def insert_subnode(self, namespace, subnode):
"""Insert a subnode into this component
:param subnode: An object of type ``DynamicsClass``.
:param namespace: A `string` specifying the name of the component in
this components namespace.
:raises: ``NineMLRuntimeException`` if there is already a subcomponent
at the same namespace location
.. note::
This method will clone the subnode.
"""
if not isinstance(namespace, basestring):
err = 'Invalid namespace: %s' % type(subnode)
raise NineMLRuntimeError(err)
if not isinstance(subnode, DynamicsClass):
err = 'Attempting to insert invalid '
err += 'object as subcomponent: %s' % type(subnode)
raise NineMLRuntimeError(err)
if namespace in self.subnodes:
err = 'Key already exists in namespace: %s' % namespace
raise NineMLRuntimeError(err)
self.subnodes[namespace] = DynamicsClonerVisitor().visit(subnode)
self.subnodes[namespace].set_parent_model(self)
self._validate_self()
def __init__(self, filename):
cls = TestableComponent
# If we recieve a filename like 'iaf', that doesn't
# end in '.py', then lets prepend the component directory
# and append .py
if not filename.endswith('.py'):
compdir = LocationMgr.getComponentDir()
filename = os.path.join(compdir, '%s.py' % filename)
self.filename = filename
self.mod = load_py_module(filename)
# Get the component functor:
if cls.functor_name not in self.mod.__dict__.keys():
err = """Can't load TestableComponnet from %s""" % self.filename
err += """Can't find required method: %s""" % cls.functor_name
raise NineMLRuntimeError(err)
self.component_functor = self.mod.__dict__[cls.functor_name]
# Check the functor will actually return us an object:
try:
c = self.component_functor()
except Exception:
raise NineMLRuntimeError('component_functor() threw an exception')
if not isinstance(c, DynamicsClass):
raise NineMLRuntimeError('Functor does not return Component Class')
# Try and get the meta-data
self.metadata = None
if cls.metadata_name in self.mod.__dict__.keys():
self.metadata = self.mod.__dict__[cls.metadata_name]
def set_flattener(self, flattener):
"""Specifies the flattening object used to create this component, if
this component was flattened from a hierarchical component"""
if not flattener:
raise NineMLRuntimeError('Setting flattener to None??')
if self.flattener:
raise NineMLRuntimeError('Trying to change flattener')
self._flattener = flattener
def standardize_units(self):
"""
Standardized the units into a single set (no duplicates). Used to avoid
naming conflicts when writing to file.
"""
# Get the set of all units and dimensions that are used in the document
# Note that Dimension & Unit objects are equal even if they have
# different names so when this set is traversed the dimension/unit will
# be substituted for the first equivalent dimension/unit.
all_units = set(chain(*[o.all_units for o in self.itervalues()]))
all_dimensions = set(
chain([u.dimension for u in all_units],
*[o.all_dimensions for o in self.itervalues()]))
# Delete unused units from the document
for k, o in self.items():
if ((isinstance(o, nineml.abstraction_layer.Unit)
and o not in all_units)
or (isinstance(o, nineml.abstraction_layer.Dimension)
and o not in all_dimensions)):
del self[k]
# Add missing units and dimensions to the document
for unit in all_units:
if unit.name in self:
if unit != self[unit.name]:
raise NineMLRuntimeError(
"Name of unit '{}' conflicts with existing object of "
"differring value or type '{}' and '{}'".format(
unit.name, unit, self[unit.name]))
self[unit.name] = unit
for dimension in all_dimensions:
if dimension.name in self:
if dimension != self[dimension.name]:
raise NineMLRuntimeError(
"Name of dimension '{}' conflicts with existing object"
" of differring value or type '{}' and '{}'".format(
dimension.name, dimension, self[unit.name]))
self[dimension.name] = dimension
# Replace units and dimensions with those in the superset
for obj in self.itervalues():
