aboutsummaryrefslogtreecommitdiff
path: root/tests/unit/computations/test_datasets.py
diff options
context:
space:
mode:
authorAlexander Kabui2021-03-31 22:29:37 +0300
committerAlexander Kabui2021-03-31 22:29:37 +0300
commitf6c6851504f14a1a163b6eeb5e3653a5ec3f5ceb (patch)
treef4a4bfc24055065357b7bb59e73ded19f5a97b35 /tests/unit/computations/test_datasets.py
parentb88d63ac06f157a97cc88bee0ea702949a5a0c64 (diff)
downloadgenenetwork3-f6c6851504f14a1a163b6eeb5e3653a5ec3f5ceb.tar.gz
add datasets functions and endpoints
Diffstat (limited to 'tests/unit/computations/test_datasets.py')
-rw-r--r--tests/unit/computations/test_datasets.py83
1 files changed, 83 insertions, 0 deletions
diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py
index 408f13b..7135041 100644
--- a/tests/unit/computations/test_datasets.py
+++ b/tests/unit/computations/test_datasets.py
@@ -1,10 +1,18 @@
"""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
class TestDatasets(TestCase):
@@ -74,3 +82,78 @@ class TestDatasets(TestCase):
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()
+ # found 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)