Merge pull request #15 from cfe-lab/ReformatBBLabAlleles

Incorporated David's suggestion that allows us to eliminate the shim …

Author: va7eex

src/hla_algorithm/hla_algorithm.py

@@ -1,9 +1,9 @@
 import csv
-import os
 from collections.abc import Generator, Iterable, Sequence
 from datetime import datetime
 from io import TextIOBase
 from operator import attrgetter
+from pathlib import Path
 from typing import Final, Optional, TypedDict, cast
 
 import numpy as np
@@ -49,6 +49,8 @@ class HLAAlgorithm:
 
     COLUMN_IDS: Final[dict[str, int]] = {"A": 0, "B": 2, "C": 4}
 
+    DEFAULT_CONFIG_DIR: Final[Path] = Path(__file__).parent / "default_data"
+
     def __init__(
         self,
         loaded_standards: Optional[LoadedStandards] = None,
@@ -136,12 +138,7 @@ def load_default_hla_standards() -> LoadedStandards:
         :return: List of known HLA standards
         :rtype: list[HLAStandard]
         """
-        standards_filename: str = HLAAlgorithm._path_join_shim(
-            os.path.dirname(__file__),
-            "default_data",
-            "hla_standards.yaml",
-        )
-        with open(standards_filename) as standards_file:
+        with open(HLAAlgorithm.DEFAULT_CONFIG_DIR / "hla_standards.yaml") as standards_file:
             return HLAAlgorithm.read_hla_standards(standards_file)
 
     FREQUENCY_LOCUS_COLUMNS: dict[HLA_LOCUS, tuple[str, str]] = {
@@ -194,13 +191,6 @@ def read_hla_frequencies(
                     hla_freqs[locus][protein_pair] += 1
         return hla_freqs
 
-    @staticmethod
-    def _path_join_shim(*args) -> str:
-        """
-        A shim for os.path.join which allows us to mock out the method easily in testing.
-        """
-        return os.path.join(*args)
-
     @staticmethod
     def load_default_hla_frequencies() -> dict[HLA_LOCUS, dict[HLAProteinPair, int]]:
         """
@@ -210,12 +200,7 @@ def load_default_hla_frequencies() -> dict[HLA_LOCUS, dict[HLAProteinPair, int]]
         :rtype: dict[HLA_LOCUS, dict[HLAProteinPair, int]]
         """
         hla_freqs: dict[HLA_LOCUS, dict[HLAProteinPair, int]]
-        default_frequencies_filename: str = HLAAlgorithm._path_join_shim(
-            os.path.dirname(__file__),
-            "default_data",
-            "hla_frequencies.csv",
-        )
-        with open(default_frequencies_filename, "r") as f:
+        with open(HLAAlgorithm.DEFAULT_CONFIG_DIR / "hla_frequencies.csv") as f:
             hla_freqs = HLAAlgorithm.read_hla_frequencies(f)
         return hla_freqs
 

tests/hla_algorithm_test.py

@@ -1781,12 +1781,6 @@ def test_interpret_error_cases(
 }
 
 
-def test_path_join_shim():
-    expected_result: str = "/foo/bar/baz"
-    result: str = HLAAlgorithm._path_join_shim("/foo/bar", "baz")
-    assert expected_result == result
-
-
 @pytest.mark.parametrize(
     "raw_standards, raw_expected_result",
     [
@@ -1900,7 +1894,7 @@ def test_read_hla_standards(
     # Also try reading it from a file.
     p = tmp_path / "hla_standards.yaml"
     p.write_text(standards_file_str)
-    mocker.patch.object(HLAAlgorithm, "_path_join_shim", return_value=str(p))
+    mocker.patch.object(HLAAlgorithm, "DEFAULT_CONFIG_DIR", tmp_path)
     load_result: LoadedStandards = HLAAlgorithm.load_default_hla_standards()
     assert load_result == expected_result
 
@@ -2233,7 +2227,7 @@ def test_read_hla_frequencies(
     # Now try loading these from a file.
     p = tmp_path / "hla_frequencies.csv"
     p.write_text(frequencies_str)
-    mocker.patch.object(HLAAlgorithm, "_path_join_shim", return_value=str(p))
+    mocker.patch.object(HLAAlgorithm, "DEFAULT_CONFIG_DIR", tmp_path)
     load_result: dict[HLA_LOCUS, dict[HLAProteinPair, int]] = (
         HLAAlgorithm.load_default_hla_frequencies()
     )
@@ -2328,11 +2322,7 @@ def test_use_config_all_defaults(
     freq_path: Path = tmp_path / "hla_frequencies.csv"
     freq_path.write_text(fake_frequencies_str)
 
-    mocker.patch.object(
-        HLAAlgorithm,
-        "_path_join_shim",
-        side_effect=[os.fspath(standards_path), os.fspath(freq_path)],
-    )
+    mocker.patch.object(HLAAlgorithm, "DEFAULT_CONFIG_DIR", tmp_path)
 
     hla_algorithm: HLAAlgorithm = HLAAlgorithm.use_config()