Update app.py

app.py

@@ -13,7 +13,10 @@ import matplotlib.pyplot as plt
 import seaborn as sns
 from typing import Optional, Dict, List, Any
 import os
+import logging
 
+# Setup logging
+logging.basicConfig(level=logging.ERROR) #Log only errors
 
 # API Endpoints (Centralized Configuration)
 API_ENDPOINTS = {
@@ -63,6 +66,7 @@ def _query_api(endpoint: str, params: Optional[Dict] = None) -> Optional[Dict]:
         return response.json()
     except requests.exceptions.RequestException as e:
         st.error(f"API request failed: {e} for endpoint {endpoint}. Please check connectivity and the endpoint.")
+        logging.error(f"API request failed: {e} for endpoint {endpoint}.")
         return None
 
 def _query_pubmed(query: str, email: Optional[str] = PUBMED_EMAIL) -> Optional[Dict]:
@@ -105,6 +109,7 @@ def _draw_molecule(smiles: str) -> Optional[any]:
             return None
     except Exception as e:
         st.error(f"Error generating molecule image: {str(e)}")
+        logging.error(f"Error generating molecule image: {str(e)}")
         return None
 
 
@@ -159,32 +164,34 @@ def _get_pharmgkb_data(gene:str) -> Optional[Dict]:
     if data and 'clinicalAnnotations' in data:
          return data
     else:
-         return None
-
+        return None
 
 def _get_bioportal_data(ontology: str, term: str) -> Optional[Dict]:
     """Fetches data from BioPortal."""
     if not BIOPORTAL_API_KEY:
-        st.error("BioPortal API key not found. Please set the BIOPORTAL_API_KEY environment variable.")
-        return None
+      st.error("BioPortal API key not found. Please add the BIOPORTAL_API_KEY to secrets.")
+      return None
     if not term:
-        st.error("Please provide a search term")
-        return None
+      st.error("Please provide a search term.")
+      return None
+    
     headers = {
         "Authorization": f"apikey token={BIOPORTAL_API_KEY}"
         }
     params = {
-      "q": term,
-      "ontologies": ontology,
-      "apikey": BIOPORTAL_API_KEY
+        "q": term,
+        "ontologies": ontology
     }
+
     url = f"{API_ENDPOINTS['bioportal']}/search"
+
     try:
-      response = requests.get(url, headers=headers, params=params, timeout=15)
-      response.raise_for_status()
-      return response.json()
+        response = requests.get(url, headers=headers, params=params, timeout=15)
+        response.raise_for_status()
+        return response.json()
     except requests.exceptions.RequestException as e:
-        st.error(f"BioPortal API request failed: {e}. Please check connectivity and ensure you have the correct API Key.")
+        st.error(f"BioPortal API request failed: {e} Please check connectivity and ensure you have the correct API Key.")
+        logging.error(f"BioPortal API request failed: {e}")
         return None
     
 def _save_pdf_report(report_content: str, filename: str):
@@ -414,7 +421,7 @@ with tabs[4]:
     if st.button("Search BioPortal"):
         with st.spinner("Searching Ontology..."):
             bioportal_data = _get_bioportal_data(ontology_select, ontology_search_term)
-            if bioportal_data and bioportal_data['collection']:
+            if bioportal_data and 'collection' in bioportal_data:
                 st.subheader(f"BioPortal Search Results for {ontology_select}")
                 for result in bioportal_data['collection']:
                     st.write(f"- {result['prefLabel']} ({result['@id']})")