diff options
Diffstat (limited to 'wqflask/tests/unit')
| -rw-r--r-- | wqflask/tests/unit/wqflask/api/test_correlation.py | 145 |
1 files changed, 79 insertions, 66 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py index cbcd006d..d0264b87 100644 --- a/wqflask/tests/unit/wqflask/api/test_correlation.py +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -1,7 +1,7 @@ import unittest from unittest import mock from wqflask import app -from collections import OrderedDict +from collections import OrderedDict from wqflask.api.correlation import init_corr_params from wqflask.api.correlation import convert_to_mouse_gene_id from wqflask.api.correlation import do_literature_correlation_for_all_traits @@ -14,14 +14,16 @@ class AttributeSetter: for k, v in obj.items(): setattr(self, k, v) + class MockDataset(AttributeSetter): def get_trait_data(self): return None - def retrieve_genes(self,id=None): + + def retrieve_genes(self, id=None): return { - "TT-1":"GH-1", - "TT-2":"GH-2", - "TT-3":"GH-3" + "TT-1": "GH-1", + "TT-2": "GH-2", + "TT-3": "GH-3" } @@ -59,8 +61,9 @@ class TestCorrelations(unittest.TestCase): rat_species_results = convert_to_mouse_gene_id( species="rat", gene_id="GH1") - mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter({"mouse": "MG-1"}),AttributeSetter({"mouse":"MG-2"})] - + mock_db.db.execute.return_value.fetchone.side_effect = [ + AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})] + self.assertEqual(convert_to_mouse_gene_id( species="mouse", gene_id="MG-4"), "MG-4") self.assertEqual(convert_to_mouse_gene_id( @@ -68,73 +71,83 @@ class TestCorrelations(unittest.TestCase): self.assertEqual(convert_to_mouse_gene_id( species="human", gene_id="H1"), "MG-2") - - @mock.patch("wqflask.api.correlation.g") @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id") - def test_do_literature_correlation_for_all_traits(self,mock_convert_to_mouse_geneid,mock_db): - mock_convert_to_mouse_geneid.side_effect=["MG-1","MG-2;","MG-3","MG-4"] - - - trait_geneid_dict={ - "TT-1":"GH-1", - "TT-2":"GH-2", - "TT-3":"GH-3" + def test_do_literature_correlation_for_all_traits(self, mock_convert_to_mouse_geneid, mock_db): + mock_convert_to_mouse_geneid.side_effect = [ + "MG-1", "MG-2;", "MG-3", "MG-4"] - } - mock_db.db.execute.return_value.fetchone.side_effect=[AttributeSetter({"value":"V1"}),AttributeSetter({"value":"V2"}),AttributeSetter({"value":"V3"})] + trait_geneid_dict = { + "TT-1": "GH-1", + "TT-2": "GH-2", + "TT-3": "GH-3" + } + mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter( + {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})] - this_trait=AttributeSetter({"geneid":"GH-1"}) + this_trait = AttributeSetter({"geneid": "GH-1"}) - target_dataset=AttributeSetter({"group":AttributeSetter({"species":"rat"})}) - results=do_literature_correlation_for_all_traits(this_trait=this_trait,target_dataset=target_dataset,trait_geneid_dict=trait_geneid_dict,corr_params={}) + target_dataset = AttributeSetter( + {"group": AttributeSetter({"species": "rat"})}) + results = do_literature_correlation_for_all_traits( + this_trait=this_trait, target_dataset=target_dataset, trait_geneid_dict=trait_geneid_dict, corr_params={}) - expected_results={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']} - self.assertEqual(results,expected_results) + expected_results = {'TT-1': ['GH-1', 0], + 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']} + self.assertEqual(results, expected_results) @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values") - def test_get_sample_r_and_p_values(self,mock_normalize): - - group=AttributeSetter({"samplelist":["S1","S2","S3","S4","S5","S6","S7"]}) - target_dataset=AttributeSetter({"group":group}) - - target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6] - trait_data={"S1":AttributeSetter({"value":2.3}),"S2":AttributeSetter({"value":1.1}),"S3":AttributeSetter({"value":6.3}),"S4":AttributeSetter({"value":3.6}),"S5":AttributeSetter({"value":4.1}),"S6":AttributeSetter({"value":5.0})} - this_trait=AttributeSetter({"data":trait_data}) - mock_normalize.return_value=([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6) - mock_normalize.side_effect=[([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,1.4], [3.4,6.2,4.1], 3)] - - results_pearsonr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson") - results_spearmanr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="spearman") - results_num_overlap=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson") - expected_pearsonr=[-0.21618688834430866, 0.680771605997119, 6] - expected_spearmanr=[-0.11595420713048969, 0.826848213385815, 6] - for i,val in enumerate(expected_pearsonr): - self.assertAlmostEqual(val,results_pearsonr[i]) - for i,val in enumerate(expected_spearmanr): - self.assertAlmostEqual(val,results_spearmanr[i]) - self.assertEqual(results_num_overlap,None) + def test_get_sample_r_and_p_values(self, mock_normalize): + + group = AttributeSetter( + {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]}) + target_dataset = AttributeSetter({"group": group}) + + target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6] + trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), + "S3": AttributeSetter( + {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), + "S6": AttributeSetter({"value": 5.0})} + this_trait = AttributeSetter({"data": trait_data}) + mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], + [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6) + mock_normalize.side_effect = [([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], + [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6), + ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], + [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6), + ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)] + + results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={ + }, target_vals=target_vals, target_dataset=target_dataset, type="pearson") + results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={ + }, target_vals=target_vals, target_dataset=target_dataset, type="spearman") + results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={ + }, target_vals=target_vals, target_dataset=target_dataset, type="pearson") + expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6] + expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6] + for i, val in enumerate(expected_pearsonr): + self.assertAlmostEqual(val, results_pearsonr[i],4) + for i, val in enumerate(expected_spearmanr): + self.assertAlmostEqual(val, results_spearmanr[i],4) + self.assertEqual(results_num_overlap, None) @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits") - def test_calculate_results(self,literature_correlation): - - literature_correlation.return_value={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]} - - - - this_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})}) - target_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})}) - this_trait=AttributeSetter({"geneid":"GH-1"}) - corr_params={"type":"literature"} - sorted_results=calculate_results(this_trait=this_trait,this_dataset=this_dataset,target_dataset=target_dataset,corr_params=corr_params) - expected_results={'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]} - - self.assertTrue(isinstance(sorted_results,OrderedDict)) - self.assertEqual(dict(sorted_results),expected_results) - - - - - - + def test_calculate_results(self, literature_correlation): + + literature_correlation.return_value = { + 'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]} + + this_dataset = MockDataset( + {"group": AttributeSetter({"species": "rat"})}) + target_dataset = MockDataset( + {"group": AttributeSetter({"species": "rat"})}) + this_trait = AttributeSetter({"geneid": "GH-1"}) + corr_params = {"type": "literature"} + sorted_results = calculate_results( + this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params) + expected_results = {'TT-2': ['GH-2', 3], + 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]} + + self.assertTrue(isinstance(sorted_results, OrderedDict)) + self.assertEqual(dict(sorted_results), expected_results) |