add tests for calling wgcna_script

1 files changed, 89 insertions, 7 deletions

diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 64f6c14..57224b3 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -11,16 +11,98 @@ from gn3.computations.wgcna import call_wgcna_script
 class TestWgcna(TestCase):
     """test class for wgcna"""
 
+    @mock.patch("gn3.computations.wgcna.run_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
-    def test_call_wgcna_script(self, mock_dump):
-        """call wgcna script"""
+    def test_call_wgcna_script(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+        """test for calling wgcna script"""
+        mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
-        mock_dump.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+        mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
 
-        results = call_wgcna_script(
-            "/home/kabui/project/genenetwork3/scripts/wgcna_analysis.R", {})
+        request_data = {
+            "trait_names": ["1455537_at", "1425637_at", "1449593_at", "1421945_a_at", "1450423_s_at", "1423841_at", "1451144_at"],
+            "trait_sample_data": [
+                {
+                    "129S1/SvImJ": 7.142,
+                    "A/J": 7.31,
+                    "AKR/J": 7.49,
+                    "B6D2F1": 6.899,
+                    "BALB/cByJ": 7.172,
+                    "BALB/cJ": 7.396
+                },
+                {
+                    "129S1/SvImJ": 7.071,
+                    "A/J": 7.05,
+                    "AKR/J": 7.313,
+                    "B6D2F1": 6.999,
+                    "BALB/cByJ": 7.293,
+                    "BALB/cJ": 7.117
+                }]}
 
-        self.assertEqual(results, "dsedf")
+        mock_run_cmd_results = {
+
+            "code": 0,
+            "output": "Flagging genes and samples with too many missing values...\n  ..step 1\nAllowing parallel execution with up to 3 working processes.\npickSoftThreshold: will use block size 7.\n pickSoftThreshold: calculating connectivity for given powers...\n   ..working on genes 1 through 7 of 7\n   Flagging genes and samples with too many missing values...\n    ..step 1\n ..Working on block 1 .\n    TOM calculation: adjacency..\n    ..will not use multithreading.\nclustering..\n ....detecting modules..\n ....calculating module eigengenes..\n ....checking kME in modules..\n ..merging modules that are too close..\n     mergeCloseModules: Merging modules whose distance is less than 0.15\n     mergeCloseModules: less than two proper modules.\n      ..color levels are turquoise\n      ..there is nothing to merge.\n       Calculating new MEs...\n"
+        }
+
+        json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"outputdata\":{\"eigengenes\":[],\"colors\":[]}}"
+
+        expected_output = {
+
+            "data": {
+                "inputdata": {
+                    "trait_sample_data ": {},
+                    "minModuleSize": 30,
+                    "TOMtype": "unsigned"
+                },
+
+                "outputdata": {
+                    "eigengenes": [],
+                    "colors": []
+                }
+            },
+
+            **mock_run_cmd_results
+
+        }
+
+        with mock.patch("builtins.open", mock.mock_open(read_data=json_output)) as mock_file:
+
+            mock_run_cmd.return_value = mock_run_cmd_results
+
+            results = call_wgcna_script(
+                "Rscript/GUIX_PATH/scripts/r_file.R", request_data)
+
+            mock_dumping_data.assert_called_once_with(request_data)
+
+            mock_compose_wgcna.assert_called_once_with(
+                "Rscript/GUIX_PATH/scripts/r_file.R", "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+            mock_run_cmd.assert_called_once_with(
+                "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+            self.assertEqual(results, expected_output)
+
+    @mock.patch("gn3.computations.wgcna.run_cmd")
+    @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+    @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+    def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+        """test for calling wgcna script fails and generates the expected error"""
+        mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+        expected_error = {
+            "code": 127,
+            "output": "could not read the json file"
+        }
+
+        with mock.patch("builtins.open", mock.mock_open(read_data="")) as mock_file:
+
+            mock_run_cmd.return_value = expected_error
+            self.assertEqual(call_wgcna_script(
+                "input_file.R", ""), expected_error)
 
     def test_compose_wgcna_cmd(self):
         """test for composing wgcna cmd"""
@@ -29,7 +111,7 @@ class TestWgcna(TestCase):
         self.assertEqual(
             wgcna_cmd, "Rscript ./scripts/wgcna.r  /tmp/wgcna.json")
 
-    @skip("to  update tests")
+    @ 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)