21402440351

Committed 27 Jan 2026 03:08PM UTC coverage: 24.281%. First build

Build # 21402440351

Build Type

Pull #84

github

Committed by

web-flow

Commit Message

Merge 6785b1ded into a27e54d58

Pull Request Pull Request #84: [WIP] Add standard pull request template and workflow for unit testing

Run Details

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30.95

/tests/test_reloading_data.py

1	import unittest	2✔
2	import os	2✔
3	from unittest.mock import Mock, patch	2✔
4	from bento.common.utils import get_logger, NODES_CREATED, RELATIONSHIP_CREATED, NODES_DELETED, RELATIONSHIP_DELETED	2✔
5	from data_loader import DataLoader	2✔
6	from icdc_schema import ICDC_Schema	2✔
7	from props import Props	2✔
8	from neo4j import Driver	2✔
9
10
11	class MockNeo4jDriver(Driver):	2✔
12	"""Mock Neo4j driver for testing without a database connection"""
13	def __init__(self):	2✔
14	# Don't call super().__init__ to avoid actual connection
NEW 15	pass	×
16
17	def session(self, **kwargs):	2✔
NEW 18	session = Mock()	×
NEW 19	session.__enter__ = Mock(return_value=session)	×
NEW 20	session.__exit__ = Mock(return_value=False)	×
NEW 21	return session	×
22
23	def close(self):	2✔
NEW 24	pass	×
25
26	def verify_connectivity(self):	2✔
NEW 27	return True	×
28
29
30	class TestLoaderReload(unittest.TestCase):	2✔
31	def setUp(self):	2✔
32	# Use mock Neo4j driver instead of requiring environment variable
NEW 33	self.driver = MockNeo4jDriver()	×
34
35	# Use paths relative to the tests directory
NEW 36	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 37	self.data_folder = os.path.join(test_dir, 'data', 'COTC007B')	×
NEW 38	props_path = os.path.join(test_dir, 'data', 'props-icdc.yml')	×
NEW 39	model_path = os.path.join(test_dir, 'data', 'icdc-model.yml')	×
NEW 40	model_props_path = os.path.join(test_dir, 'data', 'icdc-model-props.yml')	×
41
NEW 42	props = Props(props_path)	×
NEW 43	self.schema = ICDC_Schema([model_path, model_props_path], props)	×
44	self.log = get_logger('Test Loader')	×
45	self.loader = DataLoader(self.driver, self.schema)	×
46	self.file_list = [	×
47	"data/Dataset/COP-program.txt",
48	"data/Dataset/COTC007B-case.txt",
49	"data/Dataset/COTC007B-cohort.txt",
50	"data/Dataset/COTC007B-cycle.txt",
51	"data/Dataset/COTC007B-demographic.txt",
52	"data/Dataset/COTC007B-diagnostic.txt",
53	"data/Dataset/COTC007B-enrollment.txt",
54	"data/Dataset/COTC007B-extent_of_disease.txt",
55	"data/Dataset/COTC007B-physical_exam.txt",
56	"data/Dataset/COTC007B-principal_investigator.txt",
57	"data/Dataset/COTC007B-prior_surgery.txt",
58	"data/Dataset/COTC007B-study.txt",
59	"data/Dataset/COTC007B-study_arm.txt",
60	"data/Dataset/COTC007B-vital_signs.txt",
61	"data/Dataset/NCATS-COP01-blood_samples.txt",
62	"data/Dataset/NCATS-COP01-case.txt",
63	"data/Dataset/NCATS-COP01-demographic.txt",
64	"data/Dataset/NCATS-COP01-diagnosis.txt",
65	"data/Dataset/NCATS-COP01-enrollment.txt",
66	"data/Dataset/NCATS-COP01-normal_samples.txt",
67	"data/Dataset/NCATS-COP01-tumor_samples.txt",
68	"data/Dataset/NCATS-COP01_20170228-GSL-079A-PE-Breen-NCATS-MEL-Rep1-Lane3.tar-file_neo4j.txt",
69	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep1-Lane1.tar-file_neo4j.txt",
70	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep1-Lane2.tar-file_neo4j.txt",
