Merge pull request #38 from genenetwork/feature/wgcna_analysis

script for wgcna analysis

1 files changed, 73 insertions, 0 deletions

diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
new file mode 100644
index 0000000..078449d
--- /dev/null
+++ b/tests/integration/test_wgcna.py
@@ -0,0 +1,73 @@
+"""integration tests for wgcna"""
+
+from unittest import TestCase
+from unittest import mock
+
+from gn3.app import create_app
+
+
+class WgcnaIntegrationTest(TestCase):
+    """class contains wgcna integration tests"""
+
+    def setUp(self):
+        self.app = create_app().test_client()
+
+    @mock.patch("gn3.api.wgcna.call_wgcna_script")
+    def test_wgcna_endpoint(self, mock_wgcna_script):
+        """test /api/wgcna/run_wgcna endpoint"""
+
+        wgcna_output_data = {
+            "code": 0,
+            "output": "run script successfully",
+            "data": {
+                "ModEigens": {
+                    "MEturquoise": [
+                        0.0646677768085351,
+                        0.137200224277058,
+                        0.63451113720732,
+                        -0.544002665501479,
+                        -0.489487590361863,
+                        0.197111117570427
+                    ]
+                },
+                "net_colors": {
+                    "X1": "turquoise",
+                    "X2": "turquoise",
+                    "X3": "turquoise",
+                    "X4": "turquoise"
+                },
+                "imageLoc": "/WGCNAoutput_1uujpTIpC.png"
+            }
+        }
+
+        request_data = {
+            "trait_names": [
+                "1455537_at",
+                "1425637_at"
+            ],
+            "trait_sample_data": [
+                {
+                    "129S1/SvImJ": 6.142,
+                    "A/J": 5.31,
+                    "AKR/J": 3.49,
+                    "B6D2F1": 2.899,
+                    "BALB/cByJ": 1.172,
+                    "BALB/cJ": 7.396
+                },
+                {
+                    "129S1/SvImJ": 1.42,
+                    "A/J": 2.31,
+                    "AKR/J": 5.49,
+                    "B6D2F1": 3.899,
+                    "BALB/cByJ": 1.172,
+                    "BALB/cJ": 7.396
+                }
+            ]
+        }
+        mock_wgcna_script.return_value = wgcna_output_data
+
+        response = self.app.post("/api/wgcna/run_wgcna",
+                                 json=request_data, follow_redirects=True)
+
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.get_json(), wgcna_output_data)