def annotate_from_xml(cls, element, *args, **kwargs):
annot_elem = expect_none_or_single(
element.findall(NINEML + Annotations.element_name))
if annot_elem is not None:
# Extract the annotations
annotations = Annotations.from_xml(annot_elem)
# Get a copy of the element with the annotations stripped
element = copy(element)
element.remove(element.find(NINEML + Annotations.element_name))
else:
annotations = None
nineml_object = from_xml(cls, element, *args, **kwargs)
try:
nineml_object.annotations = annotations
except AttributeError:
raise
return nineml_object
def annotate_from_xml(cls, element, *args, **kwargs):
annot_elem = expect_none_or_single(
element.findall(NINEML + Annotations.element_name))
if annot_elem is not None:
# Extract the annotations
annotations = Annotations.from_xml(annot_elem)
# Get a copy of the element with the annotations stripped
element = copy(element)
element.remove(element.find(NINEML + Annotations.element_name))
else:
annotations = None
nineml_object = from_xml(cls, element, *args, **kwargs)
try:
nineml_object.annotations = annotations
except AttributeError:
raise
return nineml_object
def from_xml(cls, element, document):
check_tag(element, cls)
# Get Name
name = element.get('name')
# Get Source
e = expect_single(element.findall(NINEML + 'Source'))
e = expect_single(e.findall(NINEML + 'Reference'))
source = nineml.user_layer.Reference.from_xml(
e, document).user_layer_object
# Get Destination
e = expect_single(element.findall(NINEML + 'Destination'))
e = expect_single(e.findall(NINEML + 'Reference'))
destination = nineml.user_layer.Reference.from_xml(
e, document).user_layer_object
# Get Response
e = element.find(NINEML + 'Response')
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
response = Component.from_xml(component, document)
# Get Plasticity
e = expect_none_or_single(element.findall(NINEML + 'Plasticity'))
if e is not None:
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
plasticity = Component.from_xml(component, document)
else:
plasticity = None
# Get Connectivity
e = element.find(NINEML + 'Connectivity')
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
connectivity = Component.from_xml(component, document)
# Get Delay
delay = Delay.from_xml(
expect_single(element.findall(NINEML + 'Delay')), document)
# Get port connections by Loop through 'source', 'destination',
# 'response', 'plasticity' tags and extracting the "From*" elements
port_connections = []
for receive_role in cls._component_roles:
# Get element for component name
e = element.find(NINEML + receive_role.capitalize())
if e is not None: # Plasticity is not required
# Loop through all incoming port connections and add them to
# list
for sender_role in cls._component_roles:
pc_elems = e.findall(NINEML +
'From' + sender_role.capitalize())
if sender_role == receive_role and pc_elems:
msg = ("{} port connection receives from itself in "
"Projection '{}'".format(name, name))
raise NineMLRuntimeError(msg)
if (sender_role is 'plasticity' and plasticity is None and
len(pc_elems)):
msg = ("{} port connection receives from plasticity, "
"which wasn't provided for Projection '{}'"
.format(receive_role, name))
raise NineMLRuntimeError(msg)
for pc in pc_elems:
port_connections.append(
PortConnection(sender_role, receive_role,
pc.get('send_port'),
pc.get('receive_port')))
return cls(name=element.attrib["name"],
source=source,
destination=destination,
response=response,
plasticity=plasticity,
connectivity=connectivity,
delay=delay,
port_connections=port_connections)
def from_xml(cls, element, document):
check_tag(element, cls)
# Get Name
name = element.get('name')
# Get Source
e = expect_single(element.findall(NINEML + 'Source'))
e = expect_single(e.findall(NINEML + 'Reference'))
source = nineml.user_layer.Reference.from_xml(
e, document).user_layer_object
# Get Destination
e = expect_single(element.findall(NINEML + 'Destination'))
e = expect_single(e.findall(NINEML + 'Reference'))
destination = nineml.user_layer.Reference.from_xml(
e, document).user_layer_object
# Get Response
e = element.find(NINEML + 'Response')
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
response = Component.from_xml(component, document)
# Get Plasticity
e = expect_none_or_single(element.findall(NINEML + 'Plasticity'))
if e is not None:
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
plasticity = Component.from_xml(component, document)
else:
plasticity = None
# Get Connectivity
e = element.find(NINEML + 'Connectivity')
component = e.find(NINEML + 'Component')
if component is None:
component = e.find(NINEML + 'Reference')
connectivity = Component.from_xml(component, document)
# Get Delay
delay = Delay.from_xml(
expect_single(element.findall(NINEML + 'Delay')), document)
# Get port connections by Loop through 'source', 'destination',
# 'response', 'plasticity' tags and extracting the "From*" elements
port_connections = []
for receive_role in cls._component_roles:
# Get element for component name
e = element.find(NINEML + receive_role.capitalize())
if e is not None: # Plasticity is not required
# Loop through all incoming port connections and add them to
# list
for sender_role in cls._component_roles:
pc_elems = e.findall(NINEML + 'From' +
sender_role.capitalize())
if sender_role == receive_role and pc_elems:
msg = ("{} port connection receives from itself in "
"Projection '{}'".format(name, name))
raise NineMLRuntimeError(msg)
if (sender_role is 'plasticity' and plasticity is None
and len(pc_elems)):
msg = (
"{} port connection receives from plasticity, "
"which wasn't provided for Projection '{}'".format(
receive_role, name))
raise NineMLRuntimeError(msg)
for pc in pc_elems:
port_connections.append(
PortConnection(sender_role, receive_role,
pc.get('send_port'),
pc.get('receive_port')))
return cls(name=element.attrib["name"],
source=source,
destination=destination,
response=response,
plasticity=plasticity,
connectivity=connectivity,
delay=delay,
port_connections=port_connections)
