Changed MAC validation/check to use is_mac

Author: pbashyal-nmdp

pyard/ard.py

@@ -409,8 +409,8 @@ def redux(self, glstring: str, redux_type: VALID_REDUCTION_TYPES) -> str:
                     )
 
         # Handle MAC
-        if self._config["reduce_MAC"] and self.is_mac(glstring):
-            if db.is_valid_mac_code(self.db_connection, code):
+        if self._config["reduce_MAC"] and code.isalpha():
+            if self.is_mac(glstring):  # Make sure it's a valid MAC
                 if HLA_regex.search(glstring):
                     # Remove HLA- prefix
                     allele_name = glstring.split("-")[1]
@@ -487,15 +487,16 @@ def is_mac(self, allele: str) -> bool:
         if ":" in allele:
             allele_split = allele.split(":")
             if len(allele_split) == 2:  # MACs have only single :
-                locus_antigen, code = allele.split(":")
+                locus_antigen, code = allele_split
                 if code.isalpha():
                     try:
                         alleles = db.mac_code_to_alleles(self.db_connection, code)
                         if alleles:
                             if any(map(lambda a: ":" in a, alleles)):
-                                # allele specific antigen codes has ':' in the MAC mapping
+                                # allele specific antigen codes have ':' in the MAC mapping
                                 # e.g. CFWRN -> 15:01/15:98/15:157/15:202/
                                 #               15:239/15:280/15:340/35:43/35:67/35:79/35:102/35:118/35:185/51:220
+                                # Extract the antigens from the mapped alleles
                                 antigen_groups = map(lambda a: a.split(":")[0], alleles)
                                 # Rule 1: The 1st field with the most allele designations in the request is
                                 #         the 1st field of the allele code designation
@@ -746,8 +747,8 @@ def expand_mac(self, mac_code: str):
         :return: GL String of expanded alleles
         :rtype: str
         """
-        locus_antigen, code = mac_code.split(":")
-        if db.is_valid_mac_code(self.db_connection, code):
+        if self.is_mac(mac_code):  # Validate MAC first
+            locus_antigen, code = mac_code.split(":")
             if HLA_regex.search(mac_code):
                 locus_antigen = locus_antigen.split("-")[1]  # Remove HLA- prefix
                 return "/".join(

pyard/db.py

@@ -172,21 +172,6 @@ def alleles_to_mac_code(
     return None
 
 
-def is_valid_mac_code(connection: sqlite3.Connection, code: str) -> bool:
-    """
-    Check db if the MAC code exists.
-
-    :param connection: db connection of type sqlite.Connection
-    :param code: MAC code
-    :return: code is MAC code ?
-    """
-    mac_query = "SELECT count(alleles) from mac_codes where code = ?"
-    cursor = connection.execute(mac_query, (code,))
-    result = cursor.fetchone()
-    cursor.close()
-    return result[0] > 0
-
-
 def serology_to_alleles(connection: sqlite3.Connection, serology: str) -> List[str]:
     """
     Look up Serology in the database and return corresponding list of alleles.

scripts/pyard

@@ -155,6 +155,9 @@ if __name__ == "__main__":
     except InvalidTypingError as e:
         print("Typing Error:", e.message, file=sys.stderr)
         sys.exit(2)
+    except InvalidMACError as e:
+        print("MAC Error:", e.message, file=sys.stderr)
+        sys.exit(3)
     else:
         # Remove ard and close db connection
         del ard

tests/features/mac.feature

@@ -50,7 +50,14 @@ Feature: MAC (Multiple Allele Code)
       | HLA-A*02:01/HLA-A*02:09/HLA-A*02:43N | HLA-A*02:GNF  |
 
 
-  Scenario Outline: Invalid MACs
+  Scenario Outline: Validate allele specific antigen MACs
+
+  MAC validation rules for allele specific antigen codes:
+  - The 1st field with the most allele designations in the request is
+  the 1st field of the allele code designation
+  - If there is a tie in the number of alleles designations sharing the 1st field,
+  the 1st field with the lowest numeric value is selected.
+
 
     Given the MAC code is <MAC>
     When checking for validity of the MAC
@@ -59,5 +66,8 @@ Feature: MAC (Multiple Allele Code)
     Examples:
       | MAC          | Validity |
       | DRB1*07:DFJR | Invalid  |
+      | DRB1*15:DFJR | Valid    |
       | DPB1*08:BHHE | Invalid  |
+      | DPB1*19:BHHE | Valid    |
       | A*31:CMZEY   | Invalid  |
+      | A*02:CMZEY   | Valid    |