Improve error handling and default on disease matching

Author: mathieulemieux

pori_python/ipr/ipr.py

@@ -627,8 +627,14 @@ def get_kb_matches_sections(
 
 
 def get_kb_disease_matches(
-    graphkb_conn: GraphKBConnection, kb_disease_match: str = 'cancer', verbose=True
+    graphkb_conn: GraphKBConnection, kb_disease_match: str = None, verbose: bool = True
 ) -> list[str]:
+
+    if not kb_disease_match:
+        kb_disease_match = 'cancer'
+        if verbose:
+            logger.warning(f"No disease provided; will use '{kb_disease_match}'")
+
     if verbose:
         logger.info(f"Matching disease ({kb_disease_match}) to graphkb")
 

pori_python/ipr/main.py

@@ -384,13 +384,8 @@ def ipr_report(
     kb_disease_match: str = content["kbDiseaseMatch"]
 
     # Matching disease RIDs from GraphKB using term tree
-    disease_matches: list[str] = []
-    try:
-        disease_matches = get_kb_disease_matches(graphkb_conn, kb_disease_match)
-    except ValueError as err:
-        # 2nd try using deafult disease term.
-        # Will raise uncatched error if no match
-        disease_matches = get_kb_disease_matches(graphkb_conn)
+    # (Will raise uncatched error if no match)
+    disease_matches: list[str] = get_kb_disease_matches(graphkb_conn, kb_disease_match)
 
     # GKB MATCHING
     gkb_matches: List[Hashabledict] = []