diff options
Diffstat (limited to 'gn2/tests/unit/wqflask/show_trait')
| -rw-r--r-- | gn2/tests/unit/wqflask/show_trait/__init__.py | 0 | ||||
| -rw-r--r-- | gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py | 151 | ||||
| -rw-r--r-- | gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py | 15 |
3 files changed, 166 insertions, 0 deletions
diff --git a/gn2/tests/unit/wqflask/show_trait/__init__.py b/gn2/tests/unit/wqflask/show_trait/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/__init__.py diff --git a/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py new file mode 100644 index 00000000..a933d0bf --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py @@ -0,0 +1,151 @@ +import datetime +import unittest +from unittest import mock +from gn2.wqflask.show_trait.export_trait_data import dict_to_sorted_list +from gn2.wqflask.show_trait.export_trait_data import cmp_samples +from gn2.wqflask.show_trait.export_trait_data import export_sample_table +from gn2.wqflask.show_trait.export_trait_data import get_export_metadata + + +class AttributesSetter: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + + +class TestExportTraits(unittest.TestCase): + """Test methods for exporting traits and metadata""" + + @mock.patch("wqflask.show_trait.export_trait_data.datetime") + @mock.patch("wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata(self, data_mock, trait_mock, date_mock): + """test for exporting metadata with dataset.type=Publish""" + mock_dataset = AttributesSetter({"type": "Publish", + "name": "HC_M2_0606_P", + "dataset_name": "HC_M2_0606_P"}) + + mock_dataset.group = AttributesSetter({"name": "C"}) + data_mock.create_dataset.return_value = mock_dataset + + trait_data = { + "symbol": "Nr3c1", + "description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR", + "title": "Trait_1 title", + + "authors": "XL_1", + "journal": "" + + } + + date_mock.datetime.now.return_value = datetime.datetime( + 2022, 8, 8, 19, 2, 31, 628813) + trait_mock.return_value = AttributesSetter(trait_data) + + results = get_export_metadata({ + "trait_id": "1460303_at", + "trait_display_name": "1460303_at", + "dataset": "HC_M2_0606_P", + "group": "BXD", + }) + + expected = [["Phenotype ID:", "1460303_at"], + ["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"], + ["Group: ", "C"], + ["Phenotype: ", + 'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'], + ["Authors: ", "XL_1"], + ["Title: ", "Trait_1 title"], + ["Journal: ", "N/A"], + ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"], + ["Export Date: ", "August 08, 2022"], + ["Export Time: ", "19:02 GMT"]] + + self.assertEqual(results, expected) + + def test_dict_to_sortedlist(self): + """test for conversion of dict to sorted list""" + sample1 = { + "other": "exp1", + "name": "exp2" + } + sample2 = { + "se": 1, + "num_cases": 4, + "value": 6, + "name": 3 + + } + rever = { + "name": 3, + "value": 6, + "num_cases": 4, + "se": 1 + } + oneItem = { + "item1": "one" + } + + self.assertEqual(["exp2", "exp1"], dict_to_sorted_list(sample1)) + self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(sample2)) + self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(rever)) + self.assertEqual(["one"], dict_to_sorted_list(oneItem)) + """test that the func returns the values not the keys""" + self.assertFalse(["other", "name"] == dict_to_sorted_list(sample1)) + + def test_cmp_samples(self): + """test for comparing samples function""" + sampleA = [ + [ + ("value", "other"), + ("name", "test_name") + ] + ] + sampleB = [ + [ + ("value", "other"), + ("unknown", "test_name") + ] + ] + sampleC = [ + [("other", "value"), + ("name", "value") + ], + [ + ("name", "value"), + ("value", "name") + ], + [ + ("other", "value"), + ("name", "value" + )], + [ + ("name", "name1"), + ("se", "valuex") + ], + [( + "value", "name1"), + ("se", "valuex") + ], + [( + "other", "name1"), + ("se", "valuex" + ) + ], + [( + "name", "name_val"), + ("num_cases", "num_val") + ], + [( + "other_a", "val_a"), + ("other_b", "val" + ) + ] + ] + results = [cmp_samples(val[0], val[1]) for val in sampleA] + resultB = [cmp_samples(val[0], val[1]) for val in sampleB] + resultC = [cmp_samples(val[0], val[1]) for val in sampleC] + + self.assertEqual(1, *results) + self.assertEqual(-1, *resultB) + self.assertEqual([1, -1, 1, -1, -1, 1, -1, -1], resultC) diff --git a/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py new file mode 100644 index 00000000..45484f17 --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py @@ -0,0 +1,15 @@ +import pytest +import unittest + +from gn2.wqflask.show_trait.show_trait import get_max_digits + +@unittest.skip("Too complicated") +@pytest.mark.parametrize( + "trait_vals,expected", + ((( + (0, 1345, 92, 734), + (234253, 33, 153, 5352), + (3542, 24, 135)), + [3, 5, 3]),)) +def test_get_max_digits(trait_vals, expected): + assert get_max_digits(trait_vals) == expected |