Merge pull request #287 from pbashyal-nmdp/validate-non-strict

Fix `validate()` in non-strict mode

Author: mmaiers-nmdp

pyard/ard.py

@@ -184,14 +184,8 @@ def _redux_allele(
             else:
                 return redux_allele
 
-        # In non-strict mode, if the allele is not valid,
-        # try it with expression characters suffixed
-        if not self._config["strict"] and not self._is_valid_allele(allele):
-            for expr_char in expression_chars:
-                if self._is_valid_allele(allele + expr_char):
-                    if self._config["verbose_log"]:
-                        print(f"{allele} is not valid. Using {allele}{expr_char}")
-                    allele = allele + expr_char
+        if not self._config["strict"]:
+            allele = self._get_non_strict_allele(allele)
 
         # g_group maps alleles to their g_group
         # note: this includes mappings for shortened version of alleles
@@ -301,6 +295,23 @@ def _redux_allele(
             else:
                 raise InvalidAlleleError(f"{allele} is an invalid allele.")
 
+    def _get_non_strict_allele(self, allele):
+        """
+        In non-strict mode, if the allele is not valid,
+        try it with expression characters suffixed
+
+        @param allele: allele that might have non-strict version
+        @return: non-strict version of the allele if it exists
+        """
+        if not self._is_valid_allele(allele):
+            for expr_char in expression_chars:
+                if self._is_valid_allele(allele + expr_char):
+                    if self._config["verbose_log"]:
+                        print(f"{allele} is not valid. Using {allele}{expr_char}")
+                    allele = allele + expr_char
+                    break
+        return allele
+
     def _sorted_unique_gl(self, gls: List[str], delim: str) -> str:
         """
         Make a list of sorted unique GL Strings separated by delim.
@@ -695,6 +706,9 @@ def _is_valid(self, allele: str) -> bool:
             if not alphanum_allele.isalnum():
                 return False
 
+        if not self._config["strict"]:
+            allele = self._get_non_strict_allele(allele)
+
         if (
             not self.is_mac(allele)
             and not self.is_XX(allele)

tests/features/allele.feature

@@ -72,6 +72,21 @@ Feature: Alleles
       | A*24:329    | lgx   | A*24:329Q    |
       | DQB1*03:276 | lgx   | DQB1*03:01   |
 
+  Scenario Outline: Allele validation in non-strict mode
+
+    Similar to reduction, handle non-strict mode when validating an allele.
+    The test version of IPD/IMGT-HLA database (see environment.py),
+    A*11:403 is invalid and A*24:329 is valid for A*24:329Q
+
+    Given the allele as <Allele>
+    When checking for validity of the allele in non-strict mode
+    Then the validness of the allele is <Validity>
+
+    Examples:
+      | Allele   | Validity |
+      | A*11:403 | Invalid  |
+      | A*24:329 | Valid    |
+
 
   Scenario Outline: Single field MICA, MICB Alleles
 

tests/features/mac.feature

@@ -61,7 +61,7 @@ Feature: MAC (Multiple Allele Code)
 
     Given the MAC code is <MAC>
     When checking for validity of the MAC
-    Then the validness is <Validity>
+    Then the validness of MAC is <Validity>
 
     Examples:
       | MAC          | Validity |

tests/steps/mac.py

@@ -42,7 +42,7 @@ def step_impl(context):
         context.is_valid = False
 
 
-@then("the validness is {validity}")
+@then("the validness of MAC is {validity}")
 def step_impl(context, validity):
     valid = validity == "Valid"
     assert_that(context.is_valid, is_(valid))

tests/steps/redux_allele.py

@@ -112,3 +112,17 @@ def step_impl(context, expanded_alleles):
 def step_impl(context, level):
     context.level = level
     context.redux_allele = context.ard_non_strict.redux(context.allele, level)
+
+
+@when("checking for validity of the allele in non-strict mode")
+def step_impl(context):
+    try:
+        context.is_valid = context.ard_non_strict.validate(context.allele)
+    except InvalidAlleleError:
+        context.is_valid = False
+
+
+@then("the validness of the allele is {validity}")
+def step_impl(context, validity):
+    valid = validity == "Valid"
+    assert_that(context.is_valid, is_(valid))