def test_importer(self):
from libcellml import Importer, Parser, Printer
parser = Parser()
i = Importer()
m = parser.parseModel(file_contents('importer/diamond.cellml'))
printer = Printer()
i.resolveImports(m, resource_path('importer/'))
self.assertFalse(m.hasUnresolvedImports())
# Library should contain left, right, and one instance (not two) of the point.
self.assertEqual(3, i.libraryCount())
self.assertEqual(resource_path('importer/diamond_left.cellml'),
i.key(0))
self.assertEqual(resource_path('importer/diamond_point.cellml'),
i.key(1))
self.assertEqual(resource_path('importer/diamond_right.cellml'),
i.key(2))
# Access library items by their URL.
left = i.library(resource_path('importer/diamond_left.cellml'))
self.assertEqual(file_contents('importer/diamond_left.cellml'),
printer.printModel(left))
def test_algebraic_eqn_computed_var_on_rhs(self):
from libcellml import Analyser
from libcellml import AnalyserModel
from libcellml import Generator
from libcellml import GeneratorProfile
from libcellml import Parser
from test_resources import file_contents
p = Parser()
m = p.parseModel(
file_contents(
'generator/algebraic_eqn_computed_var_on_rhs/model.cellml'))
a = Analyser()
a.analyseModel(m)
am = a.model()
self.assertEqual(AnalyserModel.Type.ALGEBRAIC, am.type())
g = Generator()
self.assertIsNone(g.model())
g.setModel(am)
self.assertIsNotNone(g.model())
self.assertEqual(
file_contents(
"generator/algebraic_eqn_computed_var_on_rhs/model.h"),
g.interfaceCode())
self.assertEqual(
file_contents(
"generator/algebraic_eqn_computed_var_on_rhs/model.c"),
g.implementationCode())
self.assertEqual(GeneratorProfile.Profile.C, g.profile().profile())
profile = GeneratorProfile(GeneratorProfile.Profile.PYTHON)
g.setProfile(profile)
self.assertEqual("", g.interfaceCode())
self.assertEqual(
file_contents(
"generator/algebraic_eqn_computed_var_on_rhs/model.py"),
g.implementationCode())
self.assertEqual(GeneratorProfile.Profile.PYTHON,
g.profile().profile())
def test_is_unique(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
model = parser.parseModel(file_contents("annotator/unique_ids.cellml"))
annotator.setModel(model)
self.assertTrue(annotator.isUnique("variable_3"))
model = parser.parseModel(file_contents("annotator/lots_of_duplicate_ids.cellml"))
annotator.setModel(model)
self.assertFalse(annotator.isUnique("duplicateId2"))
def test_replace_model(self):
from libcellml import Component, Importer, Model, Parser
parser = Parser()
model = parser.parseModel(
file_contents('importer/generic_no_source.cellml'))
importer = Importer()
wrongSourceModel = Model('wrong')
rightSourceModel = Model('right')
rightSourceModel.addComponent(Component('a'))
rightSourceModel.addComponent(Component('b'))
rightSourceModel.addComponent(Component('c'))
rightSourceModel.addComponent(Component('d'))
self.assertTrue(
importer.addModel(wrongSourceModel, 'i_dont_exist.cellml'))
self.assertFalse(
importer.replaceModel(rightSourceModel, 'not_in_library'))
self.assertTrue(
importer.replaceModel(rightSourceModel, 'i_dont_exist.cellml'))
importer.resolveImports(model, '')
self.assertEqual(0, importer.issueCount())
self.assertFalse(model.hasUnresolvedImports())
def test_replace_model(self):
from libcellml import Component, Importer, Model, Parser
parser = Parser()
model = parser.parseModel(
file_contents("importer/generic_no_source.cellml"))
importer = Importer()
wrongSourceModel = Model("wrong")
rightSourceModel = Model("right")
rightSourceModel.addComponent(Component("a"))
rightSourceModel.addComponent(Component("b"))
rightSourceModel.addComponent(Component("c"))
rightSourceModel.addComponent(Component("d"))
self.assertTrue(
importer.addModel(wrongSourceModel, "i_dont_exist.cellml"))
self.assertFalse(
importer.replaceModel(rightSourceModel, "not_in_library"))
self.assertTrue(
importer.replaceModel(rightSourceModel, "i_dont_exist.cellml"))
importer.resolveImports(model, "")
self.assertEqual(0, importer.issueCount())
self.assertFalse(model.hasUnresolvedImports())
def test_coverage(self):
from libcellml import Issue
from libcellml import Parser
from test_resources import file_contents
self.assertRaises(AttributeError, Issue)
p = Parser()
p.parseModel(file_contents('invalid_cellml_2.0.xml'))
self.assertEqual(2, p.issueCount())
i = p.issue(0)
self.assertEqual(Issue.Level.ERROR, i.level())
self.assertNotEqual(None, i.item())
self.assertEqual("1.2.1", i.referenceHeading())
self.assertEqual(1, i.referenceRule())
self.assertEqual(
"https://cellml-specification.readthedocs.io/en/latest/reference/formal_and_informative/specA02.html?issue=XML",
i.url())
self.assertEqual(2, p.errorCount())
self.assertEqual(None, p.error(4))
self.assertEqual(0, p.warningCount())
self.assertEqual(None, p.warning(0))
self.assertEqual(0, p.messageCount())
self.assertEqual(None, p.message(0))
def test_ids(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
model = parser.parseModel(file_contents("annotator/unique_ids.cellml"))
annotator.setModel(model)
self.assertEqual(24, len(annotator.ids()))
def test_duplicate_count(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
model = parser.parseModel(file_contents("annotator/lots_of_duplicate_ids.cellml"))
annotator.setModel(model)
self.assertEqual(8, annotator.itemCount("duplicateId1"))
self.assertEqual(7, annotator.itemCount("duplicateId3"))
