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"""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)
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