for a in obj.attributes_with_dimension:
try:
std_dim = next(d for d in all_dimensions
if d == a.dimension)
except StopIteration:
assert False, \
("Did not find matching dimension in supposed superset"
" of dimensions")
a.set_dimension(std_dim)
for a in obj.attributes_with_units:
try:
std_units = next(u for u in all_units if u == a.units)
except StopIteration:
assert False, \
("Did not find matching unit in supposed superset"
" of units")
a.set_units(std_units)
def __init__(self, lhs, rhs):
ExpressionWithLHS.__init__(self, rhs)
if not MathUtil.is_single_symbol(lhs):
err = 'Expecting a single symbol on the LHS; got: %s' % lhs
raise NineMLRuntimeError(err)
if not is_valid_lhs_target(lhs):
err = 'Invalid LHS target: %s' % lhs
raise NineMLRuntimeError(err)
self._lhs = lhs.strip()
def add(self, element):
try:
if not isinstance(element, TopLevelObject):
raise NineMLRuntimeError(
"Could not add {} as it is not a document level NineML "
"object ('{}') ".format(element.element_name,
"', '".join(self.top_level_types)))
except AttributeError:
raise NineMLRuntimeError("Could not add {} as it is not a NineML "
"object".format(element))
if element.name in self:
raise NineMLRuntimeError(
"Could not add element '{}' as an element with that name "
"already exists in the document".format(element.name))
self[element.name] = element
def from_xml(cls, element, url=None):
if element.tag != NINEML + cls.element_name:
raise Exception("Not a NineML root ('{}')".format(element.tag))
# Initialise the document
elements = {'_url': url}
# Loop through child elements, determine the class needed to extract
# them and add them to the dictionary
annotations = None
for child in element.getchildren():
if child.tag.startswith(NINEML):
element_name = child.tag[len(NINEML):]
if element_name == Annotations.element_name:
assert annotations is None, \
"Multiple annotations tags found"
annotations = Annotations.from_xml(child)
continue
try:
child_cls = getattr(nineml.user_layer, element_name)
except AttributeError:
try:
child_cls = getattr(nineml.abstraction_layer,
element_name)
except AttributeError:
raise NineMLRuntimeError(
"Did not find matching NineML class for '{}' "
"element".format(element_name))
if not issubclass(child_cls, TopLevelObject):
raise NineMLRuntimeError(
"'{}' is not a valid top-level NineML element".format(
element_name))
else:
raise NotImplementedError(
"Cannot load '{}' element (extensions not implemented)".
format(child.tag))
# Units use 'symbol' as their unique identifier (from LEMS) all
# other elements use 'name'
name = child.attrib.get('name', child.attrib.get('symbol'))
if name in elements:
raise NineMLRuntimeError(
"Duplicate identifier '{ob1}:{name}'in NineML file '{url}'"
.format(name=name,
ob1=elements[name].cls.element_name,
ob2=child_cls.element_name,
url=url or ''))
elements[name] = cls._Unloaded(name, child, child_cls)
document = cls(**elements)
document.annotations = annotations
return document
def __init__(self, name, dimension=None, reduce_op='+'):
if reduce_op not in self._reduce_op_map.keys():
err = ("%s('%s')" + "specified undefined reduce_op: '%s'") %\
(self.__class__.__name__, name, str(reduce_op))
raise NineMLRuntimeError(err)
super(AnalogReducePort, self).__init__(name, dimension)
self._reduce_op = reduce_op
def action_componentclass(self, componentclass, namespace):
unresolved_aliases = dict((a.lhs, a) for a in componentclass.aliases)
def alias_contains_unresolved_symbols(alias):
unresolved = [sym for sym in alias.rhs_atoms
if sym in unresolved_aliases]
return len(unresolved) != 0
def get_resolved_aliases():
return [alias for alias in unresolved_aliases.values()
if not alias_contains_unresolved_symbols(alias)]
while(unresolved_aliases):
resolved_aliases = get_resolved_aliases()
if resolved_aliases:
for r in resolved_aliases:
del unresolved_aliases[r.lhs]
else:
errmsg = "Unable to resolve all aliases in %s. " % namespace
errmsg += "You may have a recursion issue."
