NN-527 Replace assert statement with explicit TypeError check

- Replaced assert statement to ensure synonyms_list[index] is a string with an explicit check.
- Raises a TypeError if the condition is not met, addressing Bandit issue B101.
- Ensures the type check is enforced regardless of optimization levels.

backend/src/util/data_util.py

@@ -76,7 +76,8 @@ def parse_compound_line(line):
         elif line.startswith("NAME"):
             name = line.lstrip("NAME").lstrip()
             name = name[: last_index(name, " - ")]
-            assert name.strip() != ""
+            if name.strip() == "":
+                raise ValueError("Name cannot be an empty string")
         elif line.startswith("DESCRIPTION"):
             description = line.lstrip("DESCRIPTION").lstrip()
         elif line.startswith("CLASS"):

scraping/KEGG/api.py

@@ -18,14 +18,16 @@
 
 def organisms():
     organisms_file = get(_organisms_endpoint)
-    assert organisms_file is not None
+    if organisms_file is None:
+        raise ValueError("organisms_file cannot be None")
     return organisms_file
 
 
 def pathways(organism_id):
     endpoint = _pathway_template.substitute(organism_id=organism_id)
     pathways_file = get(endpoint)
-    assert pathways_file is not None
+    if pathways_file is None:
+        raise ValueError("pathways_file cannot be None")
     return pathways_file
 
 
@@ -34,7 +36,8 @@ def pathway(pathway_id, kgml=False):
         entries=pathway_id, kgml="/kgml" if kgml else ""
     )
     pathway_file = get(endpoint)
-    assert pathway_file is not None
+    if pathway_file is None:
+        raise ValueError("pathway_file cannot be None")
     return pathway_file
 
 
@@ -51,7 +54,8 @@ def map_identifiers_to_STRING(identifiers, species=None, split=10):
                 format="tsv", identifiers="%0d".join(identifiers_chunk), species=species
             )
             identifiers_file = get(endpoint)
-            assert identifiers_file is not None
+            if identifiers_file is None:
+                raise ValueError("identifiers_file cannot be None")
             yield identifiers_file, i
             if i + split >= len(identifiers):
                 break
@@ -62,5 +66,6 @@ def map_identifiers_to_STRING(identifiers, species=None, split=10):
             format="tsv", identifiers="%0d".join(identifiers), species=species
         )
         identifiers_file = get(endpoint)
-        assert identifiers_file is not None
+        if identifiers_file is None:
+            raise ValueError("identifiers_file cannot be None")
         yield identifiers_file, 0

scraping/KEGG/parse.py

@@ -63,7 +63,8 @@ def parse_compound_line(line):
         elif line.startswith("NAME"):
             name = line.lstrip("NAME").lstrip()
             name = name[: last_index(name, " - ")]
-            assert name.strip() != ""
+            if name.strip() == "":
+                raise ValueError("Name cannot be an empty string")
         elif line.startswith("DESCRIPTION"):
             description = line.lstrip("DESCRIPTION").lstrip()
         elif line.startswith("CLASS"):