diff options
Diffstat (limited to 'wqflask/tests/wqflask/show_trait/test_show_trait.py')
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_show_trait.py | 255 |
1 files changed, 0 insertions, 255 deletions
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py deleted file mode 100644 index 1291037f..00000000 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ /dev/null @@ -1,255 +0,0 @@ -"""test for wqflask/show_trait/test_show_trait.py""" -import unittest -import pytest -from unittest import mock -from wqflask.show_trait.show_trait import check_if_attr_exists -from wqflask.show_trait.show_trait import get_ncbi_summary -from wqflask.show_trait.show_trait import has_num_cases -from wqflask.show_trait.show_trait import get_table_widths -from wqflask.show_trait.show_trait import get_categorical_variables -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 get_scales_from_genofile - - -class TraitObject: - def __init__(self, obj): - self.distinct_values = [] - self.id = "" - for key, value in obj.items(): - setattr(self, key, value) - self.id += str(value) - - -@pytest.mark.parametrize( - ('trait', 'id_type', 'expected'), - ( - (TraitObject({"id_type": "id"}), "id_type", True), - (TraitObject({"sample_name": ['samp1']}), "id_type", False), - (TraitObject({"sample": ""}), "sample", False), - (TraitObject({"group": None}), "group", False), - (TraitObject({}), "any", False) - ), -) -def test_check_if_attr_exists(trait, id_type, expected): - """"test check_if_attr_exists""" - assert check_if_attr_exists(trait, id_type) == expected - - -def test_get_ncbi_summary_request(mocker): - trait = TraitObject({"geneid": "id"}) - mocker.patch("wqflask.show_trait.show_trait.check_if_attr_exists", - return_value=True) - mock_get = mocker.patch( - "wqflask.show_trait.show_trait.requests.get", - return_value=TraitObject({"content": """{ - "result":{ - "id":{ - "summary":"this is a summary of the geneid" - } - } - } - """})) - assert get_ncbi_summary(trait) == "this is a summary of the geneid" - mock_get.assert_called_once_with( - "http://eutils.ncbi.nlm.nih.gov/entrez/" - "eutils/esummary.fcgi?db=gene&id=" - f"{trait.geneid}&retmode=json" - ) - mock_get.side_effect = Exception("an error occurred") - assert get_ncbi_summary(trait) == None - - -class TestTraits(unittest.TestCase): - def test_hash_num_cases_is_probeset(self): - """test for hash num_cases with dataset.type set to Probeset""" - create_dataset = TraitObject({"type": "ProbeSet"}) - create_trait = TraitObject({"dataset": create_dataset}) - self.assertFalse(has_num_cases(create_trait)) - - def test_hash_num_cases_no_probeset(self): - """test for hash num cases with dataset.type not Probeset""" - create_dataset = TraitObject({"type": "Temp"}) - construct_data = { - "nm1": TraitObject({"num_cases": False}), - "nm2": TraitObject({"num_cases": True}), - "nm3": TraitObject({"num_cases": False}) - } - construct_data2 = { - "nm1": TraitObject({"num_cases": False}), - "nm2": TraitObject({"num_cases": False}), - "nm3": TraitObject({"num_cases": False}) - } - create_trait = TraitObject( - {"dataset": create_dataset, "data": construct_data}) - create_trait2 = TraitObject( - {"dataset": create_dataset, "data": construct_data2}) - - results = has_num_cases(create_trait) - self.assertTrue(has_num_cases(create_trait)) - self.assertFalse(has_num_cases(create_trait2)) - - def test_get_table_widths(self): - """test for getting table widths""" - sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]} - ), TraitObject( - {"se_exists": False, "attributes": ["at1", "at2"] - })] - - results_with_numcase = get_table_widths(sample_groups, True) - result_no_numcase = get_table_widths(sample_groups, False) - - results_one_sample = get_table_widths( - [TraitObject({"se_exists": True, "attributes": []})], True) - expected_with_numcase = (450, 645) - expected_no_numcase = (450, 644) - expected_one_sample = (250, 381) - self.assertEqual(results_with_numcase, expected_with_numcase) - self.assertEqual(result_no_numcase, expected_no_numcase) - self.assertEqual(results_one_sample, - expected_one_sample) - - def test_get_categorical_variables_no_sample_attributes(self): - """test for getting categorical variable names with no samples""" - trait = TraitObject({}) - sample_list = TraitObject({"se_exists": True, "attributes": []}) - self.assertEqual(get_categorical_variables(trait, sample_list), []) - - def test_get_categorical_variables_with_sample_attributes(self): - """test for getting categorical variable names with no samples""" - this_trait = TraitObject({"data": { - "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}), - "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}), - "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}}) - }}) - sample_list = TraitObject({"attributes": { - "sample_attribute_1": TraitObject({"name": "ex1"}), - "sample_attribute_2": TraitObject({"name": "ex2"}), - "sample_attribute_3": TraitObject({"name": "ex3"}), - "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"}) - }}) - results = get_categorical_variables(this_trait, sample_list) - self.assertEqual( - ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results) - - def test_get_trait_units(self): - """test for getting trait units""" - trait = TraitObject( - {"description_fmt": "[this is a description] another test [N/A]"}) - trait_no_unit_type = TraitObject({"description_fmt": ""}) - results = get_trait_units(trait) - results_no_unit = get_trait_units(trait_no_unit_type) - self.assertEqual(results, "this is a descriptionN/A") - self.assertEqual(results_no_unit, "value") - - @mock.patch("wqflask.show_trait.show_trait.database_connection") - def test_get_nearest_marker(self, mock_db): - """test for getting nearest marker with non-empty db""" - conn = mock.MagicMock() - mock_db.return_value.__enter__.return_value = conn - with conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ["Geno1", "Geno2"], ["Geno3"]] - - trait = TraitObject({ - "locus_chr": "test_chr", - "locus_mb": "test_mb" - }) - group_name = TraitObject({"name": "group_name"}) - this_db = TraitObject({"group": group_name}) - results_with_item_db = get_nearest_marker(trait, this_db) - cursor.execute.assert_called_with( - "SELECT Geno.Name FROM Geno, GenoXRef, " - "GenoFreeze WHERE Geno.Chr = %s " - "AND GenoXRef.GenoId = Geno.Id AND " - "GenoFreeze.Id = GenoXRef.GenoFreezeId " - "AND GenoFreeze.Name = %s " - "ORDER BY ABS( Geno.Mb - %s) LIMIT 1", - ('test_chr', 'group_nameGeno', 'test_mb')) - - self.assertEqual(results_with_item_db, "Geno1") - - @mock.patch("wqflask.show_trait.show_trait.database_connection") - def test_get_nearest_marker_empty_db(self, mock_db): - """test for getting nearest marker with empty db""" - conn = mock.MagicMock() - mock_db.return_value.__enter__.return_value = conn - with conn.cursor() as cursor: - cursor.fetchall.return_value = [] - trait = TraitObject({ - "locus_chr": "test_chr", - "locus_mb": "test_mb" - }) - group_name = TraitObject({"name": "group_name"}) - this_db = TraitObject({"group": group_name}) - results_empty_db = get_nearest_marker(trait, this_db) - cursor.execute.assert_called_once() - self.assertEqual(results_empty_db, "") - - @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile") - def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales): - """test for getting genotype scales with genofile as list """ - # where genofile is instance of list - genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"}, - {"filename": "file2", "location": "~/data/files/f2"}, - {"filename": "file3", "location": "~/data/files/f3"}] - - mock_get_scales.side_effect = [[["morgan", "cM"]], - [["morgan", "cM"]], - [["physic", "Mb"]]] - - results = get_genotype_scales(genofiles_list) - expected_results = { - "~/data/files/f1": [["morgan", "cM"]], - "~/data/files/f2": [["morgan", "cM"]], - "~/data/files/f3": [["physic", "Mb"]] - } - - multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'), - mock.call('~/data/files/f3')] - mock_get_scales.assert_has_calls(multiple_calls) - self.assertEqual(results, expected_results) - - @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile") - def test_genotype_scales_with_genofile_other(self, mock_get_scales): - """test for getting genotype scales with genofile as a string""" - file_location = "~/another_file_location" - mock_get_scales.return_value = [["physic", "Mb"]] - 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_ignore_location): - """"add test for get scales from genofile where file is found""" - mock_ignore_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) |