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-rw-r--r--tests/integration/test_datasets.py41
-rw-r--r--tests/integration/test_traits.py72
-rw-r--r--tests/unit/computations/test_datasets.py219
-rw-r--r--tests/unit/computations/test_trait.py84
4 files changed, 0 insertions, 416 deletions
diff --git a/tests/integration/test_datasets.py b/tests/integration/test_datasets.py
deleted file mode 100644
index f97d970..0000000
--- a/tests/integration/test_datasets.py
+++ /dev/null
@@ -1,41 +0,0 @@
-"""This module contains integration tests for datasets"""
-from unittest import TestCase
-from unittest import mock
-
-from collections import namedtuple
-from gn3.app import create_app
-
-
-class DatasetIntegrationTests(TestCase):
- """class contains integration tests for datasets"""
-
- def setUp(self):
- self.app = create_app().test_client()
-
- @mock.patch("gn3.api.datasets.create_dataset")
- def test_create_dataset(self, mock_dataset):
- """Test for creating dataset object"""
- mock_dataset_creator = namedtuple(
- 'ProbeSet', ["dataset_name", "dataset_type"])
- new_dataset = mock_dataset_creator("HC_M2_0606_P", "ProbeSet")
- mock_dataset.return_value = new_dataset
- response = self.app.get(
- "/api/dataset/create/HC_M2_0606_P/", follow_redirects=True)
- mock_dataset.assert_called_once_with(
- dataset_type=None, dataset_name="HC_M2_0606_P")
- results = response.get_json()["dataset"]
- self.assertEqual(results[1], "ProbeSet")
- self.assertEqual(response.status_code, 200)
-
- @mock.patch("gn3.api.datasets.get_traits_data")
- @mock.patch("gn3.api.datasets.database_connector")
- def test_fetch_traits_data(self, mock_db, mock_get_trait_data):
- """Test api/dataset/fetch_traits_data/d_name/d_type"""
-
- mock_get_trait_data.return_value = {}
- mock_db.return_value = (mock.Mock(), mock.Mock())
- response = self.app.get(
- "/api/dataset/fetch_traits_data/Aging-Brain-UCIPublish/Publish", follow_redirects=True)
-
- self.assertEqual(response.status_code, 200)
- self.assertEqual(response.get_json(), {"results": {}})
diff --git a/tests/integration/test_traits.py b/tests/integration/test_traits.py
deleted file mode 100644
index 410ba22..0000000
--- a/tests/integration/test_traits.py
+++ /dev/null
@@ -1,72 +0,0 @@
-"""module contains integration tests for trait endpoints"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.app import create_app
-
-
-class TraitIntegrationTest(TestCase):
- """class contains integration tests for\
- traits"""
-
- def setUp(self):
- self.app = create_app().test_client()
-
- @mock.patch("gn3.api.traits.fetch_trait")
- @mock.patch("gn3.api.traits.database_connector")
- def test_create_trait(self, mock_database, mock_fetch_trait):
- """test the endpoint for creating traits\
- endpoint requires trait name and dataset name"""
- mock_database.return_value = (mock.Mock(), mock.Mock())
- trait_results = {
- "dataset": None,
- "trait_name": "1449593_at",
- "trait_data": {
- "BXD11": 8.464,
- "BXD12": 8.414,
- "BXD13": 8.753,
- "BXD15": 8.5,
- "BXD16": 8.832
- }
-
- }
- mock_fetch_trait.return_value = trait_results
-
- results = self.app.get(
- "/api/trait/1449593_at/HC_M2_0606_P", follow_redirects=True)
-
- trait_data = results.get_json()
-
- self.assertEqual(mock_database.call_count, 1)
- self.assertEqual(results.status_code, 200)
- self.assertEqual(trait_data, trait_results)
-
- @mock.patch("gn3.api.traits.get_trait_info_data")
- def test_retrieve_trait_info(self, mock_get_trait_info):
- """integration test for endpoints for retrieving\
- trait info expects the dataset of trait to have been
- created"""
-
- trait_post_data = {
- "trait": {"trait_name": ""},
- "trait_dataset": {"dataset_name": ""}
- }
-
- expected_api_results = {
- "description": "trait description",
- "chr": "",
- "locus": "",
- "mb": "",
- "abbreviation": "trait_abbreviation",
- "trait_display_name": "trait_name"
-
- }
- mock_get_trait_info.return_value = expected_api_results
-
- trait_info = self.app.post(
- "/api/trait/trait_info/144_at", json=trait_post_data, follow_redirects=True)
-
- trait_info_results = trait_info.get_json()
-
- self.assertEqual(trait_info.status_code, 200)
- self.assertEqual(trait_info_results, expected_api_results)
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)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:53:56 +0000