diff options
Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 160 |
1 files changed, 160 insertions, 0 deletions
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py new file mode 100644 index 0000000..ec81d94 --- /dev/null +++ b/tests/unit/computations/test_wgcna.py @@ -0,0 +1,160 @@ +"""module contains python code for wgcna""" +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.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_dumping_data, + mock_compose_wgcna, + mock_run_cmd): + """test for calling wgcna script""" + + # pylint: disable = line-too-long + 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" + + 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 + }]} + + 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)): + + 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""" + # pylint: disable = line-too-long, + 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": 2, + "output": "could not read the json file" + } + + with mock.patch("builtins.open", mock.mock_open(read_data="")): + + 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""" + wgcna_cmd = compose_wgcna_cmd( + "wgcna.r", "/tmp/wgcna.json") + self.assertEqual( + wgcna_cmd, "Rscript ./scripts/wgcna.r /tmp/wgcna.json") + + @mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp") + @mock.patch("gn3.computations.wgcna.uuid.uuid4") + def test_create_json_file(self, file_name_generator): + """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 + } + + with mock.patch("builtins.open", mock.mock_open()) as file_handler: + + file_name_generator.return_value = "facb73ff-7eef-4053-b6ea-e91d3a22a00c" + + results = dump_wgcna_data( + expected_input) + + file_handler.assert_called_once_with( + "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w') + + self.assertEqual( + results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json") |