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"""Tests for gn3/db/datasets.py"""
from unittest import mock, TestCase
from gn3.db.datasets import (
retrieve_dataset_name,
retrieve_group_fields,
retrieve_geno_group_fields,
retrieve_publish_group_fields,
retrieve_probeset_group_fields)
class TestDatasetsDBFunctions(TestCase):
"""Test cases for datasets functions."""
def test_retrieve_dataset_name(self):
"""Test that the function is called correctly."""
for trait_type, thresh, trait_name, dataset_name, columns, table, expected in [
["ProbeSet", 9, "probesetTraitName", "probesetDatasetName",
"Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze",
{"dataset_id": None, "dataset_name": "probesetDatasetName",
"dataset_fullname": "probesetDatasetName"}],
["Geno", 3, "genoTraitName", "genoDatasetName",
"Id, Name, FullName, ShortName", "GenoFreeze", {}],
["Publish", 6, "publishTraitName", "publishDatasetName",
"Id, Name, FullName, ShortName", "PublishFreeze", {}],
["Temp", 4, "tempTraitName", "tempTraitName",
"Id, Name, FullName, ShortName", "TempFreeze", {}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_type=trait_type):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = {}
self.assertEqual(
retrieve_dataset_name(
trait_type, thresh, trait_name, dataset_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
"SELECT {cols} "
"FROM {table} "
"WHERE public > %(threshold)s AND "
"(Name = %(name)s "
"OR FullName = %(name)s "
"OR ShortName = %(name)s)".format(
table=table, cols=columns),
{"threshold": thresh, "name": dataset_name})
def test_retrieve_probeset_group_fields(self):
"""
Test that the `group` and `group_id` fields are retrieved appropriately
for the 'ProbeSet' trait type.
"""
for trait_name, expected in [
["testProbeSetName", {}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
retrieve_probeset_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, ProbeSetFreeze, ProbeFreeze"
" WHERE ProbeFreeze.InbredSetId = InbredSet.Id"
" AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId"
" AND ProbeSetFreeze.Name = %(name)s"),
{"name": trait_name})
def test_retrieve_group_fields(self):
"""
Test that the group fields are set up correctly for the different trait
types.
"""
for trait_type, trait_name, dataset_info, expected in [
["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"},
{"dataset_name": "pubDBName01", "group": ""}],
["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"},
{"dataset_name": "prbDBName01", "group": ""}],
["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"},
{"dataset_name": "genoDBName01", "group": ""}],
["Temp", "tempTraitName01", {}, {"group": ""}],
]:
db_mock = mock.MagicMock()
with self.subTest(
trait_type=trait_type, trait_name=trait_name,
dataset_info=dataset_info):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ("group_name", 0)
self.assertEqual(
retrieve_group_fields(
trait_type, trait_name, dataset_info, db_mock),
expected)
def test_retrieve_publish_group_fields(self):
"""
Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Publish' trait type.
"""
for trait_name, expected in [
["testPublishName", {}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
retrieve_publish_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, PublishFreeze"
" WHERE PublishFreeze.InbredSetId = InbredSet.Id"
" AND PublishFreeze.Name = %(name)s"),
{"name": trait_name})
def test_retrieve_geno_group_fields(self):
"""
Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Geno' trait type.
"""
for trait_name, expected in [
["testGenoName", {}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
retrieve_geno_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, GenoFreeze"
" WHERE GenoFreeze.InbredSetId = InbredSet.Id"
" AND GenoFreeze.Name = %(name)s"),
{"name": trait_name})
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