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import unittest
from unittest import mock
from dataclasses import dataclass
from gn2.wqflask.marker_regression.rqtl_mapping import run_rqtl
@dataclass
class MockGroup:
name: str
genofile: str
@dataclass
class MockDataset:
group: MockGroup
class TestRqtlMapping(unittest.TestCase):
"""Tests for functions in rqtl_mapping.py"""
@mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.requests.post")
@mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.locate")
@mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
"""Test for run_rqtl with permutations > 0"""
dataset_group = MockGroup("GP1", "file_geno")
dataset = MockDataset(dataset_group)
mock_write_pheno_file.return_value = "pheno_filename"
mock_locate.return_value = "geno_filename"
mock_post.return_value = mock.Mock(ok=True)
mock_post.return_value.json.return_value = {"perm_results": [],
"suggestive": 3,
"significant": 4,
"results" : []}
results = run_rqtl(trait_name="the_trait", vals=[], samples=[],
dataset=dataset, pair_scan=False, mapping_scale="cM", model="normal", method="hk",
num_perm=5, perm_strata_list=[], do_control="false", control_marker="",
manhattan_plot=True, cofactors="")
mock_write_pheno_file.assert_called_once()
mock_locate.assert_called_once()
mock_post.assert_called_once()
self.assertEqual(results, ([], 3, 4, []))
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