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import datetime
import unittest
from unittest import mock
from gn2.wqflask.show_trait.export_trait_data import dict_to_sorted_list
from gn2.wqflask.show_trait.export_trait_data import cmp_samples
from gn2.wqflask.show_trait.export_trait_data import export_sample_table
from gn2.wqflask.show_trait.export_trait_data import get_export_metadata
class AttributesSetter:
def __init__(self, obj):
for key, value in obj.items():
setattr(self, key, value)
class TestExportTraits(unittest.TestCase):
"""Test methods for exporting traits and metadata"""
@mock.patch("gn2.wqflask.show_trait.export_trait_data.datetime")
@mock.patch("gn2.wqflask.show_trait.export_trait_data.create_trait")
@mock.patch("gn2.wqflask.show_trait.export_trait_data.data_set")
def test_get_export_metadata(self, data_mock, trait_mock, date_mock):
"""test for exporting metadata with dataset.type=Publish"""
mock_dataset = AttributesSetter({"type": "Publish",
"name": "HC_M2_0606_P",
"dataset_name": "HC_M2_0606_P"})
mock_dataset.group = AttributesSetter({"name": "C"})
data_mock.create_dataset.return_value = mock_dataset
trait_data = {
"symbol": "Nr3c1",
"description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR",
"title": "Trait_1 title",
"authors": "XL_1",
"journal": ""
}
date_mock.datetime.now.return_value = datetime.datetime(
2022, 8, 8, 19, 2, 31, 628813)
trait_mock.return_value = AttributesSetter(trait_data)
results = get_export_metadata({
"trait_id": "1460303_at",
"trait_display_name": "1460303_at",
"dataset": "HC_M2_0606_P",
"group": "BXD",
})
expected = [["Phenotype ID:", "1460303_at"],
["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"],
["Group: ", "C"],
["Phenotype: ",
'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'],
["Authors: ", "XL_1"],
["Title: ", "Trait_1 title"],
["Journal: ", "N/A"],
["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"],
["Export Date: ", "August 08, 2022"],
["Export Time: ", "19:02 GMT"]]
self.assertEqual(results, expected)
def test_dict_to_sortedlist(self):
"""test for conversion of dict to sorted list"""
sample1 = {
"other": "exp1",
"name": "exp2"
}
sample2 = {
"se": 1,
"num_cases": 4,
"value": 6,
"name": 3
}
rever = {
"name": 3,
"value": 6,
"num_cases": 4,
"se": 1
}
oneItem = {
"item1": "one"
}
self.assertEqual(["exp2", "exp1"], dict_to_sorted_list(sample1))
self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(sample2))
self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(rever))
self.assertEqual(["one"], dict_to_sorted_list(oneItem))
"""test that the func returns the values not the keys"""
self.assertFalse(["other", "name"] == dict_to_sorted_list(sample1))
def test_cmp_samples(self):
"""test for comparing samples function"""
sampleA = [
[
("value", "other"),
("name", "test_name")
]
]
sampleB = [
[
("value", "other"),
("unknown", "test_name")
]
]
sampleC = [
[("other", "value"),
("name", "value")
],
[
("name", "value"),
("value", "name")
],
[
("other", "value"),
("name", "value"
)],
[
("name", "name1"),
("se", "valuex")
],
[(
"value", "name1"),
("se", "valuex")
],
[(
"other", "name1"),
("se", "valuex"
)
],
[(
"name", "name_val"),
("num_cases", "num_val")
],
[(
"other_a", "val_a"),
("other_b", "val"
)
]
]
results = [cmp_samples(val[0], val[1]) for val in sampleA]
resultB = [cmp_samples(val[0], val[1]) for val in sampleB]
resultC = [cmp_samples(val[0], val[1]) for val in sampleC]
self.assertEqual(1, *results)
self.assertEqual(-1, *resultB)
self.assertEqual([1, -1, 1, -1, -1, 1, -1, -1], resultC)
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