def test_raise_not_found_issue(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
message = 'Could not find an item with an id of \'i_dont_exist\' in the model.'
model = parser.parseModel(file_contents('annotator/unique_ids.cellml'))
annotator.setModel(model)
annotator.item('i_dont_exist')
self.assertEqual(1, annotator.issueCount())
self.assertEqual(message, annotator.issue(0).description())
def test_raise_non_unique_issue(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
non_unique_message = 'The identifier \'duplicateId\' occurs 29 times in the model so a unique item cannot be located.'
model = parser.parseModel(file_contents('annotator/duplicate_ids.cellml'))
annotator.setModel(model)
annotator.item('duplicateId')
self.assertEqual(1, annotator.issueCount())
self.assertEqual(non_unique_message, annotator.issue(0).description())
def test_item(self):
from libcellml import Annotator, CellmlElementType, Model, Parser
annotator = Annotator()
model = Model()
parser = Parser()
model_string = file_contents("annotator/unique_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
self.assertEqual(CellmlElementType.UNDEFINED, annotator.item("not_an_id").type())
self.assertEqual(CellmlElementType.UNDEFINED, annotator.item("not_an_id", 3).type())
self.assertEqual(CellmlElementType.MAP_VARIABLES, annotator.item("map_variables_2").type())
def test_assign_id(self):
from libcellml import Annotator, Component, Model, Units
from libcellml import Unit, CellmlElementType
annotator = Annotator()
model = Model()
component1 = Component("c1")
component2 = Component("c2")
component3 = Component("c3")
component3.setId("id3")
units = Units("u1")
units.addUnit("volt")
model.addComponent(component1)
model.addComponent(component2)
component2.addComponent(component3)
model.addUnits(units)
annotator.setModel(model)
self.assertEqual("", component1.id())
self.assertEqual("", component2.id())
self.assertEqual("", units.unitId(0))
annotator.assignId(component1)
self.assertEqual("b4da55", component1.id())
self.assertEqual("", component2.id())
self.assertEqual("", units.unitId(0))
annotator.assignId(Unit(units, 0))
self.assertEqual("b4da55", component1.id())
self.assertEqual("", component2.id())
self.assertEqual("b4da56", units.unitId(0))
self.assertEqual("",
annotator.assignId(None, CellmlElementType.UNDEFINED))
item = annotator.item("id3")
annotator.assignId(item)
self.assertEqual("b4da57", component3.id())
# For coverage only.
annotator._assignId(component2)
# 2.a
# Create an Annotator item and use the setModel function to pass in the parsed
# mystery model.
annotator = Annotator()
annotator.setModel(model)
# end 2.a
# The item function returns a AnyItem, a std.pair whose:
# - first attribute is a CellmlElementType enumeration and
# - second attribute is a std.any cast of the item itself.
# 2.b
# Retrieve the item with an id of 'marco'. Use the helper function
# cellmlElementTypeAsString to convert the enumeration of its type into a
# string for printing to the terminal.
marco_item = annotator.item('marco')
print('The item with ID "marco" is a {}'.format(
cellmlElementTypeAsString(marco_item.type())))
# The item with ID 'marco' is a variable
# 2.c
# Check that the annotator has not reported any issues.
print_issues(annotator)
# 2.d
# Now that we know the marco item's type using its first attribute (it should
# be a CellmlElementType.VARIABLE) we can name its second attribute so we know
# what it is.
marco_variable = marco_item.variable()
def test_any_cellml_element(self):
from libcellml import Annotator, AnyCellmlElement, Parser
from libcellml.enums import CellmlElementType
self.assertRaises(AttributeError, AnyCellmlElement)
parser = Parser()
model = parser.parseModel(file_contents('annotator/unique_ids.cellml'))
annotator = Annotator()
annotator.setModel(model)
item = annotator.item('component_1')
self.assertEqual(CellmlElementType.COMPONENT, item.type())
self.assertEqual('component1', item.component().name())
item = annotator.item('component_ref_1')
self.assertEqual(CellmlElementType.COMPONENT_REF, item.type())
self.assertEqual('component2', item.component().name())
item = annotator.item('connection_1')
self.assertEqual(CellmlElementType.CONNECTION, item.type())
self.assertEqual('variable1', item.variablePair().variable1().name())
self.assertEqual('variable1', item.variablePair().variable2().name())
self.assertTrue(item.variablePair().isValid())
item = annotator.item('encapsulation_1')
self.assertEqual(CellmlElementType.ENCAPSULATION, item.type())
self.assertEqual('everything', item.model().name())
item = annotator.item('import_1')
self.assertEqual(CellmlElementType.IMPORT, item.type())
self.assertEqual('some-other-model.xml', item.importSource().url())
item = annotator.item('map_variables_1')
self.assertEqual(CellmlElementType.MAP_VARIABLES, item.type())
self.assertEqual('variable1', item.variablePair().variable1().name())
self.assertEqual('variable1', item.variablePair().variable2().name())
self.assertTrue(item.variablePair().isValid())
item = annotator.item('model_1')
self.assertEqual(CellmlElementType.MODEL, item.type())
self.assertEqual('everything', item.model().name())
resetItem = annotator.item('reset_1')
self.assertEqual(CellmlElementType.RESET, resetItem.type())
self.assertEqual(1, resetItem.reset().order())
item = annotator.item('reset_value_1')
self.assertEqual(CellmlElementType.RESET_VALUE, item.type())
self.assertEqual(resetItem.reset().resetValue(), item.reset().resetValue())
item = annotator.item('test_value_1')
self.assertEqual(CellmlElementType.TEST_VALUE, item.type())
self.assertEqual(resetItem.reset().testValue(), item.reset().testValue())
item = annotator.item('unit_1')
self.assertEqual(CellmlElementType.UNIT, item.type())
self.assertEqual('units2', item.unitsItem().units().name())
self.assertTrue(item.unitsItem().isValid())
item = annotator.item('units_1')
self.assertEqual(CellmlElementType.UNITS, item.type())
self.assertEqual('units1', item.units().name())
item = annotator.item('variable_1')
self.assertEqual(CellmlElementType.VARIABLE, item.type())
self.assertEqual('variable1', item.variable().name())
# - resetValue: returns the Reset with this id on its reset value.
resetValue = annotator.resetValue('taupe')
# - testValue: returns the Reset with this id on its test value.
testValue = annotator.testValue('mauve')
# In this example reset, resetValue and testValue will be the same because the
# 'taupe' reset value and 'mauve' test value are in the 'violet' reset item.
# STEP 4
# Dealing with unique id strings where the item has an unknown type.
# Check that the id is unique in the model scope:
if annotator.isUnique('green'):
# Retrieve item from the annotator by their unique id.
itemOfUnknownType = annotator.item('green')
# Because these could be any kind of item, they are stored in an AnyItem
# type. This is a tuple, where the first item is a CellmlElementType enum
# indicating the item's type, and the second is the item itself.
# The type can be turned into a string using the Annotator.typeAsString
# function on the first item in the tuple.
print('The item with id of "green" has type of "{}".'.format(
annotator.typeAsString(itemOfUnknownType[0])))
print()
# STEP 5
# Handling duplicate ID strings.
# Find any duplicated ID strings inside the model.