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"""Tests for db/phenotypes.py"""
from unittest import TestCase
from unittest import mock
from gn3.db import fetchall
from gn3.db import fetchone
from gn3.db import update
from gn3.db import update_raw
from gn3.db import diff_from_dict
from gn3.db.phenotypes import Phenotype
from gn3.db.phenotypes import Probeset
from gn3.db.metadata_audit import MetadataAudit
class TestCrudMethods(TestCase):
"""Test cases for CRUD methods"""
def test_update_phenotype_with_no_data(self):
"""Test that a phenotype is updated correctly if an empty Phenotype dataclass
is provided
"""
db_mock = mock.MagicMock()
self.assertEqual(update(
conn=db_mock, table="Phenotype",
data=Phenotype(), where=Phenotype()), None)
def test_update_phenotype_with_data(self):
"""
Test that a phenotype is updated correctly if some
data is provided
"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
type(cursor).rowcount = 1
self.assertEqual(update(
conn=db_mock, table="Phenotype",
data=Phenotype(
pre_pub_description="Test Pre Pub",
submitter="Rob",
post_pub_description="Test Post Pub"),
where=Phenotype(id_=1, owner="Rob")), 1)
cursor.execute.assert_called_once_with(
"UPDATE Phenotype SET "
"Pre_publication_description = %s, "
"Post_publication_description = %s, "
"Submitter = %s WHERE id = %s AND Owner = %s",
('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob'))
def test_fetch_phenotype(self):
"""Test that a single phenotype is fetched properly
"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
test_data = (
35, "Test pre-publication", "Test post-publication",
"Original description A", "cm^2", "pre-abbrev",
"post-abbrev", "LAB001", "R. W.", "R. W.", "R. W."
)
cursor.fetchone.return_value = test_data
phenotype = fetchone(db_mock,
"Phenotype",
where=Phenotype(id_=35, owner="Rob"))
self.assertEqual(phenotype.id_, 35)
self.assertEqual(phenotype.pre_pub_description,
"Test pre-publication")
cursor.execute.assert_called_once_with(
"SELECT * FROM Phenotype WHERE id = %s AND Owner = %s",
(35, 'Rob'))
def test_fetchall_metadataaudit(self):
"""Test that multiple metadata_audit entries are fetched properly
"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
test_data = (
1, 35, "Rob", ('{"pages": '
'{"old": "5099-5109", '
'"new": "5099-5110"}, '
'"month": {"old": "July", '
'"new": "June"}, '
'"year": {"old": "2001", '
'"new": "2002"}}'),
"2021-06-04 09:01:05")
cursor.fetchall.return_value = (test_data,)
metadata = list(fetchall(db_mock,
"metadata_audit",
where=MetadataAudit(dataset_id=35,
editor="Rob")))[0]
self.assertEqual(metadata.dataset_id, 35)
self.assertEqual(metadata.time_stamp,
"2021-06-04 09:01:05")
cursor.execute.assert_called_once_with(
("SELECT * FROM metadata_audit WHERE "
"dataset_id = %s AND editor = %s"),
(35, 'Rob'))
# pylint: disable=R0201
def test_probeset_called_with_right_columns(self):
"""Given a columns argument, test that the correct sql query is
constructed"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchall.return_value = None
fetchone(db_mock,
"ProbeSet",
where=Probeset(name="1446112_at"),
columns=["OMIM", "Probe_set_target_region"])
cursor.execute.assert_called_once_with(
"SELECT OMIM, Probe_set_target_region FROM ProbeSet WHERE "
"Name = %s",
("1446112_at",))
def test_diff_from_dict(self):
"""Test that a correct diff is generated"""
self.assertEqual(diff_from_dict({"id": 1, "data": "a"},
{"id": 2, "data": "b"}),
{"id": {"old": 1, "new": 2},
"data": {"old": "a", "new": "b"}})
def test_update_raw(self):
"""Test a raw update query"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
type(cursor).rowcount = 1
self.assertEqual(update_raw(
conn=db_mock,
table="PublishData",
set_=[("value", 1)],
where=("StrainId = '%s' AND DataId = '%s'",
(2, 8967049))),
1)
cursor.execute.assert_called_once_with(
"UPDATE PublishData SET "
"value = '%s' WHERE "
"StrainId = '%s' AND DataId = '%s'",
(1, 2, 8967049))
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