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import unittest
from unittest import mock
from gn2.wqflask.api.mapping import initialize_parameters
from gn2.wqflask.api.mapping import do_mapping_for_api
class AttributeSetter:
def __init__(self, obj):
for key, value in obj.items():
setattr(self, key, value)
class MockGroup(AttributeSetter):
def get_marker(self):
self.markers = []
class TestMapping(unittest.TestCase):
def test_initialize_parameters(self):
expected_results = {
"format": "json",
"limit_to": False,
"mapping_method": "gemma",
"maf": 0.01,
"use_loco": True,
"num_perm": 0,
"perm_check": False,
"transform": False,
"genofile": False
}
results = initialize_parameters(
start_vars={}, dataset={}, this_trait={})
self.assertEqual(results, expected_results)
start_vars = {
"format": "F1",
"limit_to": "1",
"mapping_method": "rqtl",
"control_marker": True,
"pair_scan": "true",
"interval_mapping": "true",
"use_loco": "true",
"num_perm": "14",
"transform": "qnorm",
"genofile": "BXD.8.geno"
}
results_2 = initialize_parameters(
start_vars=start_vars, dataset={}, this_trait={})
expected_results = {
"format": "F1",
"limit_to": 1,
"mapping_method": "gemma",
"maf": 0.01,
"use_loco": True,
"num_perm": 14,
"perm_check": "ON",
"transform": "qnorm",
"genofile": "BXD.8.geno"
}
self.assertEqual(results_2, expected_results)
@mock.patch("gn2.wqflask.api.mapping.rqtl_mapping.run_rqtl")
@mock.patch("gn2.wqflask.api.mapping.gemma_mapping.run_gemma")
@mock.patch("gn2.wqflask.api.mapping.initialize_parameters")
@mock.patch("gn2.wqflask.api.mapping.retrieve_sample_data")
@mock.patch("gn2.wqflask.api.mapping.create_trait")
@mock.patch("gn2.wqflask.api.mapping.data_set.create_dataset")
def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
start_vars = {
"db": "Temp",
"trait_id": "dewf3232rff2",
"format": "F1",
"mapping_method": "gemma",
"use_loco": True
}
sampleList = ["S1", "S2", "S3", "S4"]
samplelist = ["S1", "S2", "S4"]
dataset = AttributeSetter({"group": samplelist})
this_trait = AttributeSetter({})
trait_data = AttributeSetter({
"data": {
"item1": AttributeSetter({"name": "S1", "value": "S1_value"}),
"item2": AttributeSetter({"name": "S2", "value": "S2_value"}),
"item3": AttributeSetter({"name": "S3", "value": "S3_value"}),
}
})
trait = AttributeSetter({
"data": trait_data
})
dataset.return_value = dataset
mock_trait.return_value = this_trait
mock_retrieve_sample.return_value = trait
mock_param.return_value = {
"format": "F1",
"limit_to": False,
"mapping_method": "gemma",
"maf": 0.01,
"use_loco": "True",
"num_perm": 14,
"perm_check": "ON"
}
run_gemma.return_value = ["results"]
results = do_mapping_for_api(start_vars=start_vars)
self.assertEqual(results, ("results", None))
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