --title "$ISSUE_TITLE" \ | |
| --body "$ISSUE_BODY" \ | |
| #--label "maintenance" \ | |
| #--repo $REPO_OWNER/$REPO_NAME | |
| fi | |
| exit | |
| fi |