diff options
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 40 |
1 files changed, 28 insertions, 12 deletions
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py index 57224b3..ec81d94 100644 --- a/tests/unit/computations/test_wgcna.py +++ b/tests/unit/computations/test_wgcna.py @@ -1,5 +1,4 @@ """module contains python code for wgcna""" -from unittest import skip from unittest import TestCase from unittest import mock @@ -14,8 +13,13 @@ class TestWgcna(TestCase): @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): + 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" @@ -67,7 +71,7 @@ class TestWgcna(TestCase): } - with mock.patch("builtins.open", mock.mock_open(read_data=json_output)) as mock_file: + with mock.patch("builtins.open", mock.mock_open(read_data=json_output)): mock_run_cmd.return_value = mock_run_cmd_results @@ -77,7 +81,8 @@ class TestWgcna(TestCase): 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") + "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") @@ -88,17 +93,19 @@ class TestWgcna(TestCase): @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""" + """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": 127, + "code": 2, "output": "could not read the json file" } - with mock.patch("builtins.open", mock.mock_open(read_data="")) as mock_file: + with mock.patch("builtins.open", mock.mock_open(read_data="")): mock_run_cmd.return_value = expected_error self.assertEqual(call_wgcna_script( @@ -111,8 +118,9 @@ class TestWgcna(TestCase): self.assertEqual( wgcna_cmd, "Rscript ./scripts/wgcna.r /tmp/wgcna.json") - @ skip("to update tests") - def test_create_json_file(self): + @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) @@ -138,7 +146,15 @@ class TestWgcna(TestCase): "minModuleSize": 30 } - results = dump_wgcna_data( - expected_input) + 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, {}) + self.assertEqual( + results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json") |