diff options
Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 36 |
1 files changed, 29 insertions, 7 deletions
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py index b42de50..99c2936 100644 --- a/tests/unit/computations/test_wgcna.py +++ b/tests/unit/computations/test_wgcna.py @@ -1,12 +1,16 @@ """module contains python code for wgcna""" + from unittest import TestCase from unittest import mock import pytest +import os.path + from gn3.computations.wgcna import dump_wgcna_data from gn3.computations.wgcna import compose_rscript_cmd from gn3.computations.wgcna import call_wgcna_script +from gn3.settings import R_SCRIPTS class TestWgcna(TestCase): @@ -124,14 +128,18 @@ class TestWgcna(TestCase): @pytest.mark.unit_test def test_compose_rscript_cmd(self): """test for composing wgcna cmd""" - wgcna_cmd = compose_rscript_cmd( - "wgcna.r", "/tmp/wgcna.json") - self.assertEqual( - wgcna_cmd, '"Rscript ./scripts/wgcna.r /tmp/wgcna.json"') - @pytest.mark.unit_test - @mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp") - @mock.patch("gn3.computations.wgcna.uuid.uuid4") + expected_cmd = '"Rscript /home/scripts/test_script.R tmp/wgcna.json"' + + cmd = compose_rscript_cmd(script_path="/home/scripts", + file_name="test_script.R", + temp_file_path="tmp/wgcna.json") + + self.assertEqual(cmd, expected_cmd) + + @ pytest.mark.unit_test + @ 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) @@ -170,3 +178,17 @@ class TestWgcna(TestCase): self.assertEqual( results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json") + + def test_if_scripts_file_exists(self): + """check if certain script files exists""" + + files_data = [ + ("wgcna_analysis.R", True), + ("ctl_analysis.R", True), + ("control_experiment.R", False) + ] + + for file_name, file_exists in files_data: + file_path = os.path.join(R_SCRIPTS, file_name) + self.assertIs(os.path.exists(file_path), file_exists, + f"the file {file_path} doesn't exist in path") |