errmsg += ("Remaining Aliases: %s" %
','.join(unresolved_aliases.keys()))
raise NineMLRuntimeError(errmsg)
def __init__(self, componentclass):
PerNamespaceDynamicsValidator.__init__(
self, require_explicit_overrides=False)
self.connected_regimes_from_regime = defaultdict(set)
self.regimes_in_namespace = defaultdict(set)
self.visit(componentclass)
def add_connected_regimes_recursive(regime, connected):
connected.add(regime)
for r in self.connected_regimes_from_regime[regime]:
if r not in connected:
add_connected_regimes_recursive(r, connected)
for namespace, regimes in self.regimes_in_namespace.iteritems():
# Perhaps we have no transition graph; this is OK:
if len(regimes) == 0:
continue
connected = set()
add_connected_regimes_recursive(regimes[0], connected)
if len(connected) != len(self.regimes_in_namespace[namespace]):
raise NineMLRuntimeError('Transition graph is contains '
'islands')
def from_str(cls, alias_string):
"""Creates an Alias object from a string"""
if not cls.is_alias_str(alias_string):
errmsg = "Invalid Alias: %s" % alias_string
raise NineMLRuntimeError(errmsg)
lhs, rhs = alias_string.split(':=')
return Alias(lhs=lhs.strip(), rhs=rhs.strip())
def get_new_regime(self, old_regime_string):
"""
for example:
old_regime_string = ('iaf:subthresholdregime '
'cobaInhib:cobadefaultregime '
'cobaExcit:cobadefaultregime')
"""
# Lets create a dictionary that maps 'NamespaceAddress' to regime name
# from the input string:
# old_regime_string = 'iaf:subthresholdregime'
# 'cobaInhib:cobadefaultregime'
# 'cobaExcit:cobadefaultregime'
nsstr_regimename = [l.split(':') for l in old_regime_string.split()]
ns_regimename = dict([(NamespaceAddress(ns), regime_name)
for (ns, regime_name) in nsstr_regimename])
# OK, now lets go through our old componentswithregimes,
# and find the regime that was specified.
target_regime_tuple = []
for c in self.componentswithregimes:
comp_ns = c.get_node_addr()
if comp_ns not in ns_regimename:
err = ('Looking for a regime in namespace: {}, but not found.'
.format(comp_ns))
err += ('\nNamespaces: {}'
.format(','.join([str(ns)
for ns in ns_regimename.keys()])))
err += '\nSpecified String: {}'.format(old_regime_string)
raise NineMLRuntimeError(err)
target_regime_name = ns_regimename[comp_ns]
regime_map = dict([(r.name, r) for r in c.regimes])
if target_regime_name not in regime_map:
err = 'Namespace has no regime named: %s'
err += '\nRegimes: %s' % (str(regime_map.keys()))
raise NineMLRuntimeError(err)
target_regime_tuple.append(regime_map[target_regime_name])
target_regime_tuple = tuple(target_regime_tuple)
new_regime = self.old_regime_tuple_to_new_regime_map[
target_regime_tuple]
return new_regime
def get_local_name(self):
""" Returns the local reference; i.e. the last field in the
address, as a ``string``
"""
if self.is_root_namespace():
err = "Can't call get_local_name() on root namespace"
raise NineMLRuntimeError(err)
return self.loctuple[-1]
def rename_port(cls, componentclass, old_port_name, new_port_name):
""" Renames a port in a componentclass """
if not componentclass.is_flat():
raise NineMLRuntimeError('rename_port() on non-flat '
'componentclass')
# Find the old port:
port = filter_expect_single(componentclass.analog_ports,
lambda ap: ap.name == old_port_name)
port._name = new_port_name
def __init__(self, componentclass):
PerNamespaceComponentValidator.__init__(
self, require_explicit_overrides=False)
self.available_symbols = defaultdict(list)
self.aliases = defaultdict(list)
self.time_derivatives = defaultdict(list)
self.state_assignments = defaultdict(list)
self.visit(componentclass)
excludes = get_reserved_and_builtin_symbols()
# Check Aliases:
for ns, aliases in self.aliases.iteritems():
for alias in aliases:
for rhs_atom in alias.rhs_atoms:
if rhs_atom in excludes:
continue
if rhs_atom not in self.available_symbols[ns]:
err = ('Unresolved Symbol in Alias: %s [%s]' %
(rhs_atom, alias))
raise NineMLRuntimeError(err)
# Check TimeDerivatives:
for ns, timederivatives in self.time_derivatives.iteritems():
for timederivative in timederivatives:
for rhs_atom in timederivative.rhs_atoms:
if (rhs_atom not in self.available_symbols[ns] and
rhs_atom not in excludes):
err = ('Unresolved Symbol in Time Derivative: %s [%s]'
% (rhs_atom, timederivative))
raise NineMLRuntimeError(err)
