def select(self, model_name, raw_filters=None):
"""
Select data from a certain type e.g. blocks or spiketrains from the G-Node REST API
and convert the results to a list of model objects.
:param model_name: The name of the model as string.
:type model_name: str
:param raw_filters: Filters as defined by the G-Node REST API.
:type raw_filters: dict
:returns: A list of (filtered) results.
:rtype: list
"""
results = []
raw_filters = {} if raw_filters is None else raw_filters
location = Model.get_location(model_name)
url = urlparse.urljoin(self.location, location)
headers = {}
future = self.__session.get(url, headers=headers, params=raw_filters)
response = future.result()
self.raise_for_status(response)
raw_results = convert.json_to_collections(response.content, as_list=True)
for obj in raw_results:
results.append(convert.collections_to_model(obj))
return results
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 collections_to_model(collection, as_list=False):
"""
Converts objects of nested collections (list, dict) as produced by the json module
into a model object.
:param collection: The object or list of objects to convert.
:type collection: dict|list
:param as_list: If True the result is always a list.
:type as_list: bool
:returns: The converted object or a list of converted objects.
:rtype: Model|list
:raises: ValueError
"""
def clean(ref):
if ref.lower().startswith('http'):
return urlparse.urlparse(ref).path
return ref
models = []
# adjust json object
if isinstance(collection, list):
objects = collection
elif 'selected' in collection:
objects = collection['selected']
else:
objects = [collection]
# convert
for obj in objects:
if 'resource_uri' not in obj:
raise ValueError("Object identifier is missing")
location = urlparse.urlparse(obj['resource_uri']).path
api, version, category, model_name, obj_id = location.strip('/').split('/')
model_obj = Model.create(model_name)
for field_name in model_obj:
field = model_obj.get_field(field_name)
if field.is_child:
obj_field_name = field.name_mapping or field.type_info + '_set'
else:
obj_field_name = field.name_mapping or field_name
if not obj_field_name in obj:
continue
if field.type_info in ['data', 'datafile']:
value = obj[obj_field_name]
field_val = {
"units": obj.get(obj_field_name + '__unit', None),
"data": float(value) if field.type_info == 'data' else value
}
elif field_name == 'model':
field_val = model_name
elif field.is_child and obj[obj_field_name] is not None:
field_val = [clean(ref) for ref in obj[obj_field_name]]
else:
field_val = obj[obj_field_name]
if field_val is not None:
model_obj[field_name] = field_val
models.append(model_obj)
if not as_list:
if len(models) > 0:
models = models[0]
else:
models = None
return models
def to_model(self, obj, in_memory=False):
"""
Converts a native neo or odml object into model object.
:param obj: The object to convert.
:type obj: object
:param in_memory: store array data to disk (False) or keep inside the
converted model (True)
:returns: A new model object.
:rtype: Model
"""
# TODO detect unbound (newly created and not persisted) related objects and throw an error
# get type name and create a model
model_obj = None
for model_name in NativeDriver.RW_MAP:
cls = NativeDriver.RW_MAP[model_name]
if isinstance(obj, cls):
model_obj = Model.create(model_name)
break
if model_obj is None:
raise TypeError("The type of the native object (%s) is not a compatible type!" % type(obj))
# iterate over fields and set them on the model
for field_name in model_obj:
field = model_obj.get_field(field_name)
if field.type_info != "datafile": # non-data fields
if model_obj.model == 'section' and field_name \
in ['document', 'section']:
if model_obj.document is not None or \
model_obj.section is not None:
continue
parent = getattr(obj, 'parent')
if parent is not None and hasattr(parent, 'location'):
if isinstance(parent, odml.doc.Document):
model_obj['document'] = parent.location
elif isinstance(parent, odml.section.BaseSection):
model_obj['section'] = parent.location
elif hasattr(obj, field_name):
field_val = getattr(obj, field_name, field.default)
# special treatment for the location field
if field_name == "location" and field_val is not None:
model_obj.location = field_val
model_obj.id = field_val.split("/")[-1]
# process all child relationships
elif field.is_child:
if field_val is not None:
locations = []
for val in field_val:
if hasattr(val, 'location'):
locations.append(val.location)
model_obj[field_name] = locations
# process all parent relationships
elif field.is_parent:
if field_val is not None and hasattr(field_val, 'location'):
model_obj[field_name] = field_val.location
# data fields
elif field.type_info == "data":
if field_val is not None:
data = float(field_val)
units = field_val.dimensionality.string
model_obj[field_name] = {"data": data, "units": units}
# default
else:
if isinstance(field_val, numpy.ndarray):
field_val = list(field_val)
model_obj[field_name] = field_val
else: # datafile fields
is_array_1 = (
field_name == "signal" and model_obj.model in
(Model.ANALOGSIGNAL, Model.ANALOGSIGNALARRAY,
Model.IRREGULARLYSAMPLEDSIGNAL)
)
is_array_2 = (
field_name == "times" and
model_obj.model == Model.SPIKETRAIN
)
data_array = None
units = None
if is_array_1 or is_array_2:
data_array = obj
elif hasattr(obj, field_name):
data_array = getattr(obj, field_name, field.default)
if data_array is None:
continue
if hasattr(data_array, "dimensionality"):
units = data_array.dimensionality.string
if in_memory:
location_or_obj = data_array
else:
location_or_obj = self.store.set_array(data_array, temporary=True)
model_obj[field_name] = {"units": units, "data": location_or_obj}
return model_obj
def get_model_by_obj(cls, obj):
for model_name, model in cls.RW_MAP.items():
if isinstance(obj, model):
return Model.create(model_name)