CellMLToNektar.pycml.cellml_component Class Reference

Inheritance diagram for CellMLToNektar.pycml.cellml_component:

Public Member Functions
def	__init__ (self)
def	ignore_component_name (self)
def	parent (self, relationship=u 'encapsulation', namespace=None, name=None, reln_key=None)
def	get_units_by_name (self, uname)
def	add_units (self, name, units)
def	get_all_units (self)
def	get_variable_by_name (self, varname)
Public Member Functions inherited from CellMLToNektar.pycml.element_base
def	__init__ (self)
def	__delattr__ (self, key)
def	__setattr__ (self, key, value)
def	rootNode (self)
def	cmeta_id (self)
def	xml_remove_child_at (self, index=-1)
def	xml_doc (self)
def	xml_properties (self)

Static Public Member Functions
def	create_new (elt, name)

Public Attributes
	name
Public Attributes inherited from CellMLToNektar.pycml.element_base
	xml_attributes

Private Member Functions
def	_clear_hierarchy (self, reln_key)
def	_set_parent_component (self, reln_key, parent)
def	_add_child_component (self, reln_key, child)
def	_has_child_components (self, reln_key)
def	_build_units_dictionary (self)
def	_add_variable (self, var)
def	_del_variable (self, var, keep_annotations=False)

Private Attributes
	_cml_parents
	_cml_children
	_cml_units
	_cml_created_by_pe

Detailed Description

Specialised component class, with additional helper methods.

Definition at line 1509 of file pycml.py.

Constructor & Destructor Documentation

__init__()

def CellMLToNektar.pycml.cellml_component.__init__

(

self

)

Definition at line 1514 of file pycml.py.

    def __init__(self):
        element_base.__init__(self)
        self._cml_parents = {}
        self._cml_children = {}
        self._cml_units = None
        self._cml_created_by_pe = False
    

Member Function Documentation

_add_child_component()

def CellMLToNektar.pycml.cellml_component._add_child_component (   self,   reln_key,   child  )

private

Add child to our list of children in the relationship hierarchy indexed by reln_key.

Definition at line 1566 of file pycml.py.

References CellMLToNektar.pycml.cellml_component._cml_children.

    def _add_child_component(self, reln_key, child):
        """Add child to our list of children in the relationship hierarchy indexed by reln_key."""
        if not reln_key in self._cml_children:
            self._cml_children[reln_key] = []
        self._cml_children[reln_key].append(child)
    

_add_variable()

def CellMLToNektar.pycml.cellml_component._add_variable (   self,   var  )

private

Add a variable to this component.

Definition at line 1622 of file pycml.py.

References CellMLToNektar.pycml.cellml_component.name.

    def _add_variable(self, var):
        """Add a variable to this component."""
        # Add element
        self.xml_append(var)
        # Add to dictionary
        self.xml_parent._add_variable(var, var.name, self.name)
        return

_build_units_dictionary()

def CellMLToNektar.pycml.cellml_component._build_units_dictionary (   self )

private

Create a dictionary mapping units names to objects, for all units definitions in this element.

Definition at line 1577 of file pycml.py.

References CellMLToNektar.pycml.cellml_model._cml_units, CellMLToNektar.pycml.cellml_component._cml_units, CellMLToNektar.pycml.cellml_component.get_units_by_name(), CellMLToNektar.pycml.cellml_component.name, and CellMLToNektar.pycml.cellml_model.validation_error().

Referenced by CellMLToNektar.pycml.cellml_component.add_units(), CellMLToNektar.pycml.cellml_component.get_all_units(), and CellMLToNektar.pycml.cellml_component.get_units_by_name().

    def _build_units_dictionary(self):
        """Create a dictionary mapping units names to objects, for all units definitions in this element."""
        self._cml_units = {}
        for units in getattr(self, u'units', []):
            if units.name in self._cml_units:
                self.validation_error("Units names must be unique within the parent component (5.4.1.2)."
                                      " The name '%s' in component '%s' is duplicated."
                                      % (units.name, self.name))
            try:
                if self.xml_parent.get_units_by_name(units.name).standard == u'yes':
                    self.validation_error("Units definitions must not redefine the standard units (5.4.1.2)."
                                          " The name '%s' in component '%s' is not allowed."
                                          % (units.name, self.name))
            except:
                pass
            self._cml_units[units.name] = units
            self.xml_parent._add_units_obj(units)

_clear_hierarchy()

def CellMLToNektar.pycml.cellml_component._clear_hierarchy (   self,   reln_key  )

private

Unset our parent & children in the given hierarchy.

Definition at line 1546 of file pycml.py.

