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import json
import os
import pytest
from gn3.computations.rust_correlation import CORRELATION_COMMAND
from gn3.computations.rust_correlation import generate_json_file
from gn3.computations.rust_correlation import generate_input_files
from gn3.computations.rust_correlation import run_correlation
from gn3.computations.rust_correlation import parse_correlation_output
@pytest.mark.unit_test
def test_run_correlation():
"""test calling rusts' correlation """
pass
@pytest.mark.unit_test
def test_generate_input():
"""test generating text files"""
test_dataset = [
"14_at,12.1,14.1,None",
"15_at,12.2,14.1,None",
"17_at,12.1,14.1,11.4"
]
(tmpdir, tmp_file) = generate_input_files(test_dataset, output_dir="/tmp")
with open(tmp_file, "r") as file_reader:
test_results = [line.rstrip() for line in file_reader]
os.remove(tmp_file)
assert test_results == test_dataset
@pytest.mark.unit_test
def test_json_file():
json_dict = {"tmp_dir": "/tmp/correlation",
"tmp_file": "/data.txt",
"method": "pearson",
"file_path": "/data.txt",
"x_vals": "12.1,11.3,16.5,7.5,3.2",
"file_delimiter": ","}
tmp_file = generate_json_file(**json_dict)
with open(tmp_file, "r+") as file_reader:
results = json.load(file_reader)
assert results == {
"method": "pearson",
"file_path": "/data.txt",
"x_vals": "12.1,11.3,16.5,7.5,3.2",
"file_delimiter": ","}
@pytest.mark.unit_test
def test_kwargs():
def rt(**kwargs):
return kwargs
assert rt(**{"name": "tt", "age": 12}) == {"name": "tt", "age": 12}
@pytest.mark.unit_test
def test_parse_results():
raw_data = [
["63.62", "0.97", "0.00"],
["19", "-0.96", "0.22"],
["77.92", "-0.94", "0.31"],
["84.04", "0.94", "0.11"],
["23", "-0.91", "0.11"]
]
expected_results = [{"trait_name": name, "corr_coeff": corr,
"p_val": pval} for (name, corr, pval) in raw_data]
assert parse_correlation_output(
"tests/unit/computations/data/correlation/sorted_results.txt") == expected_results
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