diff options
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 96 |
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) |