diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/integration/test_correlation.py | 4 | ||||
| -rw-r--r-- | tests/integration/test_datasets.py | 6 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 73 | ||||
| -rw-r--r-- | tests/unit/computations/test_datasets.py | 55 | ||||
| -rw-r--r-- | tests/unit/computations/test_trait.py | 16 |
5 files changed, 85 insertions, 69 deletions
diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py index 488a8a4..bc3f542 100644 --- a/tests/integration/test_correlation.py +++ b/tests/integration/test_correlation.py @@ -10,10 +10,6 @@ class CorrelationIntegrationTest(TestCase): def setUp(self): self.app = create_app().test_client() - def test_fail(self): - """initial method for class that fails""" - self.assertEqual(2, 2) - @mock.patch("gn3.api.correlation.compute_all_sample_correlation") def test_sample_r_correlation(self, mock_compute_samples): """Test /api/correlation/sample_r/{method}""" diff --git a/tests/integration/test_datasets.py b/tests/integration/test_datasets.py index 1d72234..34b7669 100644 --- a/tests/integration/test_datasets.py +++ b/tests/integration/test_datasets.py @@ -1,4 +1,4 @@ -"""this module contains integration tests for datasets""" +"""This module contains integration tests for datasets""" from unittest import TestCase from unittest import mock @@ -14,7 +14,7 @@ class DatasetIntegrationTests(TestCase): @mock.patch("gn3.api.datasets.create_dataset") def test_create_dataset(self, mock_dataset): - """test for creating dataset object""" + """Test for creating dataset object""" mock_dataset_creator = namedtuple( 'ProbeSet', ["dataset_name", "dataset_type"]) new_dataset = mock_dataset_creator("HC_M2_0606_P", "ProbeSet") @@ -29,7 +29,7 @@ class DatasetIntegrationTests(TestCase): @mock.patch("gn3.api.datasets.get_traits_data") def test_fetch_traits_data(self, mock_get_trait_data): - """test api/dataset/fetch_traits_data/d_name/d_type""" + """Test api/dataset/fetch_traits_data/d_name/d_type""" mock_get_trait_data.return_value = {} response = self.app.get( diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 84b9330..631dc18 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -1,4 +1,4 @@ -"""module contains the tests for correlation""" +"""Module contains the tests for correlation""" import unittest from unittest import TestCase from unittest import mock @@ -80,10 +80,10 @@ class DataBase(QueryableMixin): class TestCorrelation(TestCase): - """class for testing correlation functions""" + """Class for testing correlation functions""" def test_normalize_values(self): - """function to test normalizing values """ + """Function to test normalizing values """ results = normalize_values([2.3, None, None, 3.2, 4.1, 5], [3.4, 7.2, 1.3, None, 6.2, 4.1]) @@ -92,7 +92,7 @@ class TestCorrelation(TestCase): self.assertEqual(results, expected_results) def test_bicor(self): - """test for doing biweight mid correlation """ + """Test for doing biweight mid correlation """ results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6]) @@ -102,8 +102,9 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value") @mock.patch("gn3.computations.correlations.normalize_values") def test_compute_sample_r_correlation(self, norm_vals, compute_corr): - """test for doing sample correlation gets the cor\ - and p value and rho value using pearson correlation""" + """Test for doing sample correlation gets the cor\ + and p value and rho value using pearson correlation + """ primary_values = [2.3, 4.1, 5] target_values = [3.4, 6.2, 4.1] @@ -133,7 +134,7 @@ class TestCorrelation(TestCase): spearman_results, tuple, "message") def test_filter_shared_sample_keys(self): - """function to tests shared key between two dicts""" + """Function to tests shared key between two dicts""" this_samplelist = { "C57BL/6J": "6.638", @@ -162,7 +163,7 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.compute_sample_r_correlation") @mock.patch("gn3.computations.correlations.filter_shared_sample_keys") def test_compute_all_sample(self, filter_shared_samples, sample_r_corr): - """given target dataset compute all sample r correlation""" + """Given target dataset compute all sample r correlation""" filter_shared_samples.return_value = (["1.23", "6.565", "6.456"], [ "6.266", "6.565", "6.456"]) @@ -192,7 +193,6 @@ class TestCorrelation(TestCase): sample_all_results = [{"1419792_at": {"corr_coeffient": -1.0, "p_value": 0.9, "num_overlap": 6}}] - # ?corr_method: str, trait_vals, target_samples_vals self.assertEqual(compute_all_sample_correlation( this_trait=this_trait_data, target_dataset=traits_dataset), sample_all_results) @@ -204,9 +204,10 @@ class TestCorrelation(TestCase): @unittest.skip("not implemented") def test_tissue_lit_corr_for_probe_type(self): - """tests for doing tissue and lit correlation for trait list\ + """Tests for doing tissue and lit correlation for trait list\ if both the dataset and target dataset are probeset runs\ - on after initial correlation has been done""" + on after initial correlation has been done + """ results = tissue_lit_corr_for_probe_type( corr_type="tissue", top_corr_results={}) @@ -215,8 +216,9 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value") def test_tissue_correlation_for_trait_list(self, mock_compute_corr_coeff): - """test given a primary tissue values for a trait and and a list of\ - target tissues for traits do the tissue correlation for them""" + """Test given a primary tissue values for a trait and and a list of\ + target tissues for traits do the tissue correlation for them + """ primary_tissue_values = [1.1, 1.5, 2.3] target_tissues_values = [1, 2, 3] @@ -233,8 +235,9 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.fetch_lit_correlation_data") @mock.patch("gn3.computations.correlations.map_to_mouse_gene_id") def test_lit_correlation_for_trait_list(self, mock_mouse_gene_id, fetch_lit_data): - """fetch results from db call for lit correlation given a trait list\ - after doing correlation""" + """Fetch results from db call for lit correlation given a trait list\ + after doing correlation + """ target_trait_lists = [{"gene_id": 15}, {"gene_id": 17}, @@ -255,8 +258,9 @@ class TestCorrelation(TestCase): self.assertEqual(lit_results, expected_results) def test_fetch_lit_correlation_data(self): - """test for fetching lit correlation data from\ - the database where the input and mouse geneid are none""" + """Test for fetching lit correlation data from\ + the database where the input and mouse geneid are none + """ database_instance = DataBase() results = fetch_lit_correlation_data(database=database_instance, @@ -267,8 +271,9 @@ class TestCorrelation(TestCase): self.assertEqual(results, ("1", 0)) def test_fetch_lit_correlation_data_db_query(self): - """test for fetching lit corr coefficent givent the input\ - input trait mouse gene id and mouse gene id""" + """Test for fetching lit corr coefficent givent the input\ + input trait mouse gene id and mouse gene id + """ database_instance = DataBase() expected_results = ("1", 0.1) @@ -281,8 +286,9 @@ class TestCorrelation(TestCase): self.assertEqual(expected_results, lit_results) def test_query_lit_correlation_for_db_empty(self): - """test that corr coeffient returned is 0 given the\ - db value if corr coefficient is empty""" + """Test that corr coeffient returned is 0 given the\ + db value if corr coefficient is empty + """ database_instance = mock.Mock() database_instance.execute.return_value.fetchone.return_value = None @@ -294,8 +300,9 @@ class TestCorrelation(TestCase): self.assertEqual(lit_results, ("16", 0)) def test_query_formatter(self): - """test for formatting a query given the query string and also the\ - values""" + """Test for formatting a query given the query string and also the\ + values + """ query = """ SELECT VALUE FROM LCorr @@ -320,16 +327,18 @@ class TestCorrelation(TestCase): self.assertEqual(formatted_query, expected_formatted_query) def test_query_formatter_no_query_values(self): - """test for formatting a query where there are no\ - string placeholder""" + """Test for formatting a query where there are no\ + string placeholder + """ query = """SELECT * FROM USERS""" formatted_query = query_formatter(query) self.assertEqual(formatted_query, query) def test_map_to_mouse_gene_id(self): - """test for converting a gene id to mouse geneid\ - given a species which is not mouse""" + """Test for converting a gene id to mouse geneid\ + given a species which is not mouse + """ database_instance = mock.Mock() test_data = [("Human", 14), (None, 9), ("Mouse", 15), ("Rat", 14)] @@ -349,9 +358,10 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.lit_correlation_for_trait_list") def test_compute_all_lit_correlation(self, mock_lit_corr): - """test for compute all lit correlation which acts\ + """Test for compute all lit correlation which acts\ as an abstraction for lit_correlation_for_trait_list - and is used in the api/correlation/lit""" + and is used in the api/correlation/lit + """ database = mock.Mock() @@ -372,8 +382,9 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.tissue_correlation_for_trait_list") def test_compute_all_tissue_correlation(self, mock_tissue_corr): - """test for compute all tissue corelation which