71	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep2-Lane1.tar-file_neo4j.txt",
72	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep3-Lane1.tar-file_neo4j.txt",
73	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep2-Lane2.tar-file_neo4j.txt",
74	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep2-Lane3.tar-file_neo4j.txt",
75	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep3-Lane2.tar-file_neo4j.txt",
76	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep3-Lane3.tar-file_neo4j.txt",
77	"data/Dataset/NCATS-COP01_cohort_file.txt",
78	"data/Dataset/NCATS-COP01_path_report_file_neo4j.txt",
79	"data/Dataset/NCATS-COP01_study_file.txt"
80	]
81	self.file_list_unique = [	×
82	"data/Dataset/COP-program.txt",
83	"data/Dataset/COTC007B-case.txt",
84	"data/Dataset/COTC007B-cohort.txt",
85	"data/Dataset/COTC007B-cycle.txt",
86	"data/Dataset/COTC007B-demographic.txt",
87	"data/Dataset/COTC007B-diagnostic.txt",
88	"data/Dataset/COTC007B-enrollment.txt",
89	"data/Dataset/COTC007B-extent_of_disease.txt",
90	"data/Dataset/COTC007B-physical_exam.txt",
91	"data/Dataset/COTC007B-principal_investigator.txt",
92	"data/Dataset/COTC007B-prior_surgery.txt",
93	"data/Dataset/COTC007B-study.txt",
94	"data/Dataset/COTC007B-study_arm.txt",
95	"data/Dataset/COTC007B-vital_signs_unique.txt",
96	"data/Dataset/NCATS-COP01-blood_samples.txt",
97	"data/Dataset/NCATS-COP01-case.txt",
98	"data/Dataset/NCATS-COP01-demographic.txt",
99	"data/Dataset/NCATS-COP01-diagnosis.txt",
100	"data/Dataset/NCATS-COP01-enrollment.txt",
101	"data/Dataset/NCATS-COP01-normal_samples.txt",
102	"data/Dataset/NCATS-COP01-tumor_samples.txt",
103	"data/Dataset/NCATS-COP01_20170228-GSL-079A-PE-Breen-NCATS-MEL-Rep1-Lane3.tar-file_neo4j.txt",
104	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep1-Lane1.tar-file_neo4j.txt",
105	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep1-Lane2.tar-file_neo4j.txt",
106	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep2-Lane1.tar-file_neo4j.txt",
107	"data/Dataset/NCATS-COP01_GSL-076A-Breen-NCATS-MEL-Rep3-Lane1.tar-file_neo4j.txt",
108	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep2-Lane2.tar-file_neo4j.txt",
109	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep2-Lane3.tar-file_neo4j.txt",
110	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep3-Lane2.tar-file_neo4j.txt",
111	"data/Dataset/NCATS-COP01_GSL-079A-Breen-NCATS-MEL-Rep3-Lane3.tar-file_neo4j.txt",
112	"data/Dataset/NCATS-COP01_cohort_file.txt",
113	"data/Dataset/NCATS-COP01_path_report_file_neo4j.txt",
114	"data/Dataset/NCATS-COP01_study_file.txt"
115	]
116
117
118	@unittest.skip("Skipping test that requires actual Neo4j database interaction")	2✔
119	def test_load_detect_duplicate(self):	2✔
NEW 120	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 121	self.assertRaises(Exception, self.loader.load([os.path.join(test_dir, "data/COTC007B/COTC007B-vital_signs.txt")], True, False, 'new', True, 1, '/tmp', False))	×
122
123
124	@unittest.skip("Skipping test that requires actual Neo4j database interaction")	2✔
125	def test_reload_with_new_and_delete_cohorts(self):	2✔
NEW 126	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 127	file_list_unique = [os.path.join(test_dir, f) for f in self.file_list_unique]	×
