From a5d4868c6d2f38d3e6fd0409e08413c3569ce356 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Wed, 21 Jul 2021 08:44:09 +0300 Subject: Extract tests from code in GN1 Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add dummy `nearest' function * tests/unit/computations/test_slink.py: Add some tests This commit adds tests to try and reproduce the working of the `nearest' function in: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py This commit might not yet have extracted all the expected behaviour of the `nearest' function, and therefore, there is a possibility of a later commit augmenting the work in this commit. --- gn3/computations/slink.py | 8 ++ tests/unit/computations/test_slink.py | 175 ++++++++++++++++++++++++++++++++++ 2 files changed, 183 insertions(+) create mode 100644 gn3/computations/slink.py create mode 100644 tests/unit/computations/test_slink.py diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py new file mode 100644 index 0000000..bec8597 --- /dev/null +++ b/gn3/computations/slink.py @@ -0,0 +1,8 @@ +class LengthError(BaseException): + pass + +class MirrorError(BaseException): + pass + +def nearest(lists, i, j): + return None diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py new file mode 100644 index 0000000..816cd2f --- /dev/null +++ b/tests/unit/computations/test_slink.py @@ -0,0 +1,175 @@ +"""Module contains tests for slink""" +import unittest +from unittest import TestCase + +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_there_is_no_zero_at_childs_list_index_corresponding_to_its_index_in_parent(self): + # I don't like the name of this test. Make the name clearer + 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_value_at_index_j_in_list_i_does_not_equals_value_at_index_i_in_list_j(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]], + [[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="Got an unexpected negative value!"): + nearest(lst, 1, 1) + + def test_nearest_with_expected(self): + # Give this test a better name + # The lists in this tests are taken from: + # 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) -- cgit v1.2.3