aboutsummaryrefslogtreecommitdiff
path: root/tests
diff options
context:
space:
mode:
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/computations/test_correlation.py32
-rw-r--r--tests/unit/computations/test_slink.py401
-rw-r--r--tests/unit/db/test_traits.py126
3 files changed, 380 insertions, 179 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 6153c8a..9450094 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -467,26 +467,28 @@ class TestCorrelation(TestCase):
self.assertEqual(results, [expected_results])
def test_compute_correlation(self):
- for dbdata,userdata,expected in [
- [[None,None,None,None,None,None,None,None,None,None],
- [None,None,None,None,None,None,None,None,None,None],
+ """Test that the new correlation function works the same as the original
+ from genenetwork1."""
+ for dbdata, userdata, expected in [
+ [[None, None, None, None, None, None, None, None, None, None],
+ [None, None, None, None, None, None, None, None, None, None],
(0.0, 0)],
- [[None,None,None,None,None,None,None,None,None,0],
- [None,None,None,None,None,None,None,None,None,None],
+ [[None, None, None, None, None, None, None, None, None, 0],
+ [None, None, None, None, None, None, None, None, None, None],
(0.0, 0)],
- [[None,None,None,None,None,None,None,None,None,0],
- [None,None,None,None,None,None,None,None,None,0],
+ [[None, None, None, None, None, None, None, None, None, 0],
+ [None, None, None, None, None, None, None, None, None, 0],
(0.0, 1)],
- [[0,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0],
+ [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
(0, 10)],
- [[9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87],
- [9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87],
+ [[9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87],
+ [9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87],
(0.9999999999999998, 10)],
- [[9.3,2.2,5.4,7.2,6.4,7.6,3.8,1.8,8.4,0.2],
- [0.6,3.97,5.82,8.21,1.65,4.55,6.72,9.5,7.33,2.34],
+ [[9.3, 2.2, 5.4, 7.2, 6.4, 7.6, 3.8, 1.8, 8.4, 0.2],
+ [0.6, 3.97, 5.82, 8.21, 1.65, 4.55, 6.72, 9.5, 7.33, 2.34],
(-0.12720361919462056, 10)],
- [[0,1,2,3,4,5,6,7,8,9],
- [None,None,None,None,2,None,None,3,None,None],
+ [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+ [None, None, None, None, 2, None, None, 3, None, None],
(0.0, 2)]]:
with self.subTest(dbdata=dbdata, userdata=userdata):
- self.assertEqual(compute_correlation(dbdata,userdata), expected)
+ self.assertEqual(compute_correlation(dbdata, userdata), expected)
diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
index 5627767..995393b 100644
--- a/tests/unit/computations/test_slink.py
+++ b/tests/unit/computations/test_slink.py
@@ -1,5 +1,4 @@
"""Module contains tests for slink"""
-import unittest
from unittest import TestCase
from gn3.computations.slink import slink
@@ -11,210 +10,302 @@ class TestSlink(TestCase):
"""Class for testing slink functions"""
def test_nearest_expects_list_of_lists(self):
+ """Test that function only accepts a list of lists."""
# This might be better handled with type-hints and mypy
for item in [9, "some string", 5.432,
- [1,2,3], ["test", 7.4]]:
+ [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):
+ """Test that function does not accept an empty list, or any of the child
+ lists to be empty."""
for lst in [[],
- [[],[]],
- [[],[],[]],
- [[0, 1, 2],[],[1, 2, 0]]]:
+ [[], []],
+ [[], [], []],
+ [[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]]]:
+ def test_nearest_expects_children_are_same_length_as_parent(self):
+ """Test that children lists are same length as parent list."""
+ 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):
+ def test_nearest_expects_member_is_zero_distance_from_itself(self):
+ """Test that distance of a member from itself is zero"""
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]]:
+ [[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]]]:
+ def test_nearest_expects_distance_atob_is_equal_to_distance_btoa(self):
+ """Test that the distance from member A to member B is the same as that
+ from member B to member A."""
+ 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):
+ """Test that all distances are either zero, or greater than zero."""
# 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]]]:
+ 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):
+ """Test that the shortest distance is returned."""
# 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]]:
+ 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]]:
+ def test_nearest_gives_shortest_distance_between_list_of_members_and_member(self):
+ """Test that the shortest distance is returned."""
+ for members_distances, members_list, member_coordinate, expected_distance 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)
+ members_distances=members_distances,
+ members_list=members_list,
+ member_coordinate=member_coordinate,
+ expected_distance=expected_distance):
+ self.assertEqual(
+ nearest(
+ members_distances, members_list, member_coordinate),
+ expected_distance)
+ self.assertEqual(
+ nearest(
+ members_distances, member_coordinate, members_list),
+ expected_distance)
- 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]]:
+ def test_nearest_returns_shortest_distance_given_two_lists_of_members(self):
+ """Test that the shortest distance is returned."""
