Update genesis/api_clients/bioportal_api.py

genesis/api_clients/bioportal_api.py

@@ -1,22 +1,33 @@
 # genesis/api_clients/bioportal_api.py
-import requests
 import os
+import requests
 
 BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")
-BASE_URL = "https://data.bioontology.org"
+BIOPORTAL_BASE = "https://data.bioontology.org"
+
+def search_bioportal(term: str, max_results: int = 10):
+    """
+    Search BioPortal for ontology terms related to the given term.
+    Returns a list of related concept labels + IDs.
+    """
+    if not BIOPORTAL_API_KEY:
+        raise ValueError("BIOPORTAL_API_KEY is missing in environment variables")
 
-def search_bioportal(query: str):
-    """Search BioPortal for ontologies, classes, or terms."""
-    url = f"{BASE_URL}/search"
-    params = {"q": query, "apikey": BIOPORTAL_API_KEY}
-    r = requests.get(url, params=params)
-    r.raise_for_status()
-    return r.json()
+    url = f"{BIOPORTAL_BASE}/search"
+    params = {
+        "q": term,
+        "apikey": BIOPORTAL_API_KEY,
+        "pagesize": max_results
+    }
+    res = requests.get(url, params=params)
+    res.raise_for_status()
+    data = res.json()
 
-def get_ontology_list():
-    """Get list of available ontologies."""
-    url = f"{BASE_URL}/ontologies"
-    params = {"apikey": BIOPORTAL_API_KEY}
-    r = requests.get(url, params=params)
-    r.raise_for_status()
-    return r.json()
+    results = []
+    for item in data.get("collection", []):
+        results.append({
+            "label": item.get("prefLabel"),
+            "id": item.get("@id"),
+            "ontology": item.get("links", {}).get("ontology")
+        })
+    return results