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-rw-r--r--tests/unit/computations/test_datasets.py219
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diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py
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--- a/tests/unit/computations/test_datasets.py
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-"""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)