CU-869574kvp: Fix preprocessing tests.

Add patch for files/folders where applicable.
Change the paths of attributes where applicable.

tests/utils/test_preprocess_snomed.py

@@ -1,8 +1,11 @@
 import os
 from typing import Dict
+import contextlib
+
 from medcat.utils import preprocess_snomed
 
 import unittest
+from unittest.mock import patch
 
 
 EXAMPLE_REFSET_DICT: Dict = {
@@ -46,22 +49,51 @@ def test_example_no_codfe_fails(self):
         with self.assertRaises(KeyError):
             preprocess_snomed.get_direct_refset_mapping(EXAMPLE_REFSET_DICT_NO_CODE)
 
+
 EXAMPLE_SNOMED_PATH_OLD = "SnomedCT_InternationalRF2_PRODUCTION_20220831T120000Z"
 EXAMPLE_SNOMED_PATH_NEW = "SnomedCT_UKClinicalRF2_PRODUCTION_20231122T000001Z"
 
 
-class TestSnomedVersionsOPCS4(unittest.TestCase):
+@contextlib.contextmanager
+def patch_fake_files(path: str, subfiles: list = [],
+                     subdirs: list = ["Snapshot"]):
+    def cur_listdir(file_path: str, *args, **kwargs) -> list:
+        if file_path == path:
+            return subfiles + subdirs
+        for sd in subdirs:
+            subdir = os.path.join(path, sd)
+            if subdir == path:
+                return []
+        raise FileNotFoundError(path)
 
-    def test_old_gets_old_OPCS4_mapping_nonuk_ext(self):
-        snomed = preprocess_snomed.Snomed(EXAMPLE_SNOMED_PATH_OLD, uk_ext=False)
-        self.assertEqual(snomed.opcs_refset_id, "1126441000000105")
+    def cur_isfile(file_path: str, *args, **kwargs) -> bool:
+        print("CUR isfile", file_path)
+        return file_path == path or file_path in [os.path.join(path, subfiles)]
+
+    def cur_isdir(file_path: str, *args, **kwrags) -> bool:
+        print("CUR isdir", file_path)
+        return file_path == path or file_path in [os.path.join(path, subdirs)]
+
+    with patch("os.listdir", new=cur_listdir):
+        with patch("os.path.isfile", new=cur_isfile):
+            with patch("os.path.isdir", new=cur_isdir):
+                yield
+
+
+class TestSnomedVersionsOPCS4(unittest.TestCase):
 
-    def test_old_gets_old_OPCS4_mapping_uk_ext(self):
-        snomed = preprocess_snomed.Snomed(EXAMPLE_SNOMED_PATH_OLD, uk_ext=True)
+    def test_old_gets_old_OPCS4_mapping(self):
+        with patch_fake_files(EXAMPLE_SNOMED_PATH_OLD):
+            snomed = preprocess_snomed.Snomed(EXAMPLE_SNOMED_PATH_OLD)
+        snomed._set_extension(snomed._determine_release(EXAMPLE_SNOMED_PATH_OLD),
+                              snomed._determine_extension(EXAMPLE_SNOMED_PATH_OLD))
         self.assertEqual(snomed.opcs_refset_id, "1126441000000105")
 
-    def test_new_gets_new_OCPS4_mapping_uk_ext(self):
-        snomed = preprocess_snomed.Snomed(EXAMPLE_SNOMED_PATH_NEW, uk_ext=True)
+    def test_new_gets_new_OCPS4_mapping(self):
+        with patch_fake_files(EXAMPLE_SNOMED_PATH_NEW):
+            snomed = preprocess_snomed.Snomed(EXAMPLE_SNOMED_PATH_NEW)
+        snomed._set_extension(snomed._determine_release(EXAMPLE_SNOMED_PATH_NEW),
+                              snomed._determine_extension(EXAMPLE_SNOMED_PATH_NEW))
         self.assertEqual(snomed.opcs_refset_id, "1382401000000109")
 
 
@@ -86,15 +118,19 @@ def _pathify(self, in_list: list) -> list:
         return [os.path.join(self.PATH, folder) for folder in in_list]
 
     def assert_got_version(self, snomed: preprocess_snomed.Snomed, raw_name: str):
-        rel = snomed.release
+        rel_list = snomed.snomed_releases
+        self.assertIsInstance(rel_list, list)
+        self.assertEqual(len(rel_list), 1)
+        rel = rel_list[0]
         self.assertIsInstance(rel, str)
         self.assertIn(rel, raw_name)
         self.assertEqual(rel, raw_name[-16:-8])
 
     def assert_all_work(self, all_paths: list):
         for path in all_paths:
             with self.subTest(f"Rrelease name: {path}"):
-                snomed = preprocess_snomed.Snomed(path)
+                with patch_fake_files(path):
+                    snomed = preprocess_snomed.Snomed(path)
                 self.assert_got_version(snomed, path)
 
     def test_gets_model_form_basename(self):
@@ -123,8 +159,8 @@ def test_fails_on_incorrect_paths_strict(self):
     def assert_all_get_no_version(self, folder_paths: list):
         for folder_path in folder_paths:
             with self.subTest(f"Folder: {folder_path}"):
-                snomed = preprocess_snomed.Snomed(folder_path)
-                self.assertEqual(snomed.release, preprocess_snomed.Snomed.NO_VERSION_DETECTED)
+                det_rel = preprocess_snomed.Snomed._determine_release(folder_path, strict=False)
+                self.assertEqual(det_rel, preprocess_snomed.Snomed.NO_VERSION_DETECTED)
 
     def test_gets_no_version_incorrect_names_nonstrict(self):
         self.assert_all_get_no_version(self.FAILING_BASE_NAMES)