Consolidate HLA- prefix handling

Clean up imports

Author: pbashyal-nmdp

pyard/ard.py

@@ -28,11 +28,9 @@
 from collections import Counter
 from typing import Iterable, List, Union
 
-import pyard.serology
 from . import data_repository as dr
 from . import db
 from . import smart_sort
-from .serology import SerologyMapping
 from .constants import (
     HLA_regex,
     VALID_REDUCTION_TYPES,
@@ -47,6 +45,7 @@
     is_2_field_allele,
     validate_reduction_type,
 )
+from .serology import SerologyMapping
 
 default_config = {
     "reduce_serology": True,

pyard/ard_refactored.py

@@ -159,16 +159,6 @@ def _redux_allele(
         self, allele: str, redux_type: VALID_REDUCTION_TYPE, re_ping=True
     ) -> str:
         """Core allele reduction with ping logic"""
-        # Handle HLA- prefix
-        if HLA_regex.search(allele):
-            hla, allele_name = allele.split("-")
-            redux_allele = self._redux_allele(allele_name, redux_type)
-            if redux_allele:
-                if "/" in redux_allele:
-                    return "/".join([f"HLA-{ra}" for ra in redux_allele.split("/")])
-                return f"HLA-{redux_allele}"
-            return redux_allele
-
         if not self._config["strict"]:
             allele = self._get_non_strict_allele(allele)
 
@@ -217,31 +207,32 @@ def redux(self, glstring: str, redux_type: VALID_REDUCTION_TYPE = "lgx") -> str:
         if processed_gl != glstring or self.is_glstring(processed_gl):
             return processed_gl
 
+        # Remove HLA- prefix for processing the allele
+        is_hla_prefix = HLA_regex.search(glstring)
+        if is_hla_prefix:
+            allele = glstring.split("-")[1]
+        else:
+            allele = glstring
         # Handle ignored allele suffixes
         if self._config["ignore_allele_with_suffixes"]:
-            _, fields = glstring.split("*")
+            _, fields = allele.split("*")
             if fields in self._config["ignore_allele_with_suffixes"]:
-                return glstring
+                return allele
 
         # Handle V2 to V3 mapping
-        if self.v2_handler.is_v2(glstring):
-            glstring = self.v2_handler.map_v2_to_v3(glstring)
-            return self.redux(glstring, redux_type)
+        if self.v2_handler.is_v2(allele):
+            allele = self.v2_handler.map_v2_to_v3(allele)
+            return self.redux(allele, redux_type)
 
         # Handle Serology
         if self._config["reduce_serology"] and self.serology_handler.is_serology(
-            glstring
+            allele
         ):
-            alleles = self.serology_handler.get_alleles_from_serology(glstring)
+            alleles = self.serology_handler.get_alleles_from_serology(allele)
             if alleles:
                 return self.redux("/".join(alleles), redux_type)
             return ""
 
-        is_hla_prefix = HLA_regex.search(glstring)
-        if is_hla_prefix:
-            allele = glstring.split("-")[1]
-        else:
-            allele = glstring
         # Validate format
         if ":" in allele:
             loc_allele = allele.split(":")
@@ -259,7 +250,7 @@ def redux(self, glstring: str, redux_type: VALID_REDUCTION_TYPE = "lgx") -> str:
             if "*" in allele:
                 locus, _ = allele.split("*")
                 if locus not in G_GROUP_LOCI:
-                    return glstring
+                    return allele
             raise InvalidTypingError(
                 f"{glstring} is not a valid V2 or Serology typing."
             )
@@ -289,11 +280,17 @@ def redux(self, glstring: str, redux_type: VALID_REDUCTION_TYPE = "lgx") -> str:
 
         # Handle short nulls
         if self._config["reduce_shortnull"] and self.shortnull_handler.is_shortnull(
-            glstring
+            allele
         ):
-            return self.redux("/".join(self.shortnulls[glstring]), redux_type)
+            return self.redux("/".join(self.shortnulls[allele]), redux_type)
 
-        return self._redux_allele(glstring, redux_type)
+        redux_allele = self._redux_allele(allele, redux_type)
+        # Add back 'HLA-' prefix when redux is done if needed
+        if is_hla_prefix:
+            if "/" in redux_allele:
+                return "/".join([f"HLA-{ra}" for ra in redux_allele.split("/")])
+            redux_allele = f"HLA-{redux_allele}"
+        return redux_allele
 
     @staticmethod
     def is_glstring(gl_string: str) -> bool:

pyard/data_repository.py

@@ -23,24 +23,18 @@
 import copy
 import functools
 import sqlite3
-import itertools
 
 import pyard.loader
 import pyard.loader.cwd
 import pyard.loader.mac_codes
 import pyard.loader.serology
-from pyard.smart_sort import smart_sort_comparator
 from . import db
 from .constants import expression_chars
 from .loader.allele_list import load_allele_list
+from .loader.g_group import load_g_group
+from .loader.p_group import load_p_group
 from .loader.serology import load_serology_mappings, load_serology_broad_split_mapping
 from .loader.version import load_latest_version
-
-from .loader.p_group import load_p_group
-from .loader.g_group import load_g_group
-
-from .simple_table import Table
-
 from .mappings import (
     ars_mapping_tables,
     ARSMapping,
@@ -56,6 +50,7 @@
     get_1field_allele,
 )
 from .serology import broad_splits_dna_mapping, SerologyMapping
+from .simple_table import Table
 from .smart_sort import smart_sort_comparator
 
 

pyard/handlers/__init__.py

@@ -4,9 +4,9 @@
 from .gl_string_processor import GLStringProcessor
 from .mac_handler import MACHandler
 from .serology_handler import SerologyHandler
+from .shortnull_handler import ShortNullHandler
 from .v2_handler import V2Handler
 from .xx_handler import XXHandler
-from .shortnull_handler import ShortNullHandler
 
 __all__ = [
     "AlleleReducer",

pyard/handlers/mac_handler.py

@@ -5,9 +5,9 @@
 from collections import Counter
 from typing import Iterable, TYPE_CHECKING
 
+from .. import db
 from ..constants import HLA_regex, DEFAULT_CACHE_SIZE
 from ..exceptions import InvalidMACError
-from .. import db
 
 if TYPE_CHECKING:
     from ..ard import ARD

pyard/handlers/serology_handler.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 from typing import Iterable, TYPE_CHECKING
+
 from .. import db
 
 if TYPE_CHECKING:

pyard/handlers/v2_handler.py

@@ -2,6 +2,7 @@
 
 import re
 from typing import TYPE_CHECKING
+
 from .. import db
 
 if TYPE_CHECKING:

pyard/loader/allele_list.py

@@ -1,9 +1,10 @@
-from urllib.request import urlopen
-from urllib.error import URLError
 import csv
 import sys
-from ..simple_table import Table
+from urllib.error import URLError
+from urllib.request import urlopen
+
 from ..loader import IMGT_HLA_URL
+from ..simple_table import Table
 
 
 def load_allele_list(imgt_version):

pyard/loader/cwd.py

@@ -1,5 +1,5 @@
-import os
 import csv
+import os
 
 
 def load_cwd2():

pyard/loader/mac_codes.py

@@ -1,8 +1,9 @@
+import io
 import sys
+import zipfile
 from urllib.error import URLError
 from urllib.request import urlopen
-import zipfile
-import io
+
 from ..simple_table import Table