def set(self, entity, avoid_collisions=False):
"""
Update or create an entity on the G-Node REST API. If an etag/guid is provided by the entity it
will be included in the header with 'If-match' if avoid_collisions is True.
:param entity: The entity to persist.
:type entity: Model
:param avoid_collisions: Try to avoid collisions (lost update problem)
:type avoid_collisions: bool
:returns: The updated entity.
:rtype: Model
:raises: RuntimeError If the changes collide with remote changes of the entity.
"""
if hasattr(entity, "location") and entity.location is not None:
method = 'put'
url = urlparse.urljoin(self.location, entity.location)
else:
method = 'post'
url = urlparse.urljoin(self.location, Model.get_location(entity.model))
data = convert.model_to_json_response(entity)
headers = {'Content-Type': 'application/json'}
if avoid_collisions and entity.guid is not None:
headers['If-match'] = entity.guid
future = getattr(self.__session, method)(url, data=data, headers=headers)
response = future.result()
if response.status_code == 304:
result = entity
else:
self.raise_for_status(response)
result = convert.collections_to_model(convert.json_to_collections(response.content))
return result
def dump(self, entity):
def get_children_fields(native, local):
child_field_names = filter(
lambda x: hasattr(native, x), local.child_fields
)
child_fields = [
getattr(native, x, []) for x in child_field_names
]
return filter(lambda x: (x is not None) and
not (hasattr(x, '_is_loaded') and not getattr(x, '_is_loaded')),
child_fields
)
name = uuid.uuid1().hex + ".h5"
path = os.path.join(tmp.gettempdir(), name) # FIXME get proper temppath
f = h5py.File(path)
todo = [entity] # a stack of objects to submit
processed = [] # collector of locations of processed objects
to_clean = [] # collector of objects to clean their fake IDs
while len(todo) > 0:
current_native = todo[0]
model = self.__driver.get_model_by_obj(current_native)
location = getattr(current_native, 'location', None)
if location is not None:
if location in processed:
continue # workaround to avoid duplicate processing for Neo
else:
location = os.path.join(
model.get_location(model.model),
"TEMP" + str(id(current_native))
) + "/" # fake location is needed to keep references
setattr(current_native, 'location', location)
to_clean.append(current_native)
current_local = self.__driver.to_model(current_native, in_memory=True)
current_group = f.create_group(name=location.replace("/", "-"))
current_group.create_dataset(
name="json", data=convert.model_to_json_response(current_local)
)
for field_name in current_local.datafile_fields:
field_val = current_local[field_name]
if field_val is not None and field_val["data"] is not None:
current_group.create_dataset(
name=field_name, data=field_val["data"]
)
processed.append(location)
todo.remove(current_native)
todo_ids = [id(obj) for obj in todo]
for children in get_children_fields(current_native, current_local):
for obj in children:
loc = getattr(obj, 'location', None)
if not (loc is not None and loc in processed) and \
not id(obj) in todo_ids:
todo.append(obj)
f.close()
for obj in to_clean:
delattr(obj, 'location')
return path
