diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/test_rqtl2.py | 109 |
1 files changed, 109 insertions, 0 deletions
diff --git a/tests/unit/test_rqtl2.py b/tests/unit/test_rqtl2.py new file mode 100644 index 0000000..5e4f657 --- /dev/null +++ b/tests/unit/test_rqtl2.py @@ -0,0 +1,109 @@ +"""Module contains the unittest for rqtl2 functions """ +# pylint: disable=C0301 +from unittest import mock +import pytest +from gn3.computations.rqtl2 import compose_rqtl2_cmd +from gn3.computations.rqtl2 import generate_rqtl2_files +from gn3.computations.rqtl2 import prepare_files +from gn3.computations.rqtl2 import validate_required_keys + + +@pytest.mark.unit_test +@mock.patch("gn3.computations.rqtl2.write_to_csv") +def test_generate_rqtl2_files(mock_write_to_csv): + """Test for generating rqtl2 files from set of inputs""" + + mock_write_to_csv.side_effect = ( + "/tmp/workspace/geno_file.csv", + "/tmp/workspace/pheno_file.csv" + ) + data = {"crosstype": "riself", + "geno_data": [], + "pheno_data": [], + "alleles": ["L", "C"], + "geno_codes": { + "L": 1, + "C": 2 + }, + "na.strings": ["-", "NA"] + } + + test_results = generate_rqtl2_files(data, "/tmp/workspace") + expected_results = {"geno_file": "/tmp/workspace/geno_file.csv", + "pheno_file": "/tmp/workspace/pheno_file.csv", + **data + } + assert test_results == expected_results + + +@pytest.mark.unit_test +def test_validate_required_keys(): + """Test to validate required keys are in a dataset""" + required_keys = ["geno_data", "pheno_data", "geno_codes"] + assert ((False, + "Required key(s) missing: geno_data, pheno_data, geno_codes") + == validate_required_keys(required_keys, {}) + ) + assert ((True, + "") + == validate_required_keys(required_keys, { + "geno_data": [], + "pheno_data": [], + "geno_codes": {} + }) + ) + + +@pytest.mark.unit_test +def test_compose_rqtl2_cmd(): + """Test for composing rqtl2 command""" + input_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/input_file.json" + output_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/output_file.json" + directory = "/tmp/575732e-691e-49e5-8d82-30c564927c95" + expected_results = f"Rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 12 --threshold 0.05 --cores 1" + + # test for using default configs + assert compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", + input_file=input_file, + output_file=output_file, + workspace_dir=directory, + data={ + "nperm": 12, + "threshold": 0.05 + }, + config={}) == expected_results + + # test for default permutation and threshold and custom configs + expected_results = f"/bin/rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 0 --threshold 1 --cores 12" + assert (compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", + input_file=input_file, + output_file=output_file, + workspace_dir=directory, + data={}, + config={"MULTIPROCESSOR_PROCS": 12, "RSCRIPT": "/bin/rscript"}) + == expected_results) + + +@pytest.mark.unit_test +@mock.patch("gn3.computations.rqtl2.os.makedirs") +@mock.patch("gn3.computations.rqtl2.create_file") +@mock.patch("gn3.computations.rqtl2.uuid") +def test_preparing_rqtl_files(mock_uuid, mock_create_file, mock_mkdir): + """test to create required rqtl files""" + mock_create_file.return_value = None + mock_mkdir.return_value = None + mock_uuid.uuid4.return_value = "2fc75611-1524-418e-970f-67f94ea09846" + assert ( + ( + "/tmp/2fc75611-1524-418e-970f-67f94ea09846", + "/tmp/2fc75611-1524-418e-970f-67f94ea09846/rqtl2-input-2fc75611-1524-418e-970f-67f94ea09846.json", + "/tmp/2fc75611-1524-418e-970f-67f94ea09846/rqtl2-output-2fc75611-1524-418e-970f-67f94ea09846.json", + "/tmp/rqtl2-log-2fc75611-1524-418e-970f-67f94ea09846" + ) == prepare_files(tmpdir="/tmp/") + ) + # assert method to create files is called + expected_calls = [mock.call("/tmp/2fc75611-1524-418e-970f-67f94ea09846/rqtl2-input-2fc75611-1524-418e-970f-67f94ea09846.json"), + mock.call( + "/tmp/2fc75611-1524-418e-970f-67f94ea09846/rqtl2-output-2fc75611-1524-418e-970f-67f94ea09846.json"), + mock.call("/tmp/rqtl2-log-2fc75611-1524-418e-970f-67f94ea09846")] + mock_create_file.assert_has_calls(expected_calls) |