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"""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": [{"NAME": "Ge_code_1"}],
"pheno_data": [{"NAME": "14343_at"}],
"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
# assert data is written to the csv
expected_calls = [mock.call(
"/tmp/workspace",
"geno_file.csv",
[{"NAME": "Ge_code_1"}]
),
mock.call(
"/tmp/workspace",
"pheno_file.csv",
[{"NAME": "14343_at"}]
)]
mock_write_to_csv.assert_has_calls(expected_calls)
@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 --method LMM --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,
"method" : "LMM"
},
config={}) == expected_results
# test for default permutation, method 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 --method HK --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)
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