2 files changed, 99 insertions, 0 deletions
diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
new file mode 100644
index 0000000..39dabb2
--- /dev/null
+++ b/tests/integration/test_wgcna.py
@@ -0,0 +1,37 @@
+"""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_api):
+        """test /api/wgcna/run_wgcna endpoint"""
+
+        wgcna_api_data = {
+            "eigengenes": ["1224_at", "121412_at", "32342342-at"],
+            "dendrogram_file_location": "/tmp/dend1.png"
+
+        }
+        mock_wgcna_api.return_value = wgcna_api_data
+
+        request_data = {
+
+            "trait_sample_data": [],
+
+
+        }
+
+        response = self.app.post("/api/wgcna/run_wgcna",
+                                 json=request_data, follow_redirects=True)
+
+        self.assertEqual(response.status_code, 401)
+        self.assertEqual(response.get_json(), wgcna_api_data)
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
new file mode 100644
index 0000000..64f6c14
--- /dev/null
+++ b/tests/unit/computations/test_wgcna.py
@@ -0,0 +1,62 @@
+"""module contains python code for wgcna"""
+from unittest import skip
+from unittest import TestCase
+from unittest import mock
+
+from gn3.computations.wgcna import dump_wgcna_data
+from gn3.computations.wgcna import compose_wgcna_cmd
+from gn3.computations.wgcna import call_wgcna_script
+
+
+class TestWgcna(TestCase):
+    """test class for wgcna"""
+
+    @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+    def test_call_wgcna_script(self, mock_dump):
+        """call wgcna script"""
+
+        mock_dump.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        results = call_wgcna_script(
+            "/home/kabui/project/genenetwork3/scripts/wgcna_analysis.R", {})
+
+        self.assertEqual(results, "dsedf")
+
+    def test_compose_wgcna_cmd(self):
+        """test for composing wgcna cmd"""
+        wgcna_cmd = compose_wgcna_cmd(
+            "wgcna.r", "/tmp/wgcna.json")
+        self.assertEqual(
+            wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
+
+    @skip("to  update tests")
+    def test_create_json_file(self):
+        """test for writing the data to a csv file"""
+        # # All the traits we have data for (should not contain duplicates)
+        # All the strains we have data for (contains duplicates)
+
+        trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142,
+                                            "A/J": 7.31, "AKR/J": 7.49,
+                                            "B6D2F1": 6.899, "BALB/cByJ": 7.172,
+                                            "BALB/cJ": 7.396},
+                             "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05,
+                                            "AKR/J": 7.313,
+                                            "B6D2F1": 6.999, "BALB/cByJ": 7.293,
+                                            "BALB/cJ": 7.117},
+                             "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246,
+                                            "AKR/J": 7.754,
+                                            "B6D2F1": 6.866, "BALB/cByJ": 6.752,
+                                            "BALB/cJ": 7.269}
+
+                             }
+
+        expected_input = {
+            "trait_sample_data": trait_sample_data,
+            "TOMtype": "unsigned",
+            "minModuleSize": 30
+        }
+
+        results = dump_wgcna_data(
+            expected_input)
+
+        self.assertEqual(results, {})