Little g alleles are valid in only non-strict mode (#375)

* Little g alleles are not valid nomenclature.

Allow validation of little-g alleles when in non-strict mode.

* Little g alleles are not valid nomenclature.

Allow validation of little-g alleles when in non-strict mode.

Author: pbashyal-nmdp

pyard/ard.py

@@ -346,7 +346,9 @@ def _is_allele_in_db(self, allele: str) -> bool:
         return allele in self.allele_group.alleles
 
     def is_valid_allele(self, allele: str) -> bool:
-        if allele.endswith(("P", "G", "g")):
+        if allele.endswith(("P", "G")):
+            allele = allele[:-1]
+        if not self.config.strict and allele.endswith("g"):
             allele = allele[:-1]
         if "*" in allele:
             _, fields = allele.split("*")

tests/features/allele.feature

@@ -58,6 +58,21 @@ Feature: Alleles
       | A*24:329    | lgx   | A*24:329Q    |
       | DQB1*03:276 | lgx   | DQB1*03:01   |
 
+  Scenario Outline: Allele validation in strict mode
+
+    liggle g alleles are valid in non-strict mode
+
+    Given the allele as <Allele>
+    When checking for validity of the allele in strict mode
+    Then the validness of the allele is <Validity>
+
+    Examples:
+      | Allele        | Validity |
+      | A*24:329      | InValid  |
+      | DRBX*NNNN     | Invalid  |
+      | A*30:02g      | Invalid  |
+      | HLA-A*01:04Ng | Invalid  |
+
   Scenario Outline: Allele validation in non-strict mode
 
   Similar to reduction, handle non-strict mode when validating an allele.
@@ -69,10 +84,12 @@ Feature: Alleles
     Then the validness of the allele is <Validity>
 
     Examples:
-      | Allele    | Validity |
-      | A*11:403  | Invalid  |
-      | A*24:329  | Valid    |
-      | DRBX*NNNN | Invalid  |
+      | Allele        | Validity |
+      | A*11:403      | Invalid  |
+      | A*24:329      | Valid    |
+      | DRBX*NNNN     | Invalid  |
+      | A*30:02g      | Valid    |
+      | HLA-A*01:04Ng | Valid    |
 
   Scenario Outline: Single field MICA, MICB Alleles
 
@@ -131,10 +148,10 @@ Feature: Alleles
 
   Scenario Outline: Alleles with 'g' suffix
 
-  Alleles with 'g' suffix are valid alleles
+  Alleles with 'g' suffix are valid alleles in non-strict mode
 
     Given the allele as <Allele>
-    When reducing on the <Level> level
+    When reducing on the <Level> level in non-strict mode
     Then the reduced allele is found to be <Redux Allele>
 
     Examples:

tests/features/p_g_group.feature

@@ -97,4 +97,4 @@ Feature: P and G Groups
       | DQA1*03:03    | lgx   | DQA1*03:01   |
       | DQA1*03:03    | lg    | DQA1*03:01g  |
       | DQA1*03:03:09 | lgx   | DQA1*03:01   |
-      | DQA1*03:03:09 | lg    | DQA1*03:01g  |
+      | DQA1*03:03:09 | lg    | DQA1*03:03g  |

tests/steps/redux_allele.py

@@ -134,6 +134,14 @@ def step_impl(context):
         context.is_valid = False
 
 
+@when("checking for validity of the allele in strict mode")
+def step_impl(context):
+    try:
+        context.is_valid = context.ard.validate(context.allele)
+    except InvalidAlleleError:
+        context.is_valid = False
+
+
 @when("reducing on the {level} level in ignore_suffix mode")
 def step_impl(context, level):
     context.level = level