diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py | 56 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 93 |
2 files changed, 0 insertions, 149 deletions
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py index 33601990..e29b18ca 100644 --- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py +++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py @@ -1,7 +1,6 @@ import unittest from unittest import mock from wqflask.correlation.show_corr_results import get_header_fields -from wqflask.correlation.show_corr_results import generate_corr_json class AttributeSetter: @@ -41,58 +40,3 @@ class TestShowCorrResults(unittest.TestCase): result2 = get_header_fields("Other", "Other") self.assertEqual(result1, expected[0]) self.assertEqual(result2, expected[1]) - - @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac") - def test_generate_corr_json(self, mock_data_hmac): - mock_data_hmac.return_value = "hajsdiau" - - dataset = AttributeSetter({"name": "the_name"}) - this_trait = AttributeSetter( - {"name": "trait_test", "dataset": dataset}) - target_dataset = AttributeSetter({"type": "Publish"}) - corr_trait_1 = AttributeSetter({ - "name": "trait_1", - "dataset": AttributeSetter({"name": "dataset_1"}), - "view": True, - "abbreviation": "T1", - "description_display": "Trait I description", - "authors": "JM J,JYEW", - "pubmed_id": "34n4nn31hn43", - "pubmed_text": "2016", - "pubmed_link": "https://www.load", - "lod_score": "", - "mean": "", - "LRS_location_repr": "BXBS", - "additive": "", - "sample_r": 10.5, - "num_overlap": 2, - "sample_p": 5 - - - - - }) - corr_results = [corr_trait_1] - - dataset_type_other = { - "location": "cx-3-4", - "sample_4": 12.32, - "num_overlap": 3, - "sample_p": 10.34 - } - - expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]' - - results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait, - dataset=dataset, target_dataset=target_dataset, for_api=True) - self.assertEqual(expected_results, results1) - - def test_generate_corr_json_view_false(self): - trait = AttributeSetter({"view": False}) - corr_results = [trait] - this_trait = AttributeSetter({"name": "trait_test"}) - dataset = AttributeSetter({"name": "the_name"}) - - results_where_view_is_false = generate_corr_json( - corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False) - self.assertEqual(results_where_view_is_false, "[]") diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index a1b45ff6..cda34bee 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -222,99 +222,6 @@ def correlation_json_for_table(start_vars, correlation_data, this_trait, this_da return json.dumps(results_list) -def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False): - results_list = [] - for i, trait in enumerate(corr_results): - if trait.view == False: - continue - results_dict = {} - results_dict['index'] = i + 1 - results_dict['trait_id'] = trait.name - results_dict['dataset'] = trait.dataset.name - results_dict['hmac'] = hmac.data_hmac( - '{}:{}'.format(trait.name, trait.dataset.name)) - if target_dataset.type == "ProbeSet": - results_dict['symbol'] = trait.symbol - results_dict['description'] = "N/A" - results_dict['location'] = trait.location_repr - results_dict['mean'] = "N/A" - results_dict['additive'] = "N/A" - if bool(trait.description_display): - results_dict['description'] = trait.description_display - if bool(trait.mean): - results_dict['mean'] = f"{float(trait.mean):.3f}" - try: - results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}" - except: - results_dict['lod_score'] = "N/A" - results_dict['lrs_location'] = trait.LRS_location_repr - if bool(trait.additive): - results_dict['additive'] = f"{float(trait.additive):.3f}" - results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" - results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" - results_dict['lit_corr'] = "--" - results_dict['tissue_corr'] = "--" - results_dict['tissue_pvalue'] = "--" - if bool(trait.lit_corr): - results_dict['lit_corr'] = f"{float(trait.lit_corr):.3f}" - if bool(trait.tissue_corr): - results_dict['tissue_corr'] = f"{float(trait.tissue_corr):.3f}" - results_dict['tissue_pvalue'] = f"{float(trait.tissue_pvalue):.3e}" - elif target_dataset.type == "Publish": - results_dict['abbreviation_display'] = "N/A" - results_dict['description'] = "N/A" - results_dict['mean'] = "N/A" - results_dict['authors_display'] = "N/A" - results_dict['additive'] = "N/A" - if for_api: - results_dict['pubmed_id'] = "N/A" - results_dict['year'] = "N/A" - else: - results_dict['pubmed_link'] = "N/A" - results_dict['pubmed_text'] = "N/A" - - if bool(trait.abbreviation): - results_dict['abbreviation_display'] = trait.abbreviation - if bool(trait.description_display): - results_dict['description'] = trait.description_display - if bool(trait.mean): - results_dict['mean'] = f"{float(trait.mean):.3f}" - if bool(trait.authors): - authors_list = trait.authors.split(',') - if len(authors_list) > 6: - results_dict['authors_display'] = ", ".join( - authors_list[:6]) + ", et al." - else: - results_dict['authors_display'] = trait.authors - if bool(trait.pubmed_id): - if for_api: - results_dict['pubmed_id'] = trait.pubmed_id - results_dict['year'] = trait.pubmed_text - else: - results_dict['pubmed_link'] = trait.pubmed_link - results_dict['pubmed_text'] = trait.pubmed_text - try: - results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}" - except: - results_dict['lod_score'] = "N/A" - results_dict['lrs_location'] = trait.LRS_location_repr - if bool(trait.additive): - results_dict['additive'] = f"{float(trait.additive):.3f}" - results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" - results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" - else: - results_dict['location'] = trait.location_repr - results_dict['sample_r'] = f"{float(trait.sample_r):.3f}" - results_dict['num_overlap'] = trait.num_overlap - results_dict['sample_p'] = f"{float(trait.sample_p):.3e}" - - results_list.append(results_dict) - - return json.dumps(results_list) - - def get_formatted_corr_type(corr_type, corr_method): formatted_corr_type = "" if corr_type == "lit": |