Merge pull request #273 from pbashyal-nmdp/add_strict_flag

Add non-strict mode

Author: mmaiers-nmdp

Dockerfile

@@ -4,7 +4,7 @@ LABEL MAINTAINER="Pradeep Bashyal"
 
 WORKDIR /app
 
-ARG PY_ARD_VERSION=1.0.4
+ARG PY_ARD_VERSION=1.0.5
 
 COPY requirements.txt /app
 RUN pip install --no-cache-dir --upgrade pip && \

api-spec.yaml

@@ -2,7 +2,7 @@ openapi: 3.0.3
 info:
   title: ARD Reduction
   description: Reduce to ARD Level
-  version: "1.0.4"
+  version: "1.0.5"
 servers:
   - url: 'http://localhost:8080'
 tags:

pyard/__init__.py

@@ -27,7 +27,7 @@
 from .misc import get_imgt_db_versions as db_versions
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = "1.0.4"
+__version__ = "1.0.5"
 
 
 def init(

pyard/ard.py

@@ -54,8 +54,9 @@
     "reduce_shortnull": True,
     "ping": False,
     "map_drb345_to_drbx": True,
-    "verbose_log": True,
+    "verbose_log": False,
     "ARS_as_lg": False,
+    "strict": True,
 }
 
 
@@ -181,6 +182,15 @@ 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
+
         # g_group maps alleles to their g_group
         # note: this includes mappings for shortened version of alleles
         # C*12:02:02:01 => C*12:02:01G
@@ -335,7 +345,8 @@ def redux(self, glstring: str, redux_type: VALID_REDUCTION_TYPES) -> str:
 
         validate_reduction_type(redux_type)
 
-        self.validate(glstring)
+        if self._config["strict"]:
+            self.validate(glstring)
 
         if "^" in glstring:
             return self._sorted_unique_gl(

scripts/pyard

@@ -76,12 +76,29 @@ if __name__ == "__main__":
     parser.add_argument(
         "--lookup-mac", dest="lookup_mac", help="Lookup MAC for an Allele List"
     )
+    parser.add_argument(
+        "--non-strict",
+        dest="non_strict",
+        action="store_true",
+        help="Use non-strict mode",
+    )
+    parser.add_argument(
+        "--verbose", dest="verbose", action="store_true", help="Use verbose mode"
+    )
 
     args = parser.parse_args()
 
     imgt_version = get_imgt_version(args.imgt_version)
     data_dir = get_data_dir(args.data_dir)
-    ard = pyard.init(imgt_version=imgt_version, data_dir=data_dir)
+
+    new_config = {}
+    if args.non_strict:
+        new_config["strict"] = False
+
+    if args.verbose:
+        new_config["verbose_log"] = True
+
+    ard = pyard.init(imgt_version=imgt_version, data_dir=data_dir, config=new_config)
 
     if args.version:
         version = ard.get_db_version()
@@ -114,8 +131,8 @@ if __name__ == "__main__":
         sys.exit(0)
 
     try:
-        if args.validate:
-            ard.validate(args.cwd)
+        if args.validate and args.gl_string:
+            ard.validate(args.gl_string)
         if args.cwd:
             if args.validate:
                 ard.validate(args.cwd)

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.4
+current_version = 1.0.5
 commit = True
 tag = True
 

setup.py

@@ -36,7 +36,7 @@
 
 setup(
     name="py-ard",
-    version="1.0.4",
+    version="1.0.5",
     description="ARD reduction for HLA with Python",
     long_description=readme,
     long_description_content_type="text/markdown",

tests/environment.py

@@ -36,3 +36,9 @@ def before_all(context):
         "ARS_as_lg": True,
     }
     context.ard_ars = pyard.init("3440", data_dir="/tmp/py-ard", config=lg_ars_config)
+
+    # use non-strict mode
+    non_strict_config = {"strict": False}
+    context.ard_non_strict = pyard.init(
+        "3440", data_dir="/tmp/py-ard", config=non_strict_config
+    )

tests/features/allele.feature

@@ -57,3 +57,17 @@ Feature: Alleles
       | DRB1*14:06:01  | lg    | DRB1*14:06ARS  |
       | C*02:02        | lg    | C*02:02ARS     |
       | C*02:10        | lg    | C*02:02ARS     |
+
+  Scenario Outline: Allele reduction in non-strict mode
+
+  The canon of HLA Nomenclature includes Deleted Alleles like A*24:329 that were renamed to add an expression character. https://hla.alleles.org/alleles/deleted.html
+  Such alleles can be included by using non-strict mode where py-ard will try alleles with expression characters when the original allele is not valid
+
+    Given the allele as <Allele>
+    When reducing on the <Level> level in non-strict mode
+    Then the reduced allele is found to be <Redux Allele>
+
+    Examples:
+      | Allele      | Level | Redux Allele |
+      | A*24:329    | lgx   | A*24:329Q    |
+      | DQB1*03:276 | lgx   | DQB1*03:01   |

tests/steps/redux_allele.py

@@ -92,3 +92,9 @@ def step_impl(context, level):
 @then("the expanded allele is found to be {expanded_alleles}")
 def step_impl(context, expanded_alleles):
     assert_that(context.expanded_alleles, is_(expanded_alleles))
+
+
+@when("reducing on the {level} level in non-strict mode")
+def step_impl(context, level):
+    context.level = level
+    context.redux_allele = context.ard_non_strict.redux(context.allele, level)