def test_validate_metadata_file_invalid_ontology(self, mock_storage_client,
mock_storage_blob):
"""Unconventional metadata file should fail validation
This basic test ensures that the external dependency
`scp-ingest-pipeline` in our public CLI works as expected.
"""
invalid_metadata_path = 'tests/data/invalid_array_v1.1.3.tsv'
with self.assertRaises(SystemExit) as cm:
validate_metadata_file(invalid_metadata_path)
self.assertEqual(cm.exception.code, 1)
def test_validate_metadata_file_invalid_ontology(self):
"""Unconventional metadata file should fail validation
This basic test ensures that the external dependency
`scp-ingest-pipeline` in our public CLI works as expected.
"""
convention_path = '../demo_data/AMC_v1.1.0.json'
invalid_metadata_path = 'tests/data/metadata_invalid_ontology.tsv'
with self.assertRaises(SystemExit) as cm:
validate_metadata_file(convention_path, invalid_metadata_path)
self.assertEqual(cm.exception.code, 1)
def test_validate_metadata_file_invalid_ontology(
self, mock_succeeded, mock_get_api_base,
):
"""Unconventional metadata file should fail validation
This basic test ensures that the external dependency
`scp-ingest-pipeline` in our public CLI works as expected.
"""
parsed_args = self.set_up_manage_study(
'upload-metadata',
'--study-name',
'CLI test',
'--file',
'tests/data/invalid_array_v1.1.3.tsv',
'--use-convention',
)
print(parsed_args)
SCPAPIManager = Mock()
SCPAPIManager.get_study_attribute.return_value = 'SCP555'
invalid_metadata_path = 'tests/data/invalid_array_v1.1.3.tsv'
with self.assertRaises(SystemExit) as cm:
validate_metadata_file(parsed_args, mock_get_connection())
self.assertEqual(cm.exception.code, 1)
def test_validate_metadata_file_valid_ontology(
self, mock_succeeded, mock_get_api_base,
):
"""Conventional metadata file should pass validation
This basic test ensures that the external dependency
`scp-ingest-pipeline` in our public CLI works as expected.
"""
parsed_args = self.set_up_manage_study(
'upload-metadata',
'--study-name',
'CLI test',
'--file',
'tests/data/valid_array_v20.0.0.tsv',
'--use-convention',
)
SCPAPIManager = Mock()
SCPAPIManager.get_study_attribute.return_value = 'SCP555'
valid_metadata_path = 'tests/data/valid_array_v20.0.0.tsv'
not self.assertRaises(
SystemExit, validate_metadata_file(parsed_args, mock_get_connection())
)
def test_validate_metadata_file_valid_ontology(self, mock_storage_client,
mock_storage_blob):
"""Conventional metadata file should pass validation
"""
valid_metadata_path = 'tests/data/valid_array_v1.1.3.tsv'
validate_metadata_file(valid_metadata_path)
def test_validate_metadata_file_valid_ontology(self):
"""Conventional metadata file should pass validation
"""
convention_path = '../demo_data/AMC_v1.1.0.json'
valid_metadata_path = 'tests/data/metadata_valid_ontology.tsv'
validate_metadata_file(convention_path, valid_metadata_path)