# Check StateAssignments
for ns, state_assignments in self.state_assignments.iteritems():
for state_assignment in state_assignments:
for rhs_atom in state_assignment.rhs_atoms:
if (rhs_atom not in self.available_symbols[ns] and
rhs_atom not in excludes):
err = ('Unresolved Symbol in Assignment: %s [%s]' %
(rhs_atom, state_assignment))
raise NineMLRuntimeError(err)
def check_conflicting_dimension(self, dimension):
try:
if dimension != self.dimensions[dimension.name]:
err = ("Duplication of dimension name '{}' for differing "
"dimensions ('{}', '{}')".format(
dimension.name, dimension,
self.dimensions[dimension.name]))
raise NineMLRuntimeError(err)
except KeyError:
self.dimensions[dimension.name] = dimension
def resolve_transitions(self):
while self.unresolved_transitions:
transition, regime_index = self.unresolved_transitions.pop()
if regime_index in self.changed_regime_indices:
raise NineMLRuntimeError(
'Something has gone wrong with event resolution. '
'Changing Regime Twice!')
self.changed_regime_indices.add(regime_index)
self.resolve_transition(transition, regime_index)
def remap_port_to_parameter(cls, componentclass, port_name):
""" Renames a port in a componentclass """
if not componentclass.is_flat():
raise NineMLRuntimeError('rename_port_to_parameter() on non-flat '
'componentclass')
# Find the old port:
port = filter_expect_single(componentclass.analog_ports,
lambda ap: ap.name == port_name)
componentclass._analog_ports.remove(port)
# Add a new parameter:
componentclass._parameters[port_name] = Parameter(port_name)
def __init__(self, componentclass):
PerNamespaceDynamicsValidator.__init__(
self, require_explicit_overrides=False)
self.sv_declared = defaultdict(list)
self.state_assignments_lhses = defaultdict(list)
self.visit(componentclass)
for namespace, state_assignments_lhs in self.state_assignments_lhses.\
iteritems():
for td in state_assignments_lhs:
if td not in self.sv_declared[namespace]:
err = 'Not Assigning to state-variable: {}'.format(td)
raise NineMLRuntimeError(err)
def __init__(self, componentclass):
PerNamespaceDynamicsValidator.__init__(
self, require_explicit_overrides=False)
self.sv_declared = defaultdict(list)
self.time_derivatives_used = defaultdict(list)
self.visit(componentclass)
for namespace, time_derivatives in self.time_derivatives_used.\
iteritems():
for td in time_derivatives:
if td not in self.sv_declared[namespace]:
err = 'StateVariable not declared: %s' % td
raise NineMLRuntimeError(err)
def close_all_reduce_ports(cls, componentclass, exclude=None):
"""
Closes all the ``reduce`` ports on a componentclass by assigning them a
value of 0
"""
if not componentclass.is_flat():
raise NineMLRuntimeError('close_all_reduce_ports() on non-flat '
'componentclass')
for arp in componentclass.query.analog_reduce_ports:
if exclude and arp.name in exclude:
continue
cls.close_analog_port(componentclass=componentclass, port_name=arp.name,
value='0')
def from_str(cls, time_derivative_string):
"""Creates an TimeDerivative object from a string"""
# Note: \w = [a-zA-Z0-9_]
tdre = re.compile(r"""\s* d(?P<dependent_var>[a-zA-Z][a-zA-Z0-9_]*)/dt
\s* = \s*
(?P<rhs> .*) """, re.VERBOSE)
match = tdre.match(time_derivative_string)
if not match:
err = "Unable to load time derivative: %s" % time_derivative_string
raise NineMLRuntimeError(err)
dependent_variable = match.groupdict()['dependent_var']
rhs = match.groupdict()['rhs']
return TimeDerivative(dependent_variable=dependent_variable, rhs=rhs)
def __init__(self, name, document, url=None):
"""
docstring needed
`name` -- a name of an existing componentclass to refer to
`document` -- a Document object containing the top-level
objects in the current file
`url` -- a url of the file containing the exiting componentclass
"""
super(Reference, self).__init__(name, document, url)
if not isinstance(self._referred_to, BaseULObject):
msg = ("Reference points to a non-user-layer object '{}'".format(
self._referred_to.name))
raise NineMLRuntimeError(msg)
self._referred_to.from_reference = self
def _resolve_transition_regime_names(self):
# Check that the names of the regimes are unique:
names = [r.name for r in self.regimes]
assert_no_duplicates(names)
# Create a map of regime names to regimes:
regime_map = dict([(r.name, r) for r in self.regimes])
