def get(self, user, execution_identifier):
execution_db = get_execution(execution_identifier, db.session)
execution, error = get_execution_as_model(user.username, execution_db)
if error:
return ErrorCodeAndMessageFormatter(EXECUTION_NOT_FOUND,
execution_identifier)
return execution
def test_put_valid_execution_name(self, test_client, session,
execution_id):
response = test_client.put('/executions/{}'.format(execution_id),
headers={"apiKey": standard_user().api_key},
data=json.dumps(PATCH_VALID_EXECUTION2))
assert response.status_code == 204
execution = session.query(ExecutionDB).filter_by(
identifier=execution_id).first()
execution, _ = get_execution_as_model(standard_user().username,
execution)
assert execution.name == PATCH_VALID_EXECUTION2["name"]
def test_put_parameter_no_change(self, test_client, session, execution_id):
response = test_client.put('/executions/{}'.format(execution_id),
headers={"apiKey": standard_user().api_key},
data=json.dumps(PATCH_NO_CHANGE_PARAMETER))
assert response.status_code == 204
execution = session.query(ExecutionDB).filter_by(
identifier=execution_id).first()
execution, _ = get_execution_as_model(standard_user().username,
execution)
assert (execution.pipeline_identifier !=
PATCH_NO_CHANGE_PARAMETER["pipelineIdentifier"])
def get(self, user):
offset = request.args.get('offset', type=query_converter)
limit = request.args.get(
'limit', type=query_converter) or PLATFORM_PROPERTIES.get(
'defaultLimitListExecutions')
user_executions = get_all_executions_for_user(user.username, limit,
offset, db.session)
for i, execution in enumerate(user_executions):
exe, error = get_execution_as_model(user.username, execution)
if error:
return error
user_executions[i] = exe
return user_executions
def put(self, user, execution_identifier):
execution_db = get_execution(execution_identifier, db.session)
if not execution_db:
return ErrorCodeAndMessageFormatter(EXECUTION_NOT_FOUND,
execution_identifier)
if execution_db.creator_username != user.username:
return UNAUTHORIZED
if execution_db.status != ExecutionStatus.Initializing:
return ErrorCodeAndMessageFormatter(CANNOT_REPLAY_EXECUTION,
execution_db.status.name)
execution, error = get_execution_as_model(user.username, execution_db)
if error:
return CORRUPTED_EXECUTION
# Get the descriptor path
descriptor_path = get_descriptor_path(user.username,
execution.identifier)
# Get appriopriate descriptor object
descriptor = Descriptor.descriptor_factory_from_type(
execution_db.descriptor)
if not descriptor:
# We don't have any descriptor defined for this pipeline type
logger = logging.getLogger('server-error')
logger.error(
"Unsupported descriptor type extracted from file at {}".format(
descriptor_path))
return ErrorCodeAndMessageFormatter(UNSUPPORTED_DESCRIPTOR_TYPE,
execution_db.descriptor)
modified_inputs_path = get_absolute_path_inputs_path(
user.username, execution.identifier)
if not os.path.isfile(modified_inputs_path):
logger = logging.getLogger('server-error')
logger.error("Absolute path inputs file not found at {}".format(
descriptor_path))
return UNEXPECTED_ERROR
# The execution is valid and we are now ready to start it
start_execution(user, execution, descriptor, modified_inputs_path)
def std_file_resource(user, execution_identifier, path_to_file):
execution_db = get_execution(execution_identifier, db.session)
if not execution_db:
error = ErrorCodeAndMessageFormatter(EXECUTION_NOT_FOUND,
execution_identifier)
return marshal(error), 400
if not is_safe_for_get(user, execution_db):
return UNAUTHORIZED
execution, error = get_execution_as_model(execution_db.creator_username,
execution_db)
if error:
return marshal(error), 400
std, error = get_std_file(user.username, execution_identifier,
path_to_file)
if error:
return marshal(error), 400
return Response(std, mimetype='text/plain')
def post(self, model, user):
_, error = validate_request_model(model, request.url_root)
if error:
return error
try:
# Get the descriptor path and type
(descriptor_path,
descriptor_type), error = get_original_descriptor_path_and_type(
model.pipeline_identifier)
if error:
return error
# Insert new execution to DB
new_execution = Execution(
name=model.name,
pipeline_identifier=model.pipeline_identifier,
descriptor=descriptor_type,
timeout=model.timeout,
status=ExecutionStatus.Initializing,
study_identifier=model.study_identifier,
creator_username=user.username)
db.session.add(new_execution)
db.session.commit()
# Execution directory creation
(execution_path,
carmin_files_path), error = create_execution_directory(
new_execution, user)
if error:
db.session.rollback()
return error
# Writing inputs to inputs file in execution directory
error = write_inputs_to_file(model, carmin_files_path)
if error:
delete_execution_directory(execution_path)
db.session.rollback()
return error
# Copying pipeline descriptor to execution folder
error = copy_descriptor_to_execution_dir(carmin_files_path,
descriptor_path)
if error:
delete_execution_directory(execution_path)
db.session.rollback()
return UNEXPECTED_ERROR
# Get appriopriate descriptor object
descriptor = Descriptor.descriptor_factory_from_type(
new_execution.descriptor)
if not descriptor:
delete_execution_directory(execution_path)
db.session.rollback()
# We don't have any descriptor defined for this pipeline type
logger = logging.getLogger('server-error')
logger.error(
"Unsupported descriptor type extracted from file at {}".
format(descriptor_path))
return ErrorCodeAndMessageFormatter(
UNSUPPORTED_DESCRIPTOR_TYPE, descriptor_type)
# Create a version of the inputs file with correct links
modified_inputs_path, error = create_absolute_path_inputs(
user.username, new_execution.identifier,
new_execution.pipeline_identifier, request.url_root)
if error:
delete_execution_directory(execution_path)
db.session.rollback()
return UNEXPECTED_ERROR
# We now validate the invocation
success, error = descriptor.validate(descriptor_path,
modified_inputs_path)
if not success: # If this fails, we will change the execution status to InitializationFailed and return this error
new_execution.status = ExecutionStatus.InitializationFailed
db.session.commit()
error_code_and_message = ErrorCodeAndMessageFormatter(
INVOCATION_INITIALIZATION_FAILED, new_execution.identifier)
return ErrorCodeAndMessageAdditionalDetails(
error_code_and_message, str(error))
# Get execution from DB (for safe measure)
execution_db = get_execution(new_execution.identifier, db.session)
if not execution_db:
return UNEXPECTED_ERROR
# Get execution back as a model from the DB for response
execution, error = get_execution_as_model(user.username,
execution_db)
if error:
return UNEXPECTED_ERROR
return execution
except IntegrityError:
db.session.rollback()