diff options
Diffstat (limited to 'wqflask/tests')
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_show_trait.py | 264 |
1 files changed, 264 insertions, 0 deletions
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py new file mode 100644 index 00000000..c617e9f2 --- /dev/null +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -0,0 +1,264 @@ +"""test for wqflask/show_trait/test_show_trait.py""" +import unittest +from unittest import mock +from wqflask import app +from wqflask.show_trait.show_trait import (check_if_attr_exists, get_ncbi_summary, + has_num_cases, get_table_widths, + get_categorical_variables, + get_trait_units, get_nearest_marker, get_genotype_scales, requests) + + +class TraitObject: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + + +class TestTraits(unittest.TestCase): + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + def test_check_if_attr_exists_truthy(self): + """"test if attributes exists with true return""" + trait_obj = TraitObject({"id_type": "id"}) + trait_obj2 = TraitObject({"sample_name": ['samp1']}) + results = check_if_attr_exists(trait_obj, "id_type") + result2 = check_if_attr_exists(trait_obj2, "sample_name") + self.assertIsInstance(trait_obj, TraitObject) + self.assertIs(results, True) + self.assertIs(result2, True) + + def test_check_if_attr_exists_empty_attr(self): + """test if attributes exists with false return""" + trait_obj = TraitObject({"sample": ""}) + trait_obj2 = TraitObject({"group": None}) + result = check_if_attr_exists(trait_obj, "sample") + result2 = check_if_attr_exists(trait_obj, "group") + self.assertIs(result, False) + self.assertIs(result2, False) + + def test_check_if_attr_exists_falsey(self): + """check if attribute exists with empty attributes""" + trait_obj = TraitObject({}) + results = check_if_attr_exists(trait_obj, "any") + self.assertIs(results, False) + + @mock.patch("wqflask.show_trait.show_trait.requests.get") + @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists") + def test_get_ncbi_summary_request_success(self, mock_exists, mock_get): + """test for getting ncbi summary with + successful request""" + trait = TraitObject({"geneid": "id"}) + mock_exists.return_value = True + content_json_string = """{ + "result":{ + "id":{ + "summary":"this is a summary of the geneid" + } + } + } + """ + + get_return_obj = TraitObject({"content": content_json_string}) + + mock_get.return_value = get_return_obj + + results = get_ncbi_summary(trait) + mock_exists.assert_called_once() + mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") + + self.assertEqual(results, "this is a summary of the geneid") + + @mock.patch("wqflask.show_trait.show_trait.requests.get") + @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists") + def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail): + """test for getting ncbi summary with request fail""" + trait = TraitObject({"geneid": "id"}) + mock_exists.return_value = True + mock_get_fail.side_effect = Exception("an error occurred") + content_json_string = """{ + "result":{ + "id":{ + "summary":"this is a summary of the geneid" + } + } + } + """ + + results = get_ncbi_summary(trait) + self.assertEqual(results, None) + + 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.assertIs(has_num_cases(create_trait), False) + + 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.assertIs(has_num_cases(create_trait), True) + self.assertIs(has_num_cases(create_trait2), False) + + 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, "750px") + expected_no_numcase = (450, "670px") + expected_one_sample = (250, "540px") + + 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.g") + def test_get_nearest_marker(self, mock_db): + """test for getting nearest marker with non-empty db""" + + mock_db.db.execute.return_value.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) + + called_with_value = """SELECT Geno.Name + FROM Geno, GenoXRef, GenoFreeze + WHERE Geno.Chr = 'test_chr' AND + GenoXRef.GenoId = Geno.Id AND + GenoFreeze.Id = GenoXRef.GenoFreezeId AND + GenoFreeze.Name = 'group_nameGeno' + ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1""" + + mock_db.db.execute.assert_called_with(called_with_value) + + self.assertEqual(results_with_item_db, "Geno1") + + @mock.patch("wqflask.show_trait.show_trait.g") + def test_get_nearest_marker_empty_db(self, mock_db): + """test for getting nearest marker with empty db""" + mock_db.db.execute.return_value.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) + mock_db.db.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) |