Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

1 files changed, 80 insertions, 38 deletions

diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
index 33e0de9..488a8a4 100644
--- a/tests/integration/test_correlation.py
+++ b/tests/integration/test_correlation.py
@@ -1,57 +1,99 @@
-"""Integration tests for correlation api"""
-
-import os
-import json
-import unittest
+"""module contains integration tests for correlation"""
+from unittest import TestCase
 from unittest import mock
-
 from gn3.app import create_app
 
 
-def file_path(relative_path):
-    """getting abs path for file """
-    dir_name = os.path.dirname(os.path.abspath(__file__))
-    split_path = relative_path.split("/")
-    new_path = os.path.join(dir_name, *split_path)
-    return new_path
+class CorrelationIntegrationTest(TestCase):
+    """class for correlation integration tests"""
 
-
-class CorrelationAPITest(unittest.TestCase):
-    # currently disable
-    """Test cases for the Correlation API"""
     def setUp(self):
         self.app = create_app().test_client()
 
-        with open(file_path("correlation_data.json")) as json_file:
-            self.correlation_data = json.load(json_file)
+    def test_fail(self):
+        """initial method for class that fails"""
+        self.assertEqual(2, 2)
+
+    @mock.patch("gn3.api.correlation.compute_all_sample_correlation")
+    def test_sample_r_correlation(self, mock_compute_samples):
+        """Test /api/correlation/sample_r/{method}"""
+        this_trait_data = {
+            "trait_id": "1455376_at",
+            "trait_sample_data": {
+                "C57BL/6J": "6.138",
+                "DBA/2J": "6.266",
+                "B6D2F1": "6.434",
+                "D2B6F1": "6.55",
+                "BXS2": "6.7"
+            }}
+
+        traits_dataset = [
+            {
+                "trait_id": "14192_at",
+                "trait_sample_data": {
+                    "DBA/2J": "7.13",
+                    "D2B6F1": "5.65",
+                    "BXD2": "1.46"
+                }
+            }
+        ]
+
+        correlation_input_data = {"corr_method": "pearson",
+                                  "this_trait": this_trait_data,
+                                  "target_dataset": traits_dataset}
+
+        expected_results = [
+            {
+                "sample_r": "-0.407",
+                "p_value": "6.234e-04"
+            },
+            {
+                "sample_r": "0.398",
+                "sample_p": "8.614e-04"
+            }
+        ]
+
+        mock_compute_samples.return_value = expected_results
+
+        api_response = {
+            "corr_results": expected_results
+        }
+
+        response = self.app.post("/api/correlation/sample_r/pearson",
+                                 json=correlation_input_data, follow_redirects=True)
 
-        with open(file_path("expected_corr_results.json")) as results_file:
-            self.correlation_results = json.load(results_file)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.get_json(), api_response)
 
-    def tearDown(self):
-        self.correlation_data = ""
+    @mock.patch("gn3.api.correlation.compute_all_lit_correlation")
+    def test_lit_correlation(self, mock_compute_corr):
+        """Test api/correlation/lit_corr/{species}/{gene_id}"""
 
-        self.correlation_results = ""
+        mock_compute_corr.return_value = []
 
-    @mock.patch("gn3.api.correlation.compute_correlation")
-    def test_corr_compute(self, compute_corr):
-        """Test that the correct response in correlation"""
+        post_data = [{"gene_id": 8, "lit_corr": 1}, {
+            "gene_id": 12, "lit_corr": 0.3}]
 
-        compute_corr.return_value = self.correlation_results
-        response = self.app.post("/api/correlation/corr_compute",
-                                 json=self.correlation_data,
-                                 follow_redirects=True)
+        response = self.app.post(
+            "/api/correlation/lit_corr/mouse/16", json=post_data, follow_redirects=True)
 
+        self.assertEqual(mock_compute_corr.call_count, 1)
         self.assertEqual(response.status_code, 200)
 
-    @mock.patch("gn3.api.correlation.compute_correlation")
-    def test_corr_compute_failed_request(self, compute_corr):
-        """test taht cormpute requests fails """
+    @mock.patch("gn3.api.correlation.compute_all_tissue_correlation")
+    def test_tissue_correlation(self, mock_tissue_corr):
+        """Test api/correlation/tissue_corr/{corr_method}"""
+        mock_tissue_corr.return_value = {}
 
-        compute_corr.return_value = self.correlation_results
+        primary_dict = {"trait_id": "1449593_at", "tissue_values": [1, 2, 3]}
 
-        response = self.app.post("/api/correlation/corr_compute",
-                                 json=None,
-                                 follow_redirects=True)
+        target_tissue_dict_list = [
+            {"trait_id": "1449593_at", "tissue_values": [1, 2, 3]}]
 
-        self.assertEqual(response.status_code, 400)
+        tissue_corr_input_data = {"primary_tissue": primary_dict,
+                                  "target_tissues": target_tissue_dict_list}
+
+        response = self.app.post("/api/correlation/tissue_corr/spearman",
+                                 json=tissue_corr_input_data, follow_redirects=True)
+
+        self.assertEqual(response.status_code, 200)