itproject-code/test/test_consolidate.py

"""Test consolidators

Consolidators work on a List of Features, and Features are 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

        def move_end(self, new_end):
            """Mocked method to move the end of the interval"""
            self.end = new_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 (2)
        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 (4)
        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 (1)
        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()