abstracts - api calling the tissue_correlation for trait_list""" + """Test for compute all tissue corelation which abstracts + api calling the tissue_correlation for trait_list + """ primary_tissue_dict = {"trait_id": "1419792_at", "tissue_values": [1, 2, 3, 4, 5]} diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py index 44ff527..f9e9c2b 100644 --- a/tests/unit/computations/test_datasets.py +++ b/tests/unit/computations/test_datasets.py @@ -1,4 +1,4 @@ -"""module contains tests from datasets""" +"""Module contains tests from datasets""" import json from unittest import TestCase @@ -19,12 +19,13 @@ from gn3.computations.datasets import get_traits_data class TestDatasets(TestCase): - """class contains tests for datasets""" + """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""" + """Test retrieving sample data\ + for trait from the dataset + """ trait_name = "1419792_at" dataset_id = "HC_M2_0606_P&" dataset_type = "Publish" @@ -47,7 +48,7 @@ class TestDatasets(TestCase): self.assertEqual(results, fetch_results) def test_query_for_dataset_sample(self): - """test for getting query for sample data""" + """Test for getting query for sample data""" no_results = get_query_for_dataset_sample("does not exists") @@ -57,8 +58,9 @@ class TestDatasets(TestCase): self.assertIsInstance(query_exists, str) def test_fetch_from_db_sample_data(self): - """test for function that fetches sample\ - results from the database""" + """Test for function that fetches sample\ + results from the database + """ database_results = [('BXD31', 8.001, None, None, 'BXD31'), ('BXD32', 7.884, None, None, 'BXD32'), @@ -91,9 +93,10 @@ class TestDatasets(TestCase): @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\ + """Test function that creates/fetches required dataset\ can either be published phenotype,genotype,Microarray or\ - user defined ->Temp""" + user defined ->Temp + """ probe_name = "HC_M2_0606_P" probe_type = "ProbeSet" @@ -109,28 +112,31 @@ class TestDatasets(TestCase): self.assertEqual(dataset.dataset_type, probe_type) def test_dataset_creator_store(self): - """test for functions that actual + """Test for functions that actual function to create differerent \ - datasets""" + 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""" + """Test for fetching type of dataset given\ + the dataset name + """ redis_instance = mock.Mock() - # found in redis + # 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\ + """Test for function that test fetching\ all datasets from gn2 api in order to store\ - in redis""" + in redis + """ expected_json_results = {"datasets": { "arabidopsis": { @@ -164,8 +170,9 @@ class TestDatasets(TestCase): self.assertEqual(expected_results, results) def test_fetch_dataset_sample_id(self): - """get from the database the sample\ - id if only in the samplelists""" + """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} @@ -187,10 +194,9 @@ class TestDatasets(TestCase): @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""" - # xtodo more tests needed for this - + """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() @@ -203,8 +209,9 @@ class TestDatasets(TestCase): self.assertEqual({}, dict(results)) def test_divide_into_chunks(self): - """test for dividing a list into given number of\ - chunks for example""" + """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]] diff --git a/tests/unit/computations/test_trait.py b/tests/unit/computations/test_trait.py index cdd8078..feb97c6 100644 --- a/tests/unit/computations/test_trait.py +++ b/tests/unit/computations/test_trait.py @@ -1,4 +1,4 @@ -"""module contains tests for creating traits""" +"""Module contains tests for creating traits""" from unittest import TestCase from unittest import mock @@ -8,11 +8,11 @@ from gn3.computations.traits import get_trait_info_data class TestTrait(TestCase): - """class contains tests for creating traits""" + """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""" + """Test for creating/fetching trait""" expected_sample_data = { "A/Y": 12.3, @@ -37,8 +37,9 @@ class TestTrait(TestCase): @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""" + """Test for getting sample data from either\ + the trait's dataset or form redis + """ trait_dataset = mock.Mock() dataset_trait_sample_data = [ @@ -65,8 +66,9 @@ class TestTrait(TestCase): self.assertEqual(results, expected_results) def test_get_trait_info_data(self): - """test for getting info data related\ - to trait""" + """Test for getting info data related\ + to trait + """ results = get_trait_info_data( trait_name="AXSF_AT", trait_dataset=mock.Mock(), database_instance=None) |