Merge pull request #297 from pbashyal-nmdp/fix-serology-sort

Fix serology sort

Author: mmaiers-nmdp

Dockerfile

@@ -4,7 +4,7 @@ LABEL MAINTAINER="Pradeep Bashyal"
 
 WORKDIR /app
 
-ARG PY_ARD_VERSION=1.0.9
+ARG PY_ARD_VERSION=1.0.10
 
 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: "1.0.9"
+  version: "1.0.10"
 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__ = "1.0.9"
+__version__ = "1.0.10"
 
 
 def init(

pyard/smart_sort.py

@@ -28,6 +28,7 @@
 
 expr_regex = re.compile("[PNQLSGg]")
 glstring_chars = re.compile("[/|+^~]")
+serology_splitter = re.compile(r"(\D+)(\d+)")
 
 
 @functools.lru_cache(maxsize=constants.DEFAULT_CACHE_SIZE)
@@ -63,7 +64,11 @@ def smart_sort_comparator(a1, a2):
 
     # Handle serology
     if ":" not in a1:
-        return 1 if a1 > a2 else -1
+        serology1_match = serology_splitter.match(a1)
+        serology1_num = int(serology1_match.group(2))
+        serology2_match = serology_splitter.match(a2)
+        serology2_num = int(serology2_match.group(2))
+        return 1 if serology1_num > serology2_num else -1
 
     # Extract and Compare 1st fields first
     a1_f1 = int(a1[a1.find("*") + 1 : a1.find(":")])

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.9
+current_version = 1.0.10
 commit = True
 tag = True
 

setup.py

@@ -36,7 +36,7 @@
 
 setup(
     name="py-ard",
-    version="1.0.9",
+    version="1.0.10",
     description="ARD reduction for HLA with Python",
     long_description=readme,
     long_description_content_type="text/markdown",

tests/features/serology_redux.feature

@@ -7,16 +7,20 @@ Feature: Serology Reduction
 
     Given the allele as <Allele>
     When reducing on the <Level> level with ping
-    Then the reduced allele is found to be <Redux Allele>
+    Then the reduced allele is found to be <Redux Serology>
 
-    Examples:
-      | Allele                          | Level | Redux Allele        |
-      | A*01:01:01:01                   | S     | A1                  |
-      | A*01:01                         | S     | A1                  |
-      | A*01:AABJE                      | S     | A1/A36              |
-      | A*03:XX                         | S     | A3                  |
-      | B*44:02:01:11/B*44:02:01:12     | S     | B12/B44             |
-      | B*13:03                         | S     | B13                 |
-      | B*13:04                         | S     | B15/B21             |
-      | B*15:01/B*15:02/B*15:03/B*15:04 | S     | B15/B62/B70/B72/B75 |
-      | B*15:10                         | S     | B15/B70/B71         |
+    Examples: Alleles to Serology
+      | Allele                      | Level | Redux Serology |
+      | A*01:01:01:01               | S     | A1             |
+      | A*01:01                     | S     | A1             |
+      | A*01:AABJE                  | S     | A1/A36         |
+      | A*03:XX                     | S     | A3             |
+      | B*44:02:01:11/B*44:02:01:12 | S     | B12/B44        |
+      | B*13:03                     | S     | B13            |
+      | B*13:04                     | S     | B15/B21        |
+
+    Examples: Serology Sorted Properly
+      | Allele                                   | Level | Redux Serology      |
+      | B*15:01/B*15:02/B*15:03/B*15:04          | S     | B15/B62/B70/B72/B75 |
+      | B*15:10                                  | S     | B15/B70/B71         |
+      | A*24:03/A*24:10/A*24:23/A*24:33/A*24:374 | S     | A9/A24/A2403        |

tests/test_smart_sort.py

@@ -104,6 +104,21 @@ def test_fourth_field_comparator_ge(self):
         allele2 = "HLA-A*01:01:01:09"
         self.assertEqual(smart_sort_comparator(allele1, allele2), 1)
 
+    def test_serology_ge(self):
+        serology1 = "Cw10"
+        serology2 = "Cw3"
+        self.assertEqual(smart_sort_comparator(serology1, serology2), 1)
+
+    def test_serology_le(self):
+        serology1 = "A10"
+        serology2 = "A25"
+        self.assertEqual(smart_sort_comparator(serology1, serology2), -1)
+
+    def test_serology_eq(self):
+        serology1 = "B70"
+        serology2 = "B70"
+        self.assertEqual(smart_sort_comparator(serology1, serology2), 0)
+
 
 if __name__ == "__main__":
     unittest.main()