improved error catching in manifest

src/clinical_etl/CSVConvert.py

@@ -642,13 +642,25 @@ def csv_convert(input_path, manifest_file, minify=False, index_output=False, ver
     # read manifest data
     print(f"{Bcolors.OKGREEN}Starting conversion...{Bcolors.ENDC}", end="")
     manifest = load_manifest(manifest_file)
-    mappings.IDENTIFIER_FIELD = manifest["identifier"]
-    if mappings.IDENTIFIER_FIELD is None:
+    try:
+        mappings.IDENTIFIER_FIELD = manifest["identifier"]
+        if manifest["identifier"] is None:
+            raise TypeError
+    except KeyError as e:
         sys.exit("Need to specify what the main identifier column name is as 'identifier' in the manifest file, "
                  "see README for more details.")
-    mappings.DATE_FORMAT = manifest["date_format"]
-    if mappings.DATE_FORMAT is None:
-        sys.exit("Need to specify what the date format is in the manifest file, "
+    except TypeError as e:
+        sys.exit("'identifier' in the manifest file cannot be blank, see README for more details.")
+    try:
+        mappings.DATE_FORMAT = manifest["date_format"]
+        if manifest["date_format"] is None:
+            raise TypeError
+        if sorted(manifest["date_format"]) != sorted("DMY"):
+            raise TypeError
+    except KeyError as e:
+        sys.exit("'date_format' in the manifest file cannot be blank, see README for more details.")
+    except TypeError as e:
+        sys.exit("Need to specify a valid value for the date format in the manifest file, "
                  "see README for more details.")
 
     # read the schema (from the url specified in the manifest) and generate