diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/testSampleList.py | 18 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_show_trait.py | 55 |
2 files changed, 73 insertions, 0 deletions
diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py new file mode 100644 index 00000000..4cc8c4da --- /dev/null +++ b/wqflask/tests/wqflask/show_trait/testSampleList.py @@ -0,0 +1,18 @@ +import unittest +import re +from unittest import mock +from wqflask.show_trait.SampleList import natural_sort + + +class TestSampleList(unittest.TestCase): + def test_natural_sort(self): + "Sort the list into natural alphanumeric order." + + characters_list = ["z", "f", "q", "s", "t", "a", "g"] + names_list = ["temp1", "publish", "Sample", "Dataset"] + + natural_sort(characters_list) + natural_sort(names_list) + + self.assertEqual(characters_list, ["a", "f", "g", "q", "s", "t", "z"]) + self.assertEqual(names_list, ["Dataset", "Sample", "publish", "temp1"]) diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py index 24150738..b1a91bbe 100644 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -11,6 +11,7 @@ from wqflask.show_trait.show_trait import get_trait_units from wqflask.show_trait.show_trait import get_nearest_marker from wqflask.show_trait.show_trait import get_genotype_scales from wqflask.show_trait.show_trait import requests +from wqflask.show_trait.show_trait import get_scales_from_genofile class TraitObject: @@ -240,3 +241,57 @@ class TestTraits(unittest.TestCase): expected_results = {f"{file_location}": [["physic", "Mb"]]} self.assertEqual(get_genotype_scales(file_location), expected_results) mock_get_scales.assert_called_once_with(file_location) + + @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error") + def test_get_scales_from_genofile_found(self, mock_location_ignore): + # test no complete to be continued with + # a .geno file + mock_location_ignore.return_value = True + mock_file_with_one_line = mock.mock_open( + read_data="Some data from opened file") + + mock_file = """#@scale and random data:is here_returned\n + This is second with spaced with tabs\n """ + mock_file_result = mock.mock_open(read_data=mock_file) + + with mock.patch("builtins.open", mock_file_with_one_line): + result = get_scales_from_genofile("~/data/file") + self.assertEqual(result, [['morgan', 'cM']]) + + with mock.patch("builtins.open", mock_file_result): + results = get_scales_from_genofile("~data/file_geno") + self.assertEqual(results, [['physic', 'Mb']]) + + @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error") + def test_get_scales_from_genofile_found(self, mock_ingore_location): + """"add test for get scales from genofile where file is found""" + mock_ingore_location.return_value = True + geno_file = """ + #sample line with no @scales:other\n + #sample line @scales and :separated by semicolon\n + This attempts to check whether\n + """ + + geno_file_string = "@line start with @ and has @scale:morgan" + + file_location = "~/data/file.geno" + + mock_open_geno_file = mock.mock_open(read_data=geno_file) + with mock.patch("builtins.open", mock_open_geno_file): + results = get_scales_from_genofile(file_location) + self.assertEqual(results, [["morgan", "cM"]]) + + mock_open_string = mock.mock_open(read_data=geno_file_string) + + with mock.patch("builtins.open", mock_open_string): + result2 = get_scales_from_genofile(file_location) + self.assertEqual([['morgan', 'cM']], result2) + + @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error") + def test_get_scales_from_genofile_not_found(self, mock_location_ignore): + mock_location_ignore.return_value = False + + expected_results = [["physic", "Mb"]] + results = get_scales_from_genofile("~/data/file") + mock_location_ignore.assert_called_once_with("~/data/file", "genotype") + self.assertEqual(results, expected_results) |