def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls()
machinery_node = get_unique_child(node, MachineryComposition.tag)
result.machinery_composition \
= MachineryComposition.from_xml_node(machinery_node)
capacity_node = get_unique_child(node, Capacity.tag)
result.capacity = Capacity.from_xml_node(capacity_node)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'))
n = get_unique_child(node, ConstantCost.tag, False)
if n is not None:
result.constant_cost = ConstantCost.from_xml_node(n)
n = get_unique_child(node, ListOfCosts.tag)
result.costs = ListOfCosts.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls()
n = get_unique_child(node, ListOfReactants.tag, False)
if n is not None:
result.reactants = ListOfReactants.from_xml_node(n)
n = get_unique_child(node, ListOfProducts.tag, False)
if n is not None:
result.products = ListOfProducts.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'))
n = get_unique_child(node, ConstantProcessing.tag, False)
if n is not None:
result.constant_processing = ConstantProcessing.from_xml_node(n)
n = get_unique_child(node, ListOfComponentProcessings.tag)
result.component_processings \
= ListOfComponentProcessings.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'), node.get('name'))
n = get_unique_child(node, Machinery.tag, False)
if n is not None:
result.machinery = Machinery.from_xml_node(n)
n = get_unique_child(node, Processings.tag, False)
if n is not None:
result.processings = Processings.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""
Constructor from xml node.
"""
result = cls(node.get('id'), is_true(node.get('reversible')))
n = get_unique_child(node, ListOfReactants.tag, False)
if n is not None:
result.reactants = ListOfReactants.from_xml_node(n)
n = get_unique_child(node, ListOfProducts.tag, False)
if n is not None:
result.products = ListOfProducts.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
try:
proc_cost = float(node.get('processingCost'))
except TypeError:
proc_cost = 0.0
result = cls(node.get('component'), proc_cost)
n = get_unique_child(node, ListOfReactants.tag, False)
if n is not None:
result.reactants = ListOfReactants.from_xml_node(n)
n = get_unique_child(node, ListOfProducts.tag, False)
if n is not None:
result.products = ListOfProducts.from_xml_node(n)
return result
def from_file(cls, input_stream):
"""
Constructor from XML structure.
Parameters
----------
input_stream : file or buffer
Location containing XML structure.
"""
node = etree.ElementTree(file=input_stream).getroot()
result = cls()
n = get_unique_child(node, ListOfComponents.tag)
result.components = ListOfComponents.from_xml_node(n)
n = get_unique_child(node, ListOfMacromolecules.tag)
result.macromolecules = ListOfMacromolecules.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""
Constructor from xml node.
"""
result = cls(node.get('id'), node.get('compartment'))
comp_node = get_unique_child(node, Composition.tag)
result.composition = Composition.from_xml_node(comp_node)
return result
def from_file(cls, input_stream):
"""
Build object from XML structure.
Parameters
----------
input_stream : file or buffer
Location containing XML structure.
"""
node = etree.ElementTree(file=input_stream).getroot()
result = cls()
n = get_unique_child(node, ListOfFunctions.tag)
result.functions = ListOfFunctions.from_xml_node(n)
n = get_unique_child(node, ListOfAggregates.tag)
result.aggregates = ListOfAggregates.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'), node.get('type'), {},
node.get('variable'))
n = get_unique_child(node, 'listOfParameters', False)
if n is not None:
result.parameters = ListOfParameters.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'))
n = get_unique_child(node, result.concentrations.tag, False)
if n is not None:
result.concentrations = result.concentrations.from_xml_node(n)
n = get_unique_child(node, result.production_fluxes.tag, False)
if n is not None:
result.production_fluxes \
= result.production_fluxes.from_xml_node(n)
n = get_unique_child(node, result.degradation_fluxes.tag, False)
if n is not None:
result.degradation_fluxes \
= result.degradation_fluxes.from_xml_node(n)
n = get_unique_child(node, result.reaction_fluxes.tag, False)
if n is not None:
result.reaction_fluxes = result.reaction_fluxes.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build from xml node."""
result = cls(node.get('id'), node.get('reaction'),
node.get('forward_efficiency'),
node.get('backward_efficiency'),
is_true(node.get('zeroCost')))
n = get_unique_child(node, MachineryComposition.tag, False)
if n is not None:
result.machinery_composition \
= MachineryComposition.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('id'), node.get('type'))
n = get_unique_child(node, ListOfFunctionReferences.tag)
result.function_references = ListOfFunctionReferences.from_xml_node(n)
return result
def from_xml_node(cls, node):
"""Build object from xml node."""
result = cls(node.get('processingMap'), node.get('set'))
n = get_unique_child(node, ListOfInputs.tag)
result.inputs = ListOfInputs.from_xml_node(n)
return result
