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Build Dependencies Table #6

Build Dependencies Table

Build Dependencies Table #6

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."