NEW 128	load_result = self.loader.load(file_list_unique, True, False, 'new', True, 1, '/tmp', False)	×
129	self.assertIsInstance(load_result, dict, msg='Load data failed!')	×
130	self.assertEqual(1832, load_result[NODES_CREATED])	×
131	self.assertEqual(1974, load_result[RELATIONSHIP_CREATED])	×
NEW 132	result = self.loader.load([os.path.join(test_dir, 'data/Dataset/COTC007B-cohort.txt')], True, False, 'delete', False, 1, '/tmp', False)	×
133	self.assertEqual(result[NODES_DELETED], 18)	×
134	self.assertEqual(result[RELATIONSHIP_DELETED], 101)	×
135
136	@unittest.skip("Skipping test that requires actual Neo4j database interaction")	2✔
137	def test_reload_with_new_and_delete_study(self):	2✔
NEW 138	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 139	file_list_unique = [os.path.join(test_dir, f) for f in self.file_list_unique]	×
NEW 140	load_result = self.loader.load(file_list_unique, True, False, 'new', True, 1, '/tmp', False)	×
141	self.assertIsInstance(load_result, dict, msg='Load data failed!')	×
142	self.assertEqual(1832, load_result[NODES_CREATED])	×
143	self.assertEqual(1974, load_result[RELATIONSHIP_CREATED])	×
NEW 144	result = self.loader.load([os.path.join(test_dir, 'data/Dataset/COTC007B-study.txt')], True, False, 'delete', False, 1, '/tmp', False)	×
145	self.assertEqual(result[NODES_DELETED], 1118)	×
146	self.assertEqual(result[RELATIONSHIP_DELETED], 1201)	×
147
NEW 148	result = self.loader.load([os.path.join(test_dir, 'data/Dataset/NCATS-COP01_study_file.txt')], True, False, 'delete', False, 1, '/tmp', False)	×
149	self.assertEqual(result[NODES_DELETED], 713)	×
150	self.assertEqual(result[RELATIONSHIP_DELETED], 773)	×
151
152	@unittest.skip("Skipping test that requires actual Neo4j database interaction")	2✔
153	def test_reload_with_new_and_delete_program(self):	2✔
NEW 154	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 155	file_list_unique = [os.path.join(test_dir, f) for f in self.file_list_unique]	×
NEW 156	load_result = self.loader.load(file_list_unique, True, False, 'new', True, 1, '/tmp', False)	×
157	self.assertIsInstance(load_result, dict, msg='Load data failed!')	×
158	self.assertEqual(1832, load_result[NODES_CREATED])	×
159	self.assertEqual(1974, load_result[RELATIONSHIP_CREATED])	×
NEW 160	result = self.loader.load([os.path.join(test_dir, 'data/Dataset/COP-program.txt')], True, False, 'delete', False, 1, '/tmp', False)	×
161	self.assertEqual(result[NODES_DELETED], 1832)	×
162	self.assertEqual(result[RELATIONSHIP_DELETED], 1974)	×
163
164
165	@unittest.skip("Skipping test that requires actual Neo4j database interaction")	2✔
166	def test_reload_upsert(self):	2✔
NEW 167	test_dir = os.path.dirname(os.path.abspath(__file__))	×
NEW 168	file_list = [os.path.join(test_dir, f) for f in self.file_list]	×
NEW 169	load_result = self.loader.load(file_list, True, False, 'upsert', True, 1, '/tmp', False)	×
170	self.assertIsInstance(load_result, dict, msg='Load data failed!')	×
171	self.assertEqual(1832, load_result[NODES_CREATED])	×
172	self.assertEqual(1974, load_result[RELATIONSHIP_CREATED])	×
173
174
175
176	if __name__ == '__main__':	2✔
177	unittest.main()	×

CBIIT / CCDI-C3DC-Dataloader / 21402440351

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