feat: add __init__, TestOverlapConsolidation suite

test/__init__.py

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+"""Test cases for highlight generator"""

test/test_consolidate.py

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+"""Test consolidators
+
+Consolidators work on a List of Faetures, and Features a constructed from Interval objects.
+As such, we need to mock an Interval object and a Feature object to test the consolidators.
+"""
+import unittest
+from pipeline.consolidators import OverlapConsolidator
+
+
+class TestOverlapConsolidation(unittest.TestCase):
+    """overlap consolidator only uses Interval .start and .end attributes, so we can mock them here"""
+    class MockInterval():
+        """Mock interval object for overlap testing -- only has start and end attributes"""
+        def __init__(self, start, end):
+            self.start = start
+            self.end = end
+    class MockFeature():
+        """Mock feature object for overlap testing -- only has interval attribute"""
+        def __init__(self, interval):
+            self.interval = interval
+
+    def setUp(self):
+        """Set up test data"""
+        self.empty_features = []
+        self.fakepath = "/tmp/fakepath"
+        self.featureA = self.MockFeature(interval=self.MockInterval(start=0, end=10))
+        self.featureB = self.MockFeature(interval=self.MockInterval(start=5, end=15))
+        self.populated_features = [self.featureA, self.featureB]
+
+    def test_init(self):
+        # test empty features
+        with self.assertRaises(ValueError):
+            OverlapConsolidator(self.empty_features)
+        # test populated features
+        consolidator = OverlapConsolidator(features=self.populated_features)
+        self.assertEqual(consolidator.features, self.populated_features)
+
+    def test_consolidate(self):
+        # 4 features for overlap test: ABCD, overlap A-B, C-D
+        self.featureA = self.MockFeature(interval=self.MockInterval(start=0, end=10))
+        self.featureB = self.MockFeature(interval=self.MockInterval(start=5, end=15))
+        self.featureC = self.MockFeature(interval=self.MockInterval(start=20, end=30))
+        self.featureD = self.MockFeature(interval=self.MockInterval(start=25, end=35))
+        self.overlapping_features = [self.featureA, self.featureB, self.featureC, self.featureD]
+        consolidator = OverlapConsolidator(features=self.overlapping_features)
+        consolidator.consolidate()
+        # check that A-B and C-D have been merged
+        self.assertEqual(len(consolidator.features), 2)
+
+        # 4 features for no overlap test
+        self.feature1 = self.MockFeature(interval=self.MockInterval(start=0, end=10))
+        self.feature2 = self.MockFeature(interval=self.MockInterval(start=15, end=25))
+        self.feature3 = self.MockFeature(interval=self.MockInterval(start=30, end=40))
+        self.feature4 = self.MockFeature(interval=self.MockInterval(start=45, end=55))
+        self.non_overlapping_features = [self.feature1, self.feature2, self.feature3, self.feature4]
+        consolidator = OverlapConsolidator(features=self.non_overlapping_features)
+        consolidator.consolidate()
+        # check that no features have been merged
+        self.assertEqual(len(consolidator.features), 4)
+
+        # 3 features for overlap test: ABC, overlap A-B, B-C
+        self.featureA = self.MockFeature(interval=self.MockInterval(start=0, end=10))
+        self.featureB = self.MockFeature(interval=self.MockInterval(start=5, end=15))
+        self.featureC = self.MockFeature(interval=self.MockInterval(start=12, end=20))
+        self.overlapping_features = [self.featureA, self.featureB, self.featureC]
+        consolidator = OverlapConsolidator(features=self.overlapping_features)
+        consolidator.consolidate()
+        # check that A-B and B-C have been merged
+        self.assertEqual(len(consolidator.features), 1)
+
+if __name__ == '__main__':
+    unittest.main()