Database, models, Swagger API

.github/scripts/api_check.py

@@ -0,0 +1,122 @@
+#!/usr/bin/env python3
+"""API check: counts, validation summary, and route health."""
+
+import json
+import sys
+import urllib.request
+from datetime import datetime, timezone
+
+BASE = "http://localhost:5050/api"
+
+
+def get(path):
+    url = f"{BASE}{path}"
+    try:
+        req = urllib.request.Request(url)
+        with urllib.request.urlopen(req, timeout=15) as r:
+            return r.status, json.loads(r.read())
+    except urllib.error.HTTPError as e:
+        return e.code, None
+    except Exception:
+        return 0, None
+
+
+errors = []
+
+# 1. Entity counts
+ENTITIES = {
+    "Tools":                "/tools/",
+    "Methods":              "/methods/",
+    "Case studies":         "/casestudies/",
+    "Regulatory questions": "/regulatory-questions/",
+    "Stage explanations":   "/stages/",
+}
+
+counts = {}
+for label, path in ENTITIES.items():
+    status, data = get(path)
+    if status == 200 and isinstance(data, list):
+        counts[label] = len(data)
+    else:
+        counts[label] = None
+        errors.append(f"GET {path} -> {status}")
+
+# 2. Validation summary
+status, validation = get("/validation/")
+if status != 200:
+    errors.append(f"GET /validation/ -> {status}")
+    validation = None
+
+# 3. Health check every route
+ROUTES = [
+    ("GET", "/tools/"),
+    ("GET", "/tools/cdkdepict"),
+    ("GET", "/methods/"),
+    ("GET", "/methods/5_cfda_assay_to_determine_cytotoxicity"),
+    ("GET", "/regulatory-questions/"),
+    ("GET", "/stages/"),
+    ("GET", "/casestudies/"),
+    ("GET", "/casestudies/kidney"),
+    ("GET", "/compounds/Q2270"),
+    ("GET", "/compounds/Q2270/properties"),
+    ("GET", "/compounds/Q2270/identifiers"),
+    ("GET", "/compounds/Q2270/toxicology"),
+    ("GET", "/compounds/Q2270/experimental-data"),
+    ("GET", "/data/"),
+    ("GET", "/validation/"),
+    ("GET", "/validation/tools"),
+]
+
+health = []
+for method, path in ROUTES:
+    status, _ = get(path)
+    ok = 200 <= status < 300
+    health.append((method, path, status, ok))
+    if not ok:
+        errors.append(f"{method} {path} -> {status}")
+
+# ── build report ──────────────────────────────────────────────────
+
+now = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M UTC")
+lines = [f"## API check -- {now}", ""]
+
+# counts
+lines.append("### Entity counts")
+lines.append("")
+lines.append("| Entity | Count |")
+lines.append("|--------|------:|")
+for label, n in counts.items():
+    lines.append(f"| {label} | {n if n is not None else 'ERR'} |")
+lines.append("")
+
+# validation
+if validation and "entities" in validation:
+    lines.append("### Validation (field completeness)")
+    lines.append("")
+    lines.append("| Entity | Entries | Avg complete | Full |")
+    lines.append("|--------|--------:|-------------:|-----:|")
+    for e in validation["entities"]:
+        lines.append(
+            f"| {e['entity']} | {e['total_entries']}"
+            f" | {e['avg_completeness_pct']}%"
+            f" | {e['fully_complete']}/{e['total_entries']} |"
+        )
+    lines.append("")
+
+# health
+lines.append("### Route health")
+lines.append("")
+lines.append("| Method | Route | Status |")
+lines.append("|--------|-------|-------:|")
+for method, path, status, ok in health:
+    mark = "ok" if ok else f"FAIL ({status})"
+    lines.append(f"| {method} | `{path}` | {mark} |")
+lines.append("")
+
+# result
+all_ok = not errors
+lines.append(f"**Result: {'PASS' if all_ok else 'FAIL'}**")
+
+print("\n".join(lines))
+if not all_ok:
+    sys.exit(1)

.github/workflows/pr-api-check.yml

@@ -0,0 +1,45 @@
+name: API check
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+  pull-requests: write
+
+jobs:
+  api-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build Docker image
+        run: docker build -t vhp4safety .
+
+      - name: Start container
+        run: |
+          docker run -d --name vhp4safety -p 5050:5050 vhp4safety
+          for i in $(seq 1 30); do
+            curl -sf http://localhost:5050/api/tools/ && break
+            sleep 2
+          done
+
+      - name: Run API checks
+        id: report
+        run: |
+          python3 .github/scripts/api_check.py > report.md
+          {
+            echo 'REPORT<<GHEOF'
+            cat report.md
+            echo 'GHEOF'
+          } >> "$GITHUB_OUTPUT"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: api-check
+          message: ${{ steps.report.outputs.REPORT }}
+
+      - name: Stop container
+        if: always()
+        run: docker stop vhp4safety && docker rm vhp4safety

.gitignore

@@ -3,6 +3,8 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# SQLite database
+data/*.db
 # C extensions
 *.so
 

Dockerfile

@@ -21,9 +21,14 @@ COPY . .
 # Install any needed packages specified in requirements.txt
 RUN pip install -r requirements.txt
 
+# Create data directory for SQLite DB
+RUN mkdir -p /usr/src/app/data
+
 # Copy entrypoint script
 COPY entrypoint.sh /usr/src/app/entrypoint.sh
 RUN chmod +x /usr/src/app/entrypoint.sh
 
+EXPOSE 5050
+
 # Define the entrypoint script
 ENTRYPOINT ["/usr/src/app/entrypoint.sh"]