diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_export_trait_data.py | 118 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 4 |
5 files changed, 138 insertions, 16 deletions
diff --git a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py index 98d599b1..41761944 100644 --- a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py +++ b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py @@ -1,10 +1,128 @@ import unittest +from unittest import mock from wqflask.show_trait.export_trait_data import dict_to_sorted_list from wqflask.show_trait.export_trait_data import cmp_samples +from wqflask.show_trait.export_trait_data import export_sample_table +from wqflask.show_trait.export_trait_data import get_export_metadata + + +class AttributesSetter: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) class TestExportTraits(unittest.TestCase): """Test methods related to converting dict to sortedlist""" + @mock.patch("wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata_no_publish(self, mock_dataset, mock_trait): + """test for exporting metadata with no publish""" + mock_dataset_attributes = AttributesSetter( + {"type": "no_publish", "dataset_name": "Temp", "name": "Temp"}) + + mock_nested_attributes = AttributesSetter({"name": "name"}) + mock_dataset_attributes.group = mock_nested_attributes + mock_dataset.create_dataset.return_value = mock_dataset_attributes + mock_trait.return_value = AttributesSetter({"symbol": "", "description_display": "Description", + "title": "research1", "journal": "", "authors": ""}) + + results = get_export_metadata("random_id", "Temp") + expected = [["Record ID: random_id"], + ["Trait URL: http://genenetwork.org/show_trait?trait_id=random_id&dataset=Temp"], + ["Dataset: Temp"], + ["Group: name"], []] + + mock_dataset.create_dataset.assert_called_with("Temp") + mock_trait.assert_called_with( + dataset=mock_dataset_attributes, name="random_id", cellid=None, get_qtl_info=False) + self.assertEqual(results, expected) + + @mock.patch("wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata_with_publish(self, data_mock, trait_mock): + """test for exporting metadata with dataset.type=Publish""" + mock_dataset_attributes = AttributesSetter({"type": "Publish", "dataset_name": "Temp", + "name": "Temp", "description_display": "Description goes here"}) + + mock_nested_attributes = AttributesSetter({"name": "name"}) + mock_dataset_attributes.group = mock_nested_attributes + data_mock.create_dataset.return_value = mock_dataset_attributes + trait_instance = AttributesSetter({"symbol": "", "description_display": "Description", + "title": "research1", "journal": "", "authors": ""}) + trait_mock.return_value = trait_instance + + results = get_export_metadata( + "29ae0615-0d77-4814-97c7-c9e91f6bfd7b", "Temp") + + expected = [['Phenotype ID: 29ae0615-0d77-4814-97c7-c9e91f6bfd7b'], + ['Phenotype URL: http://genenetwork.org/show_trait?trait_id=29ae0615-0d77-4814-97c7-c9e91f6bfd7b&dataset=Temp'], [ + 'Group: name'], ['Phenotype: Description'], + ['Authors: N/A'], ['Title: research1'], + ['Journal: N/A'], ['Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Temp'], []] + + self.assertEqual(results, expected) + + @mock.patch("wqflask.show_trait.export_trait_data.dict_to_sorted_list") + @mock.patch("wqflask.show_trait.export_trait_data.get_export_metadata") + def test_export_sample_table(self, exp_metadata, dict_list): + """test for exporting sample table""" + targs_obj = { + "export_data": """{ + "primary_samples": [ + { + "other": "germanotta", + "name": "Sauroniops", + "se":{ + "name":"S2" + }, + "num_cases":{ + "k1":"value" + + } + } + ], + "other_samples": [ + { + "se": 1, + "num_cases": 4, + "value": 6, + "name": 3 + } + ] + }""", + "trait_display_name": "Hair_color", + "trait_id": "23177fdc-312e-4084-ad0c-f3eae785fff5", + "dataset": { + } + } + exp_metadata.return_value = [ + ["Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f"], ['Group:gp1'], + ["Phenotype:p1"], [ + "Authors:N/A"], + ["Title:research1"], + ["Journal:N/A"], + ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1"], []] + expected = ('Hair_color', + [['Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f'], + ['Group:gp1'], + ['Phenotype:p1'], + ['Authors:N/A'], + ['Title:research1'], + ['Journal:N/A'], + ['Dataset Link: ' + 'http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1'], + [], + ['Name', 'Value', 'SE', 'N'], + ['Sauroniops', 'germanotta'], + [3, 6, 1, 4]]) + + dict_list.side_effect = [['Sauroniops', 'germanotta'], [3, 6, 1, 4]] + + self.assertEqual(export_sample_table(targs_obj), expected) + exp_metadata.assert_called_with( + "23177fdc-312e-4084-ad0c-f3eae785fff5", {}) + self.assertEqual(dict_list.call_count, 2) def test_dict_to_sortedlist(self): """test for conversion of dict to sorted list""" diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index d855a7fa..236cc755 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -25,6 +25,10 @@ def is_redis_available(): return True +def load_json_from_redis(item_list, column_value): + return json.loads(item_list[str.encode(column_value)]) + + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -46,7 +50,7 @@ def get_user_by_unique_column(column_name, column_value): if column_name in user_ob and user_ob[column_name] == column_value: item_details = user_ob else: - item_details = json.loads(user_list[column_value]) + item_details = load_json_from_redis(user_list, column_value) return item_details @@ -70,7 +74,7 @@ def get_users_like_unique_column(column_name, column_value): if column_value in user_ob[column_name]: matched_users.append(user_ob) else: - matched_users.append(json.loads(user_list[column_value])) + matched_users.append(load_json_from_redis(user_list, column_value)) return matched_users @@ -199,7 +203,7 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(json.loads(group_list[column_value])) + matched_groups.append(load_json_from_redis(group_list, column_value)) return matched_groups diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e710bacd..4c2b64ba 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -184,6 +184,8 @@ class CorrelationResults(object): for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + if not trait_object: + continue if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option @@ -434,15 +436,15 @@ class CorrelationResults(object): self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) - #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ - if self.corr_method == 'bicor': - sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) - elif self.corr_method == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) - else: - sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) - if num_overlap > 5: + #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ + if self.corr_method == 'bicor': + sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) + elif self.corr_method == 'pearson': + sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) + else: + sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) + if numpy.isnan(sample_r): pass else: @@ -635,3 +637,4 @@ def get_header_fields(data_type, corr_method): 'Sample p(r)'] return header_fields + diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index b5686b70..6d6572ff 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2146,9 +2146,6 @@ class DisplayMappingResults(object): LRSScale = 1.0 LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) - #make sure the user's value appears on the y-axis - #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460 - LRSAxisList.append(ceil(LRS_LOD_Max)) #ZS: Convert to int if all axis values are whole numbers all_int = True diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index edf9638c..25ba1a1d 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -228,8 +228,8 @@ class ShowTrait(object): hddn = OrderedDict() if self.dataset.group.allsamples: - hddn['allsamples'] = ''.join(self.dataset.group.allsamples) - hddn['primary_samples'] = ''.join(self.primary_sample_names) + hddn['allsamples'] = ','.join(self.dataset.group.allsamples) + hddn['primary_samples'] = ','.join(self.primary_sample_names) hddn['trait_id'] = self.trait_id hddn['trait_display_name'] = self.this_trait.display_name hddn['dataset'] = self.dataset.name |