def test_main_with_updates(self):
output = os.path.join(self.test_subdirectory, 'output.pbtxt')
with flagsaver.flagsaver(input_pattern=self.dataset1_filename,
update=True,
output=output):
process_dataset.main(())
self.assertTrue(os.path.exists(output))
dataset = message_helpers.load_message(output, dataset_pb2.Dataset)
self.assertLen(dataset.reactions, 1)
self.assertStartsWith(dataset.reactions[0].reaction_id, 'ord-')
def test_bad_dataset_id(self):
dataset = dataset_pb2.Dataset(reactions=[reaction_pb2.Reaction()],
dataset_id='not-a-real-dataset-id')
filename = os.path.join(self.test_subdirectory, 'test.pbtxt')
message_helpers.write_message(dataset, filename)
with flagsaver.flagsaver(root=self.test_subdirectory,
input_pattern=filename,
validate=False,
update=True):
with self.assertRaisesRegex(ValueError, 'malformed dataset ID'):
process_dataset.main(())
def test_main_with_updates(self):
output = os.path.join(self.test_subdirectory, 'output.pb')
with flagsaver.flagsaver(input_pattern=self.dataset1_filename,
update=True,
output=output):
process_dataset.main(())
self.assertTrue(os.path.exists(output))
with open(output, 'rb') as f:
dataset = dataset_pb2.Dataset.FromString(f.read())
self.assertLen(dataset.reactions, 1)
self.assertStartsWith(dataset.reactions[0].provenance.record_id,
'ord-')
def test_bad_dataset_id(self):
dataset = dataset_pb2.Dataset(reactions=[reaction_pb2.Reaction()],
dataset_id='not-a-real-dataset-id')
filename = os.path.join(self.test_subdirectory, 'test.pb')
with open(filename, 'wb') as f:
f.write(dataset.SerializeToString())
with flagsaver.flagsaver(root=self.test_subdirectory,
input_pattern=filename,
validate=False,
update=True):
with self.assertRaisesRegex(ValueError, 'malformed dataset ID'):
process_dataset.main(())
def test_main_with_validation_errors(self):
with flagsaver.flagsaver(input_pattern=self.dataset2_filename,
write_errors=True):
with self.assertRaisesRegex(ValueError,
'validation encountered errors'):
process_dataset.main(())
error_filename = f'{self.dataset2_filename}.error'
self.assertTrue(os.path.exists(error_filename))
expected_output = [
'Reactions should have at least 1 reaction input\n',
'Reactions should have at least 1 reaction outcome\n',
]
with open(error_filename) as f:
self.assertEqual(f.readlines(), expected_output)
def test_preserve_existing_dataset_id(self):
dataset = dataset_pb2.Dataset(
reactions=[reaction_pb2.Reaction()],
dataset_id='64b14868c5cd46dd8e75560fd3589a6b')
filename = os.path.join(self.test_subdirectory, 'test.pb')
with open(filename, 'wb') as f:
f.write(dataset.SerializeToString())
expected_filename = os.path.join(
self.test_subdirectory, 'data', '64',
'64b14868c5cd46dd8e75560fd3589a6b.pb')
self.assertFalse(os.path.exists(expected_filename))
with flagsaver.flagsaver(root=self.test_subdirectory,
input_pattern=filename,
validate=False,
update=True):
process_dataset.main(())
self.assertTrue(os.path.exists(expected_filename))
def _run_main(self, **kwargs):
subprocess.run(['git', 'add', '*.pbtxt', 'data/*/*.pbtxt'], check=True)
changed = subprocess.run(['git', 'diff', '--name-status', '--staged'],
check=True,
capture_output=True)
with open('changed.txt', 'wb') as f:
f.write(changed.stdout)
subprocess.run(['git', 'commit', '-m', 'Submission'], check=True)
run_flags = {
'input_file': 'changed.txt',
'update': True,
'cleanup': True
}
run_flags.update(kwargs)
with flagsaver.flagsaver(**run_flags):
process_dataset.main(())
return glob.glob(os.path.join(self.test_subdirectory, '**/*.pbtxt'),
recursive=True)
def test_main_with_too_many_flags(self):
with flagsaver.flagsaver(input_pattern=self.dataset1_filename,
input_file=self.dataset2_filename):
with self.assertRaisesRegex(ValueError, 'not both'):
process_dataset.main(())
def test_main_with_input_file(self):
input_file = os.path.join(self.test_subdirectory, 'input_file.txt')
with open(input_file, 'w') as f:
f.write(f'{self.dataset1_filename}\n')
with flagsaver.flagsaver(input_file=input_file):
process_dataset.main(())
def test_main_with_input_pattern(self):
with flagsaver.flagsaver(input_pattern=self.dataset1_filename):
process_dataset.main(())
