"""Module contains tests for slink""" import unittest from unittest import TestCase from gn3.computations.slink import slink from gn3.computations.slink import nearest from gn3.computations.slink import LengthError from gn3.computations.slink import MirrorError class TestSlink(TestCase): """Class for testing slink functions""" def test_nearest_expects_list_of_lists(self): # This might be better handled with type-hints and mypy for item in [9, "some string", 5.432, [1,2,3], ["test", 7.4]]: with self.subTest(item=item): with self.assertRaises(ValueError, msg="Expected list or tuple"): nearest(item, 1, 1) def test_nearest_does_not_allow_empty_lists(self): for lst in [[], [[],[]], [[],[],[]], [[0, 1, 2],[],[1, 2, 0]]]: with self.subTest(lst=lst): with self.assertRaises(ValueError): nearest(lst, 1, 1) def test_nearest_expects_exception_if_all_child_lists_are_not_of_equal_length_to_length_of_parent_list(self): for lst in [[[0,1]], [[0,1,2],[3,4,5]], [[0,1,2,3],[4,5,6],[7,8,9,0]], [[0,1,2,3,4],[5,6,7,8,9],[1,2,3,4,5],[2,3],[3,4,5,6,7]]]: with self.subTest(lst=lst): with self.assertRaises(LengthError): nearest(lst, 1, 1) def test_nearest_expects_exception_if_distance_of_child_from_itself_is_not_zero(self): for lst in [[[1]], [[1,2],[3,4]], [1,0,0],[0,0,5],[0,3,4], [0,0,0,0],[0,0,3,3],[0,1,2,3],[0,3,2,0]]: with self.subTest(lst=lst): with self.assertRaises(ValueError): nearest(lst, 1, 1) def test_nearest_expects_exception_if_distance_from_child_a_to_child_b_is_not_distance_from_child_b_to_child_a(self): for lst in [[[0,1],[2,0]], [[0,1,2],[1,0,3],[9,7,0]], [[0,1,2,3],[7,0,2,3],[2,3,0,1],[8,9,5,0]]]: with self.subTest(lst=lst): with self.assertRaises(MirrorError): nearest(lst, 1, 1) def test_nearest_expects_zero_or_positive_distances(self): # Based on: # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89 for lst in [[[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]], [[0,1,-2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]], [[0,1,2,3],[1,0,-3,4],[2,-3,0,5],[3,4,5,0]], [[0,1,2,-3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]], [[0,1,2,3],[1,0,3,-4],[2,3,0,5],[3,-4,5,0]], [[0,1,2,3],[1,0,3,4],[2,3,0,-5],[3,4,-5,0]]]: with self.subTest(lst=lst): with self.assertRaises(ValueError, msg="Distances should be positive."): nearest(lst, 1, 1) def test_nearest_returns_shortest_distance_given_coordinates_to_both_group_members(self): # This test is named wrong - at least I think it is, from the expected results # This tests distance when both `i`, and `j` are integers # We still need to add tests for when (either one/both) (is/are) not (an) integer(s) # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L39-L40 for lst, i, j, expected in [[[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 0,0,0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 0,1,9], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 0,2,3], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 0,3,6], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 0,4,11], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 1,0,9], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 1,1,0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 1,2,7], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 1,3,5], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 1,4,10], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 2,0,3], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 2,1,7], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 2,2,0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 2,3,9], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 2,4,2], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 3,0,6], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 3,1,5], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 3,2,9], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 3,3,0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 3,4,8], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 4,0,11], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 4,1,10], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 4,2,2], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 4,3,8], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], 4,4,0], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 0,0,0], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 0,1,9], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 0,2,5.5], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 0,3,6], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 0,4,11], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 1,0,9], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 1,1,0], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 1,2,7], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 1,3,5], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 1,4,10], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 2,0,5.5], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 2,1,7], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 2,2,0], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 2,3,9], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 2,4,2], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 3,0,6], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 3,1,5], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 3,2,9], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 3,3,0], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 3,4,3], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 4,0,11], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 4,1,10], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 4,2,2], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 4,3,3], [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], 4,4,0]]: with self.subTest(lst=lst): self.assertEqual(nearest(lst, i, j), expected) def test_given_a_list_or_tuple_of_members_distances_and_a_coordinate_find_closest_member_to_member_at_coordinate(self): for md, ml, mc, ed in [ [[[0,9,3],[9,0,7],[3,7,0]],(0,2,3),1,7], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,3,4],3,0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,4],3,5], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,2,4],3,6], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[2,4],3,9]]: with self.subTest( members_distances=md, members_list=ml, member_coordinate=mc, expected_distance=ed): self.assertEqual(nearest(md, ml, mc), ed) self.assertEqual(nearest(md, mc, ml), ed) def test_given_2_lists_or_tuples_of_members_distances_nearest_returns_shortest_distance(self): for md, ml, mc, ed in [ [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], [0,1,2,3,4],[0,1,2,3,4],0], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], [0,1],[3,4],6], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], [0,1],[2,3,4],3], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], [0,2],[3,4],6]]: with self.subTest( members_distances=md, members_list=ml, member_coordinate=mc, expected_distance=ed): self.assertEqual(nearest(md, ml, mc), ed) self.assertEqual(nearest(md, mc, ml), ed) def test_slink_wrong_data_returns_empty_list(self): for data in [1, "test", [], 2.945, nearest, [0]]: with self.subTest(data=data): self.assertEqual(slink(data), []) def test_slink_with_data(self): for data, expected in [ [[[0,9],[9,0]],[0,1,9]], [[[0,9,3],[9,0,7],[3,7,0]],[(0,2,3),1,7]], [[[0,9,3,6],[9,0,7,5],[3,7,0,9],[6,5,9,0]],[(0,2,3),(1,3,5),6]], [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8], [11,10,2,8,0]], [(0,(2,4,2),3),(1,3,5),6]]]: with self.subTest(data=data): self.assertEqual(slink(data), expected)