References CellMLToNektar.pycml.cellml_component._cml_children, and CellMLToNektar.pycml.cellml_component._cml_parents.

    def _clear_hierarchy(self, reln_key):
        """Unset our parent & children in the given hierarchy."""
        self._cml_parents[reln_key] = None
        self._cml_children[reln_key] = []

_del_variable()

def CellMLToNektar.pycml.cellml_component._del_variable (   self,   var,   keep_annotations = False  )

private

Remove a variable from this component.

Definition at line 1629 of file pycml.py.

References CellMLToNektar.pycml.cellml_component.name.

    def _del_variable(self, var, keep_annotations=False):
        """Remove a variable from this component."""
        if not keep_annotations:
            # Remove metadata about the variable
            var.remove_rdf_annotations()
        # Remove the element
        self.xml_remove_child(var)
        # Remove from dictionary
        self.xml_parent._del_variable(var.name, self.name)
        return

_has_child_components()

def CellMLToNektar.pycml.cellml_component._has_child_components (   self,   reln_key  )

private

Determine whether we have any children in the given relationship hierarchy.

Definition at line 1572 of file pycml.py.

References CellMLToNektar.pycml.cellml_component._cml_children.

    def _has_child_components(self, reln_key):
        """Determine whether we have any children in the given relationship hierarchy."""
        return self._cml_children.get(reln_key, []) != []

_set_parent_component()

def CellMLToNektar.pycml.cellml_component._set_parent_component (   self,   reln_key,   parent  )

private

Set the parent of this component in the relationship hierarchy indexed by reln_key to parent.
Trigger a validation error if we already have a parent in this hierarchy.
Also add ourselves to parent's children.

Definition at line 1551 of file pycml.py.

References CellMLToNektar.pycml.cellml_component._cml_parents, and CellMLToNektar.pycml.cellml_component.name.

    def _set_parent_component(self, reln_key, parent):
        """Set the parent of this component in the relationship hierarchy indexed by reln_key to parent.
        Trigger a validation error if we already have a parent in this hierarchy.
        Also add ourselves to parent's children.
        """
        if not reln_key in self._cml_parents or self._cml_parents[reln_key] is None:
            # Only set parent if we don't already have one
            self._cml_parents[reln_key] = parent
        else:
            self.xml_parent.validation_error("In a given hierarchy, a component may not be a child more"
                                             " than once (6.4.3.2). Component '%s' has multiple parents."
                                             % self.name)
        if not parent is None:
            parent._add_child_component(reln_key, self)
    

add_units()

def CellMLToNektar.pycml.cellml_component.add_units	(		self,
			name,
			units
	)

Add an entry in our units dictionary for units named `name' with element object `units'.

Definition at line 1604 of file pycml.py.

References CellMLToNektar.pycml.cellml_model._build_units_dictionary(), CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.cellml_model._cml_units, and CellMLToNektar.pycml.cellml_component._cml_units.

    def add_units(self, name, units):
        """Add an entry in our units dictionary for units named `name' with element object `units'."""
        if self._cml_units is None:
            self._build_units_dictionary()
        self._cml_units[name] = units
        self.xml_parent._add_units_obj(units)
        return

create_new()

def CellMLToNektar.pycml.cellml_component.create_new (   elt,   name  )

static

Create a new component with the given name.

Definition at line 1641 of file pycml.py.

    def create_new(elt, name):
        """Create a new component with the given name."""
        new_comp = elt.xml_create_element(u'component', NSS[u'cml'],
                                          attributes={u'name': unicode(name)})
        return new_comp

get_all_units()

def CellMLToNektar.pycml.cellml_component.get_all_units

(

self

)

Get a list of all units objects defined in this component.

Definition at line 1612 of file pycml.py.

References CellMLToNektar.pycml.cellml_model._build_units_dictionary(), CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.cellml_model._cml_units, and CellMLToNektar.pycml.cellml_component._cml_units.

    def get_all_units(self):
        """Get a list of all units objects defined in this component."""
        if self._cml_units is None:
            self._build_units_dictionary()
        return self._cml_units.values()

get_units_by_name()

def CellMLToNektar.pycml.cellml_component.get_units_by_name	(		self,
			uname
	)

Return an object representing the element that defines the units named `uname'.

Definition at line 1594 of file pycml.py.

References CellMLToNektar.pycml.cellml_model._build_units_dictionary(), CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.cellml_model._cml_units, and CellMLToNektar.pycml.cellml_component._cml_units.

