diff options
Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_datasets.py | 219 | ||||
| -rw-r--r-- | tests/unit/computations/test_trait.py | 84 |
2 files changed, 0 insertions, 303 deletions
diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py deleted file mode 100644 index f9e9c2b..0000000 --- a/tests/unit/computations/test_datasets.py +++ /dev/null @@ -1,219 +0,0 @@ -"""Module contains tests from datasets""" -import json - -from unittest import TestCase -from unittest import mock - -from collections import namedtuple - -from gn3.computations.datasets import retrieve_trait_sample_data -from gn3.computations.datasets import get_query_for_dataset_sample -from gn3.computations.datasets import fetch_from_db_sample_data -from gn3.computations.datasets import create_dataset -from gn3.computations.datasets import dataset_creator_store -from gn3.computations.datasets import dataset_type_getter -from gn3.computations.datasets import fetch_dataset_type_from_gn2_api -from gn3.computations.datasets import fetch_dataset_sample_id -from gn3.computations.datasets import divide_into_chunks -from gn3.computations.datasets import get_traits_data - - -class TestDatasets(TestCase): - """Class contains tests for datasets""" - - @mock.patch("gn3.computations.datasets.fetch_from_db_sample_data") - def test_retrieve_trait_sample_data(self, mock_fetch_sample_results): - """Test retrieving sample data\ - for trait from the dataset - """ - trait_name = "1419792_at" - dataset_id = "HC_M2_0606_P&" - dataset_type = "Publish" - - database = mock.Mock() - - dataset = { - "id": dataset_id, - "type": dataset_type, - "name": dataset_id - } - - fetch_results = [('BXD32', 8.001, None, None, 'BXD32')] - - mock_fetch_sample_results.return_value = fetch_results - - results = retrieve_trait_sample_data( - dataset, trait_name, database) - self.assertEqual(mock_fetch_sample_results.call_count, 1) - self.assertEqual(results, fetch_results) - - def test_query_for_dataset_sample(self): - """Test for getting query for sample data""" - - no_results = get_query_for_dataset_sample("does not exists") - - query_exists = get_query_for_dataset_sample("Publish") - - self.assertEqual(no_results, None) - self.assertIsInstance(query_exists, str) - - def test_fetch_from_db_sample_data(self): - """Test for function that fetches sample\ - results from the database - """ - - database_results = [('BXD31', 8.001, None, None, 'BXD31'), - ('BXD32', 7.884, None, None, 'BXD32'), - ('BXD42', 7.682, None, None, 'BXD42'), - ('BXD42', 7.682, None, None, 'BXD42'), - ('BXD40', 7.945, None, None, 'BXD40'), - ('BXD43', 7.873, None, None, 'BXD43') - ] - - database = mock.Mock() - db_cursor = mock.Mock() - db_cursor.execute.return_value = 6 - db_cursor.fetchall.return_value = database_results - database.cursor.return_value = db_cursor - - mock_pheno_query = """ - SELECT - Strain.Name, PublishData.value, PublishSE.error,NStrain.count, Strain.Name2 - WHERE - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = 1419792_at AND - PublishFreeze.Id = '12' AND PublishData.StrainId = Strain.Id - Order BY - Strain.Name - """ - fetch_results = fetch_from_db_sample_data(mock_pheno_query, database) - - self.assertEqual(fetch_results, database_results) - - @mock.patch("gn3.computations.datasets.dataset_creator_store") - @mock.patch("gn3.computations.datasets.dataset_type_getter") - def test_create_dataset(self, mock_dataset_type, mock_store): - """Test function that creates/fetches required dataset\ - can either be published phenotype,genotype,Microarray or\ - user defined ->Temp - """ - probe_name = "HC_M2_0606_P" - probe_type = "ProbeSet" - - mock_dataset_creator = namedtuple( - 'ProbeSet', ["dataset_name", "dataset_type"]) - - mock_store.return_value = mock_dataset_creator - mock_dataset_type.return_value = probe_type - dataset = create_dataset( - dataset_type=None, dataset_name=probe_name) - - self.assertEqual(dataset.dataset_name, probe_name) - self.assertEqual(dataset.dataset_type, probe_type) - - def test_dataset_creator_store(self): - """Test for functions that actual - function to create differerent \ - datasets - """ - results = dataset_creator_store("ProbeSet") - - self.assertTrue(results) - - def test_dataset_type_getter(self): - """Test for fetching type of dataset given\ - the dataset name - """ - - redis_instance = mock.Mock() - # fetched in redis - redis_instance.get.return_value = "ProbeSet" - results = dataset_type_getter("HC_M2_0_P", redis_instance) - self.assertEqual(results, "ProbeSet") - - @mock.patch("gn3.computations.datasets.requests") - def test_fetch_dataset_type_from_gn2_api(self, mock_request): - """Test for function that test fetching\ - all datasets