initial commit for creating trait and datasets

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)