# We only worry about 'target' regimes, since source regimes are taken
# care of for us by the Regime objects they are attached to.
for trans in self.transitions:
if trans.target_regime_name not in regime_map:
raise NineMLRuntimeError("Can't find regime '{}'".format(
trans.target_regime_name))
trans.set_target_regime(regime_map[trans.target_regime_name])
def __init__(self, componentclass):
super(OutputAnalogPortsDynamicsValidator,
self).__init__(require_explicit_overrides=False)
self.output_analogports = defaultdict(list)
self.available_symbols = defaultdict(list)
self.visit(componentclass)
for namespace, analogports in self.output_analogports.iteritems():
for ap in analogports:
if ap not in self.available_symbols[namespace]:
raise NineMLRuntimeError(
'Unable to find an Alias or State variable for '
'analog-port: %s' % ap)
def __init__(self, componentclass, old_symbol_name, new_symbol_name):
ComponentActionVisitor.__init__(
self, require_explicit_overrides=True)
self.old_symbol_name = old_symbol_name
self.new_symbol_name = new_symbol_name
self.namemap = {old_symbol_name: new_symbol_name}
if not componentclass.is_flat():
raise NineMLRuntimeError('Rename Symbol called on non-flat model')
self.lhs_changes = []
self.rhs_changes = []
self.port_changes = []
self.visit(componentclass)
componentclass._validate_self()
def get_parent_addr(self):
"""Return the address of an namespace higher
>>> a = NamespaceAddress('level1.level2.level3')
>>> a
NameSpaceAddress: '/level1/level2/level3/'
>>> a.get_parent_addr()
NameSpaceAddress: '/level1/level2/'
"""
if self.is_root_namespace():
err = "Can't call get_parent_addr() on root namespace"
raise NineMLRuntimeError(err)
return NamespaceAddress(loc=tuple(self.loctuple[:-1]))
def _load_blocks(self, element, blocks):
"""
Creates a dictionary that maps class-types to instantiated objects
"""
# Initialise loaded objects with empty lists
loaded_objects = dict((block, []) for block in blocks)
for t in element.iterchildren(tag=etree.Element):
# Strip namespace
tag = t.tag[len(NINEML):] if t.tag.startswith(NINEML) else t.tag
if tag not in blocks:
err = "Unexpected block tag: %s " % tag
err += '\n Expected: %s' % ','.join(blocks)
raise NineMLRuntimeError(err)
loaded_objects[tag].append(self._get_loader(tag)(self, t))
return loaded_objects
def add_on_condition(self, on_condition):
"""Add an |OnCondition| transition which leaves this regime
If the on_condition object has not had its target regime name
set in the constructor, or by calling its ``set_target_regime_name()``,
then the target is assumed to be this regime, and will be set
appropriately.
The source regime for this transition will be set as this regime.
"""
if not isinstance(on_condition, OnCondition):
err = ("Expected 'OnCondition' Obj, but got %s" %
(type(on_condition)))
raise NineMLRuntimeError(err)
self._resolve_references_on_transition(on_condition)
self._on_conditions.append(on_condition)
def load_py_module(filename):
"""Takes the fully qualified path of a python file,
loads it and returns the module object
"""
if not os.path.exists(filename):
print "CWD:", os.getcwd()
raise NineMLRuntimeError('File does not exist %s' % filename)
dirname, fname = os.path.split(filename)
sys.path = [dirname] + sys.path
module_name = fname.replace('.py', '')
module_name_short = module_name
module = __import__(module_name)
return module