test: Add unit tests

tests/test_value_matching.py

@@ -1,56 +1,97 @@
-import unittest
-import pandas as pd
 from bdikit.value_matching.polyfuzz import (
     TFIDFValueMatcher,
     EditDistanceValueMatcher,
+    FastTextValueMatcher,
+    EmbeddingValueMatcher,
 )
 
+from bdikit.value_matching.gene import Gene
 
-class ValueMatchingTest(unittest.TestCase):
 
-    def test_tfidf_value_matching(self):
+def test_textual_transformation_matching():
+    threshold = 0.5
+    for value_matcher in [
+        TFIDFValueMatcher(threshold=threshold),
+        EditDistanceValueMatcher(threshold=threshold),
+    ]:
+
         # given
-        source_values = ["Red Apple", "Banana", "Oorange", "Strawberry"]
+        source_values = ["Red Apple", "Banana", "Oorange", "dragon-fruits"]
         target_values = ["apple", "banana", "orange", "kiwi"]
 
-        tfidf_matcher = TFIDFValueMatcher()
-
         # when
-        matches = tfidf_matcher.match(source_values, target_values)
+        matches = value_matcher.match(source_values, target_values)
 
         # then
-        self.assertEqual(len(matches), 3)
+        assert len(matches) == 3
 
         mapped_matches = {match[0]: (match[1], match[2]) for match in matches}
-        self.assertNotIn("Strawberry", mapped_matches)
-        self.assertEqual(mapped_matches["Red Apple"][0], "apple"),
-        self.assertEqual(mapped_matches["Banana"][0], "banana"),
-        self.assertEqual(mapped_matches["Oorange"][0], "orange")
+        assert "dragon-fruits" not in mapped_matches
+        assert mapped_matches["Red Apple"][0] == "apple"
+        assert mapped_matches["Banana"][0] == "banana"
+        assert mapped_matches["Oorange"][0] == "orange"
 
         scores = [match[2] for match in matches]
-        self.assertTrue(all(score > 0.8 for score in scores))
+        assert all(score > threshold for score in scores)
 
-    def test_edit_distance_value_matching(self):
-        # given
-        source_values = ["Red Apple", "Banana", "Oorange", "Strawberry"]
-        target_values = ["apple", "bananana", "orange", "kiwi"]
 
-        edit_distance_matcher = EditDistanceValueMatcher(threshold=0.5)
+def test_semantic_matching():
+    threshold = 0.4
+    value_matcher = FastTextValueMatcher(threshold=threshold)
 
-        # when
-        matches = edit_distance_matcher.match(
-            source_values,
-            target_values,
-        )
+    # given
+    source_values = ["Computer", "Display", "Pencil"]
+    target_values = ["PC", "Monitor", "Football field"]
 
-        # then
-        self.assertEqual(len(matches), 3)
+    # when
+    matches = value_matcher.match(source_values, target_values)
 
-        mapped_matches = {match[0]: (match[1], match[2]) for match in matches}
-        self.assertNotIn("Strawberry", mapped_matches)
-        self.assertEqual(mapped_matches["Red Apple"][0], "apple"),
-        self.assertEqual(mapped_matches["Banana"][0], "bananana"),
-        self.assertEqual(mapped_matches["Oorange"][0], "orange")
+    # then
+    assert len(matches) == 2
 
-        scores = [match[2] for match in matches]
-        self.assertTrue(all(score > 0.5 for score in scores))
+    mapped_matches = {match[0]: (match[1], match[2]) for match in matches}
+    assert "Pencil" not in mapped_matches
+    assert mapped_matches["Computer"][0] == "PC"
+    assert mapped_matches["Display"][0] == "Monitor"
+
+    scores = [match[2] for match in matches]
+    assert all(score > threshold for score in scores)
+
+    threshold = 0.6
+    value_matcher = EmbeddingValueMatcher(threshold=threshold)
+
+    # given
+    source_values = ["Computer", "Display", "Pencil"]
+    target_values = ["PC", "Monitor", "Football field"]
+
+    # when
+    matches = value_matcher.match(source_values, target_values)
+
+    # then
+    assert len(matches) == 2
+
+    mapped_matches = {match[0]: (match[1], match[2]) for match in matches}
+    assert "Pencil" not in mapped_matches
+    assert mapped_matches["Computer"][0] == "PC"
+    assert mapped_matches["Display"][0] == "Monitor"
+
+    scores = [match[2] for match in matches]
+    assert all(score > threshold for score in scores)
+
+
+def test_gene_matching():
+    # given
+    gene_matcher = Gene()
+    source_values = ["ENSMUSG00000064341", "ENSMUSG00000064345", "ENSMUSG00000064351"]
+    target_values = ["ENSG00000198763", "ENSG00000198888", "ENSG000000000000X"]
+
+    # when
+    matches = gene_matcher.match(source_values, target_values)
+
+    # then
+    assert len(matches) == 2
+
+    mapped_matches = {match[0]: (match[1], match[2]) for match in matches}
+    assert "ENSG000000000000X" not in mapped_matches
+    assert mapped_matches["ENSMUSG00000064341"][0] == "ENSG00000198888"
+    assert mapped_matches["ENSMUSG00000064345"][0] == "ENSG00000198763"