diff options
Diffstat (limited to 'gn2/tests/wqflask')
| -rw-r--r-- | gn2/tests/wqflask/show_trait/testSampleList.py | 17 | ||||
| -rw-r--r-- | gn2/tests/wqflask/show_trait/test_show_trait.py | 255 |
2 files changed, 272 insertions, 0 deletions
diff --git a/gn2/tests/wqflask/show_trait/testSampleList.py b/gn2/tests/wqflask/show_trait/testSampleList.py new file mode 100644 index 00000000..1c5478bb --- /dev/null +++ b/gn2/tests/wqflask/show_trait/testSampleList.py @@ -0,0 +1,17 @@ +import unittest +import re +from unittest import mock +from gn2.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"] + sorted_list_a = natural_sort(characters_list) + sorted_list_b = natural_sort(names_list) + self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"]) + self.assertEqual( + sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) diff --git a/gn2/tests/wqflask/show_trait/test_show_trait.py b/gn2/tests/wqflask/show_trait/test_show_trait.py new file mode 100644 index 00000000..97618d31 --- /dev/null +++ b/gn2/tests/wqflask/show_trait/test_show_trait.py @@ -0,0 +1,255 @@ +"""test for wqflask/show_trait/test_show_trait.py""" +import unittest +import pytest +from unittest import mock +from gn2.wqflask.show_trait.show_trait import check_if_attr_exists +from gn2.wqflask.show_trait.show_trait import get_ncbi_summary +from gn2.wqflask.show_trait.show_trait import has_num_cases +from gn2.wqflask.show_trait.show_trait import get_table_widths +from gn2.wqflask.show_trait.show_trait import get_categorical_variables +from gn2.wqflask.show_trait.show_trait import get_trait_units +from gn2.wqflask.show_trait.show_trait import get_nearest_marker +from gn2.wqflask.show_trait.show_trait import get_genotype_scales +from gn2.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) |