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authorAlexander Kabui2021-03-30 18:12:58 +0300
committerAlexander Kabui2021-03-30 18:12:58 +0300
commite6f10522833cbd75441766e5b8656b3f5925d6d7 (patch)
tree99ad19a80f3a22307164c4d6e0450e527a060640
parent5151987063eab58b10a2dd8e831ec036df217531 (diff)
downloadgenenetwork3-e6f10522833cbd75441766e5b8656b3f5925d6d7.tar.gz
initial commit for creating trait and datasets
-rw-r--r--gn3/computations/traits.py59
-rw-r--r--tests/integration/test_traits.py70
-rw-r--r--tests/unit/computations/test_trait.py81
3 files changed, 210 insertions, 0 deletions
diff --git a/gn3/computations/traits.py b/gn3/computations/traits.py
new file mode 100644
index 0000000..7386745
--- /dev/null
+++ b/gn3/computations/traits.py
@@ -0,0 +1,59 @@
+"""module contains all operating related to traits"""
+
+
+def compute_sum(rhs_val: int, lhs_val: int) -> int:
+ """initial function for trait module"""
+ return rhs_val + lhs_val
+
+
+def fetch_trait(dataset, trait_name: str) -> dict:
+ """this method creates a trait by\
+ fetching required data given the\
+ dataset and trait_name"""
+
+ created_trait = {
+ "dataset": dataset,
+ "trait_name": trait_name
+ }
+
+ trait_data = get_trait_sample_data(dataset, trait_name)
+
+ created_trait["trait_data"] = trait_data
+
+ return created_trait
+
+
+def get_trait_sample_data(trait_dataset, trait_name) -> dict:
+ """first try to fetch the traits sample data from redis if that\
+ try to fetch from the traits dataset redis is only used for\
+ temp dataset type which is not used in this case """
+
+ sample_results = trait_dataset.retrieve_sample_data(trait_name)
+
+ trait_data = {}
+
+ for (name, sample_value, _variance, _numcase, _name2) in sample_results:
+
+ trait_data[name] = sample_value
+ return trait_data
+
+
+def get_trait_info_data(trait_dataset,
+ trait_name: str,
+ database_instance,
+ get_qtl_info: bool = False) -> dict:
+ """given a dataset and trait_name return a dict containing all info\
+ regarding the get trait"""
+
+ _temp_var_holder = (trait_dataset, trait_name,
+ database_instance, get_qtl_info)
+ trait_info_data = {
+ "description": "",
+ "chr": "",
+ "locus": "",
+ "mb": "",
+ "abbreviation": "",
+ "trait_display_name": ""
+
+ }
+ return trait_info_data
diff --git a/tests/integration/test_traits.py b/tests/integration/test_traits.py
new file mode 100644
index 0000000..2f3433a
--- /dev/null
+++ b/tests/integration/test_traits.py
@@ -0,0 +1,70 @@
+"""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()
+
+ def test_home(self):
+ """test for initial endpoint for trait"""
+ results = self.app.get("/api/trait", follow_redirects=True)
+
+ self.assertEqual(200, results.status_code)
+
+ @mock.patch("gn3.api.traits.fetch_trait")
+ def test_create_trait(self, mock_fetch_trait):
+ """test the endpoint for creating traits\
+ endpoint requires trait name and dataset name"""
+
+ trait_results = {
+ "dataset": None,
+ "trait_name": "1449593_at",
+ "trait_data": {}
+
+ }
+ 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(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_trait.py b/tests/unit/computations/test_trait.py
new file mode 100644
index 0000000..20f0546
--- /dev/null
+++ b/tests/unit/computations/test_trait.py
@@ -0,0 +1,81 @@
+"""module contains tests for creating traits"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.computations.traits import compute_sum
+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"""
+
+ def test_sum(self):
+ """initial faling tests"""
+ results = compute_sum(2, 5)
+ self.assertEqual(results, 7)
+
+ @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
+ }
+
+ 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")
+
+ self.assertEqual(results, expected_trait)
+ get_sample_data.assert_called_once_with(None, "AXFDSF_AT")
+
+ def test_get_trait_sample_data(self):
+ """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')]
+ trait_dataset.retrieve_sample_data.return_value = dataset_trait_sample_data
+
+ trait_name = "1426679_at"
+
+ results = get_trait_sample_data(
+ trait_dataset, trait_name)
+
+ 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)