Build Dependencies Table #6
Workflow file for this run
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| name: Build Dependencies Table | |
| on: | |
| release: | |
| types: [published] | |
| jobs: | |
| update-table: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: main | |
| - name: Fetch latest changes from main | |
| run: | | |
| git fetch origin | |
| git checkout main | |
| git pull origin main | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install requests pandas | |
| - name: Fetch attribute table | |
| run: | | |
| python - <<EOF | |
| import requests | |
| import pandas as pd | |
| from io import StringIO | |
| def fetch_and_save_attribute_table(): | |
| url = "https://schematic.api.sagebionetworks.org/v1/visualize/attributes" | |
| jsonld_url = "https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld" | |
| # Prepare parameters or request body as needed | |
| params = {'schema_url': jsonld_url} | |
| print("Fetching attribute table...") | |
| # Change to POST if required by the API | |
| response = requests.post(url, params=params) | |
| print(f"Status Code: {response.status_code}") | |
| print(f"Response Text: {response.text[:500]}") # Print first 500 characters for review | |
| if response.status_code == 200: | |
| content_type = response.headers.get('Content-Type', '') | |
| if 'text/html' in content_type: | |
| print("Response in text/html format, converting to CSV...") | |
| try: | |
| df = pd.read_csv(StringIO(response.text)) | |
| print("Fetched attribute table.") | |
| df.to_csv('HTAN.dependencies.csv', index=False) | |
| print("Saved to HTAN.dependencies.csv.") | |
| except Exception as e: | |
| print(f"Error processing CSV: {e}") | |
| else: | |
| print("Unexpected content type. Expected text/html but got:", content_type) | |
| else: | |
| print(f"Failed to fetch data. Status Code: {response.status_code}") | |
| if __name__ == "__main__": | |
| fetch_and_save_attribute_table() | |
| EOF | |
| - name: Commit changes | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git add HTAN.dependencies.csv | |
| git commit -m "Update HTAN.dependencies.csv with the latest attribute table" || echo "No changes to commit" | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: "Update HTAN.dependencies.csv" | |
| branch: update-attribute-table | |
| title: "Update HTAN.dependencies.csv" | |
| body: "This PR updates HTAN.dependencies.csv with the latest attribute table." |