+ for members_distances, members_list, member_list2, expected_distance 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)
+ members_distances=members_distances,
+ members_list=members_list,
+ member_list2=member_list2,
+ expected_distance=expected_distance):
+ self.assertEqual(
+ nearest(
+ members_distances, members_list, member_list2),
+ expected_distance)
+ self.assertEqual(
+ nearest(
+ members_distances, member_list2, members_list),
+ expected_distance)
def test_slink_wrong_data_returns_empty_list(self):
+ """Test that empty list is returned for wrong data."""
for data in [1, "test", [], 2.945, nearest, [0]]:
with self.subTest(data=data):
self.assertEqual(slink(data), [])
def test_slink_with_data(self):
+ """Test slink with example data, and expected results for each data
+ sample."""
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]]]:
+ [[[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)
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 0e69bbe..c8f28b5 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,12 +1,120 @@
-"""Tests for db/traits.py"""
-from unittest import TestCase
-from unittest import mock
+"""Tests for gn3/db/traits.py"""
+from unittest import mock, TestCase
+from gn3.db.traits import (
+ GENO_TRAIT_INFO_QUERY,
+ TEMP_TRAIT_INFO_QUERY,
+ PUBLISH_TRAIT_INFO_QUERY,
+ PROBESET_TRAIT_INFO_QUERY)
+from gn3.db.traits import (
+ retrieve_trait_info,
+ retrieve_geno_trait_info,
+ retrieve_temp_trait_info,
+ retrieve_trait_dataset_name,
+ retrieve_publish_trait_info,
+ retrieve_probeset_trait_info,
+ update_sample_data)
-from gn3.db.traits import update_sample_data
+class TestTraitsDBFunctions(TestCase):
+ "Test cases for traits functions"
+
+ def test_retrieve_trait_dataset_name(self):
+ """Test that the function is called correctly."""
+ for trait_type, thresh, trait_dataset_name, columns in [
+ ["ProbeSet", 9, "testName",
+ "Id, Name, FullName, ShortName, DataScale"],
+ ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"],
+ ["Publish", 6, "publishTraitName",
+ "Id, Name, FullName, ShortName"],
+ ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]:
+ db_mock = mock.MagicMock()
+ with self.subTest(trait_type=trait_type):
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = (
+ "testName", "testNameFull", "testNameShort",
+ "dataScale")
+ self.assertEqual(
+ retrieve_trait_dataset_name(
+ trait_type, thresh, trait_dataset_name, db_mock),
+ ("testName", "testNameFull", "testNameShort",
+ "dataScale"))
+ cursor.execute.assert_called_once_with(
+ "SELECT {cols} "
+ "FROM {ttype}Freeze "
+ "WHERE public > %(threshold)s AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format(
+ cols=columns, ttype=trait_type),
+ {"threshold": thresh, "name": trait_dataset_name})
+
+ def test_retrieve_publish_trait_info(self):
+ """Test retrieval of type `Publish` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "PublishTraitName", "trait_dataset_id": 1}
+ self.assertEqual(
+ retrieve_publish_trait_info(
+ trait_source,
+ db_mock),
+ tuple())
+ cursor.execute.assert_called_once_with(
+ PUBLISH_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_probeset_trait_info(self):
+ """Test retrieval of type `Probeset` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "ProbeSetTraitName",
+ "trait_dataset_name": "ProbeSetDatasetTraitName"}
+ self.assertEqual(
+ retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ PROBESET_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_geno_trait_info(self):
+ """Test retrieval of type `Geno` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "GenoTraitName",
+ "trait_dataset_name": "GenoDatasetTraitName"}
+ self.assertEqual(
+ retrieve_geno_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ GENO_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_temp_trait_info(self):
+ """Test retrieval of type `Temp` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {"trait_name": "TempTraitName"}
+ self.assertEqual(
+ retrieve_temp_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ TEMP_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_trait_info(self):
+ """Test that information on traits is retrieved as appropriate."""
+ for trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [
+ ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"],
+ ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"],
+ ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"],
+ ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]:
+ db_mock = mock.MagicMock()
+ with self.subTest(trait_type=trait_type):
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ self.assertEqual(
+ retrieve_trait_info(
+ trait_type, trait_name, trait_dataset_id,
+ trait_dataset_name, db_mock),
+ tuple())
-class TestTraitsSqlMethods(TestCase):
- """Test cases for sql operations that affect traits"""
def test_update_sample_data(self):
"""Test that the SQL queries when calling update_sample_data are called with
the right calls.
@@ -14,12 +122,12 @@ class TestTraitsSqlMethods(TestCase):
"""
db_mock = mock.MagicMock()
- STRAIN_ID_SQL: str = "UPDATE Strain SET Name = '%s' WHERE Id = %s"
+ STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
- "WHERE StrainId = %s AND DataId = %s")
+ "WHERE StrainId = %s AND Id = %s")
PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
"WHERE StrainId = %s AND DataId = %s")
- N_STRAIN_SQL: str = ("UPDATE NStrain SET count = '%s' "
+ N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s")
with db_mock.cursor() as cursor:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:51:58 +0000