Referenced by CellMLToNektar.pycml.cellml_component._build_units_dictionary().

    def get_units_by_name(self, uname):
        """Return an object representing the element that defines the units named `uname'."""
        if self._cml_units is None:
            self._build_units_dictionary()
        if uname in self._cml_units:
            # Units are defined in this component
            return self._cml_units[uname]
        else:
            # Look up units in model element instead
            return self.xml_parent.get_units_by_name(uname)

get_variable_by_name()

def CellMLToNektar.pycml.cellml_component.get_variable_by_name	(		self,
			varname
	)

Return the variable object with name `varname' in this component.

Definition at line 1618 of file pycml.py.

References CellMLToNektar.pycml.cellml_component.name.

    def get_variable_by_name(self, varname):
        """Return the variable object with name `varname' in this component."""
        return self.xml_parent.get_variable_by_name(self.name, varname)

ignore_component_name()

def CellMLToNektar.pycml.cellml_component.ignore_component_name

(

self

)

Whether to not include the component name in the full names of contained variables.

Definition at line 1522 of file pycml.py.

    def ignore_component_name(self):
        """Whether to not include the component name in the full names of contained variables."""
        return self._cml_created_by_pe or self.name == u''
    
    

parent()

def CellMLToNektar.pycml.cellml_component.parent	(		self,
			relationship = u'encapsulation',
			namespace = None,
			name = None,
			reln_key = None
	)

Find the parent of this component in the given hierarchy.

We default to the encapsulation hierarchy.

relationship gives the type of the hierarchy. If it is not one
of the CellML types (i.e. encapsulation or containment) then
the namespace URI must be specified.  Multiple non-encapsulation
hierarchies of the same type can be specified by giving the name
argument.

Results are cached for efficiency.

Definition at line 1527 of file pycml.py.

References CellMLToNektar.pycml.cellml_component._cml_parents.

    def parent(self, relationship=u'encapsulation', namespace=None, name=None, reln_key=None):
        """Find the parent of this component in the given hierarchy.
        
        We default to the encapsulation hierarchy.

        relationship gives the type of the hierarchy. If it is not one
        of the CellML types (i.e. encapsulation or containment) then
        the namespace URI must be specified.  Multiple non-encapsulation
        hierarchies of the same type can be specified by giving the name
        argument.

        Results are cached for efficiency.
        """
        key = reln_key or (relationship, namespace, name)
        if not key in self._cml_parents:
            assert(reln_key is None)
            self.xml_parent.build_component_hierarchy(relationship, namespace, name)
        return self._cml_parents[key]

Member Data Documentation

_cml_children

CellMLToNektar.pycml.cellml_component._cml_children

private

Definition at line 1517 of file pycml.py.

Referenced by CellMLToNektar.pycml.cellml_component._add_child_component(), CellMLToNektar.pycml.cellml_component._clear_hierarchy(), and CellMLToNektar.pycml.cellml_component._has_child_components().

_cml_created_by_pe

CellMLToNektar.pycml.cellml_component._cml_created_by_pe

private

Definition at line 1519 of file pycml.py.

_cml_parents

CellMLToNektar.pycml.cellml_component._cml_parents

private

Definition at line 1516 of file pycml.py.

Referenced by CellMLToNektar.pycml.cellml_component._clear_hierarchy(), CellMLToNektar.pycml.cellml_component._set_parent_component(), and CellMLToNektar.pycml.cellml_component.parent().

_cml_units

CellMLToNektar.pycml.cellml_component._cml_units

private

Definition at line 1518 of file pycml.py.

Referenced by CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.mathml_apply._set_in_units(), CellMLToNektar.pycml.mathml_piecewise._set_in_units(), CellMLToNektar.pycml.cellml_component.add_units(), CellMLToNektar.pycml.cellml_component.get_all_units(), CellMLToNektar.pycml.mathml_ci.get_units(), CellMLToNektar.pycml.mathml_apply.get_units(), CellMLToNektar.pycml.mathml_piecewise.get_units(), and CellMLToNektar.pycml.cellml_component.get_units_by_name().

name

CellMLToNektar.pycml.cellml_component.name

Definition at line 1524 of file pycml.py.

Referenced by CellMLToNektar.pycml.cellml_units.__repr__(), CellMLToNektar.pycml.cellml_component._add_variable(), CellMLToNektar.pycml.cellml_component._build_units_dictionary(), CellMLToNektar.pycml.cellml_component._del_variable(), CellMLToNektar.pycml.cellml_units._hash_tuple(), CellMLToNektar.pycml.cellml_component._set_parent_component(), CellMLToNektar.pycml.cellml_variable.fullname(), and CellMLToNektar.pycml.cellml_component.get_variable_by_name().