from gn2 api in order to store\ - in redis - """ - - expected_json_results = {"datasets": { - "arabidopsis": { - "BayXSha": { - "Genotypes": [ - [ - "None", - "BayXShaGeno", - "BayXSha Genotypes" - ] - ], - "Phenotypes": [ - [ - "642", - "BayXShaPublish", - "BayXSha Published Phenotypes" - ] - ] - } - } - }} - - request_results = json.dumps(expected_json_results) - mock_request.get.return_value.content = request_results - results = fetch_dataset_type_from_gn2_api("HC_M2_0_P") - expected_results = { - "BayXShaGeno": "Geno", - "642": "Publish" - } - - self.assertEqual(expected_results, results) - - def test_fetch_dataset_sample_id(self): - """Get from the database the sample\ - id if only in the samplelists - """ - - expected_results = {"B6D2F1": 1, "BXD1": 4, "BXD11": 10, - "BXD12": 11, "BXD13": 12, "BXD15": 14, "BXD16": 15} - - database_instance = mock.Mock() - database_cursor = mock.Mock() - - database_cursor.execute.return_value = 5 - database_cursor.fetchall.return_value = list(expected_results.items()) - database_instance.cursor.return_value = database_cursor - strain_list = ["B6D2F1", "BXD1", "BXD11", - "BXD12", "BXD13", "BXD16", "BXD15"] - - results = fetch_dataset_sample_id( - samplelist=strain_list, database=database_instance, species="mouse") - - self.assertEqual(results, expected_results) - - @mock.patch("gn3.computations.datasets.fetch_from_db_sample_data") - @mock.patch("gn3.computations.datasets.divide_into_chunks") - def test_get_traits_data(self, mock_divide_into_chunks, mock_fetch_samples): - """Test for for function to get data\ - of traits in dataset - """ - _expected_results = {'AT_DSAFDS': [ - 12, 14, 13, 23, 12, 14, 13, 23, 12, 14, 13, 23]} - database = mock.Mock() - sample_id = [1, 2, 7, 3, 22, 8] - mock_divide_into_chunks.return_value = [ - [1, 2, 7], [3, 22, 8], [5, 22, 333]] - mock_fetch_samples.return_value = ("AT_DSAFDS", 12, 14, 13, 23) - results = get_traits_data(sample_id, database, "HC_M2", "Publish") - - self.assertEqual({}, dict(results)) - - def test_divide_into_chunks(self): - """Test for dividing a list into given number of\ - chunks for example - """ - results = divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3) - - expected_results = [[1, 2, 7], [3, 22, 8], [5, 22, 333]] - - self.assertEqual(results, expected_results) diff --git a/tests/unit/computations/test_trait.py b/tests/unit/computations/test_trait.py deleted file mode 100644 index feb97c6..0000000 --- a/tests/unit/computations/test_trait.py +++ /dev/null @@ -1,84 +0,0 @@ -"""Module contains tests for creating traits""" -from unittest import TestCase -from unittest import mock - -from gn3.computations.traits import fetch_trait -from gn3.computations.traits import get_trait_sample_data -from gn3.computations.traits import get_trait_info_data - - -class TestTrait(TestCase): - """Class contains tests for creating traits""" - - @mock.patch("gn3.computations.traits.get_trait_sample_data") - def test_fetch_trait(self, get_sample_data): - """Test for creating/fetching trait""" - - expected_sample_data = { - "A/Y": 12.3, - "WQC": 11.1 - } - - database = mock.Mock() - - get_sample_data.return_value = expected_sample_data - - expected_trait = { - "trait_name": "AXFDSF_AT", - "dataset": None, - "trait_data": expected_sample_data - } - results = fetch_trait(dataset=None, - trait_name="AXFDSF_AT", - database=database) - - self.assertEqual(results, expected_trait) - self.assertEqual(get_sample_data.call_count, 1) - - @mock.patch("gn3.computations.traits.retrieve_trait_sample_data") - def test_get_trait_sample_data(self, mock_retrieve_sample_data): - """Test for getting sample data from either\ - the trait's dataset or form redis - """ - - trait_dataset = mock.Mock() - dataset_trait_sample_data = [ - ('129S1/SvImJ', 7.433, None, None, '129S1/SvImJ'), - ('A/J', 7.596, None, None, 'A/J'), - ('AKR/J', 7.774, None, None, 'AKR/J'), - ('B6D2F1', 7.707, None, None, 'B6D2F1')] - mock_retrieve_sample_data.return_value = dataset_trait_sample_data - - trait_name = "1426679_at" - - database = mock.Mock() - - results = get_trait_sample_data( - trait_dataset, trait_name, database) - - expected_results = { - "129S1/SvImJ": 7.433, - "A/J": 7.596, - "AKR/J": 7.774, - "B6D2F1": 7.707 - } - - self.assertEqual(results, expected_results) - - def test_get_trait_info_data(self): - """Test for getting info data related\ - to trait - """ - - results = get_trait_info_data( - trait_name="AXSF_AT", trait_dataset=mock.Mock(), database_instance=None) - expected_trait_info = { - "description": "", - "trait_display_name": "", - "abbreviation": "", - "chr": "", - "mb": "", - "locus": "" - } - - self.assertEqual(results, expected_trait_info) |