Minor cleanups

Author: pbashyal-nmdp

api-spec.yaml

@@ -14,6 +14,8 @@ tags:
     description: Expand MAC to alleles
   - name: DRBX Blender
     description: Blend DRBX based on DRB1 and DRB3/4/5
+  - name: Validation
+    description: Validate a GL String or Allele
 paths:
   /version:
     get:
@@ -134,7 +136,7 @@ paths:
   /validate:
     post:
       tags:
-        - ARD Reduction
+        - Validation
       operationId: api.validate_controller
       summary: Validate GL String
       description: |

pyard/__init__.py

@@ -25,6 +25,7 @@
 from .blender import blender as dr_blender
 from .broad_splits import find_splits as find_broad_splits
 from .misc import get_imgt_db_versions as db_versions
+from .misc import DEFAULT_CACHE_SIZE
 
 __author__ = """NMDP Bioinformatics"""
 __version__ = "0.9.1"
@@ -34,7 +35,7 @@ def init(
     imgt_version: str = "Latest",
     data_dir: str = None,
     load_mac: bool = True,
-    cache_size: int = 1_000,
+    cache_size: int = DEFAULT_CACHE_SIZE,
     config: dict = None,
 ):
     from .ard import ARD

pyard/exceptions.py

@@ -3,28 +3,28 @@ class PyArdError(Exception):
     Base Class for All py-ard Errors
     """
 
-    pass
+    def __init__(self, message: str) -> None:
+        self.message = message
 
 
 class InvalidAlleleError(PyArdError):
     def __init__(self, message: str) -> None:
-        self.message = message
+        super().__init__(message)
 
     def __str__(self) -> str:
         return f"Invalid Allele: {self.message}"
 
 
 class InvalidMACError(PyArdError):
     def __init__(self, message: str) -> None:
-        self.message = message
+        super().__init__(message)
 
     def __str__(self) -> str:
         return f"Invalid MAC Code: {self.message}"
 
 
 class InvalidTypingError(PyArdError):
     def __init__(self, message: str, cause=None) -> None:
-        self.message = message
         self.cause = cause
 
     def __str__(self) -> str:

scripts/pyard-import

@@ -30,13 +30,13 @@ from pyard import db, data_repository
 from pyard.misc import get_data_dir
 
 
-def get_imgt_version(imgt_version):
-    if imgt_version:
-        version = imgt_version.replace(".", "")
-        if version.isdigit():
-            return version
+def get_imgt_version(version_number):
+    if version_number:
+        version_no_digit = version_number.replace(".", "")
+        if version_no_digit.isdigit():
+            return version_no_digit
         raise RuntimeError(
-            f"{imgt_version} is not a valid IMGT database version number"
+            f"{version_number} is not a valid IMGT database version number"
         )
     return "Latest"