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authorBonfaceKilz2020-11-04 10:59:09 +0300
committerGitHub2020-11-04 10:59:09 +0300
commit510e66de705b90341cd773e666e51dfcf033a958 (patch)
treea80c572548bd5808a231b5fe09231e669e3c948e /wqflask
parent55bb282311d82abf842d95a44c61d744803cf4a2 (diff)
parent3f08f54fe3d42eca0ccf98831e4e339defa17720 (diff)
downloadgenenetwork2-510e66de705b90341cd773e666e51dfcf033a958.tar.gz
Merge pull request #475 from Alexanderlacuna/test-showtrait
Add more tests for show trait module
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/tests/wqflask/show_trait/test_show_trait.py242
1 files changed, 242 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..24150738
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -0,0 +1,242 @@
+"""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
+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 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.assertTrue(results)
+ self.assertTrue(result2)
+
+ 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.assertFalse(result)
+ self.assertFalse(result2)
+
+ 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.assertFalse(results)
+
+ @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.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, "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)