def test_has_model(self):
from libcellml import Annotator, Parser
annotator = Annotator()
parser = Parser()
self.assertFalse(annotator.hasModel())
model = parser.parseModel(file_contents("annotator/unique_ids.cellml"))
annotator.setModel(model)
self.assertTrue(annotator.hasModel())
def test_remove_all_models(self):
from libcellml import Parser, Importer
parser = Parser()
model = parser.parseModel(file_contents('importer/diamond.cellml'))
importer = Importer()
importer.resolveImports(model, resource_path('importer/'))
self.assertEqual(3, importer.libraryCount())
importer.removeAllModels()
self.assertEqual(0, importer.libraryCount())
def test_flatten(self):
from libcellml import Importer, Parser
parser = Parser()
importer = Importer()
model = parser.parseModel(file_contents('importer/diamond.cellml'))
importer.resolveImports(model, resource_path('importer/'))
flattenedModel = importer.flattenModel(model)
self.assertEqual(2, flattenedModel.componentCount())
def test_auto_ids(self):
from libcellml import Annotator, Parser, Variable
annotator = Annotator()
parser = Parser()
model_string = file_contents("annotator/unique_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
annotator.clearAllIds()
annotator.assignAllIds()
self.assertEqual("b4da55", model.id())
self.assertEqual("b4da56", model.importSource(0).id())
self.assertEqual("b4da57", model.importSource(1).id())
self.assertEqual("b4da58", model.units(0).id())
self.assertEqual("b4da59", model.units(1).id())
self.assertEqual("b4da5a", model.units(2).id())
self.assertEqual("b4da5b", model.units(3).id())
self.assertEqual("b4da5c", model.units(1).unitId(0))
self.assertEqual("b4da5d", model.component(0).id())
self.assertEqual("b4da5e", model.component(1).id())
self.assertEqual("b4da5f", model.component(1).component(0).id())
self.assertEqual("b4da60", model.component(1).variable(0).id())
self.assertEqual("b4da61", model.component(1).variable(1).id())
self.assertEqual("b4da62",
model.component(1).component(0).variable(0).id())
self.assertEqual("b4da63",
model.component(1).component(0).variable(1).id())
self.assertEqual("b4da64", model.component(1).reset(0).id())
self.assertEqual("b4da65", model.component(1).reset(0).resetValueId())
self.assertEqual("b4da66", model.component(1).reset(0).testValueId())
c2v1 = model.component("component2").variable("variable1")
c2v2 = model.component("component2").variable("variable2")
c3v1 = model.component("component3").variable("variable1")
c3v2 = model.component("component3").variable("variable2")
self.assertEqual("b4da67",
Variable.equivalenceConnectionId(c2v1, c3v1))
self.assertEqual("b4da67",
Variable.equivalenceConnectionId(c2v2, c3v2))
self.assertEqual("b4da68", Variable.equivalenceMappingId(c2v1, c3v1))
self.assertEqual("b4da69", Variable.equivalenceMappingId(c2v2, c3v2))
self.assertEqual("b4da6a",
model.component("component2").encapsulationId())
self.assertEqual("b4da6b",
model.component("component3").encapsulationId())
self.assertEqual("b4da6c", model.encapsulationId())
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_resolve_imports(self):
from libcellml import Importer
from libcellml import Parser
i = Importer()
p = Parser()
m1 = p.parseModel(file_contents('importer/units_imported.cellml'))
m2 = p.parseModel(file_contents('importer/units_imported.cellml'))
m3 = p.parseModel(file_contents('importer/units_imported.cellml'))
self.assertEqual(0, p.issueCount())
self.assertTrue(m1.hasUnresolvedImports())
i.resolveImports(m1, resource_path('importer/'))
self.assertFalse(m1.hasUnresolvedImports())
self.assertTrue(m2.hasUnresolvedImports())
i.resolveImports(m2, resource_path('importer'))
self.assertFalse(m2.hasUnresolvedImports())
self.assertTrue(m3.hasUnresolvedImports())
i.resolveImports(m3, resource_path('importer\\'))
self.assertFalse(m3.hasUnresolvedImports())
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_resolve_imports(self):
from libcellml import Importer
from libcellml import Parser
i = Importer()
p = Parser()
m = p.parseModel(file_contents('sine_approximations_import.xml'))
self.assertEqual(0, p.issueCount())
self.assertTrue(m.hasUnresolvedImports())
i.resolveImports(m, resource_path())
self.assertFalse(m.hasUnresolvedImports())
def test_is_resolved_component(self):
from libcellml import Importer, Parser
parser = Parser()
importer = Importer()
model = parser.parseModel(
file_contents("importer/component_importer_unresolved.cellml"))
self.assertEqual(0, parser.issueCount())
importer.resolveImports(model, resource_path("importer/"))
self.assertEqual(1, importer.issueCount())
c = model.component(0)
self.assertFalse(c.isResolved())
def test_requirements(self):
from libcellml import Parser, Importer
keys = [
'complicatedComponents.cellml',
'complicatedUnits.cellml',
]
parser = Parser()
model = parser.parseModel(file_contents('import-requirements/complicatedExample.cellml'))
self.assertEqual(0, parser.issueCount())
requirements = model.importRequirements()
i = 0
for r in requirements:
self.assertEqual(keys[i], r)
i += 1
def test_clear_imports(self):
from libcellml import Importer, Parser
parser = Parser()
importer = Importer()
model = parser.parseModel(
file_contents('importer/nested_components.cellml'))
self.assertEqual(0, parser.issueCount())
importer.resolveImports(model, resource_path('importer/'))
self.assertEqual(0, importer.issueCount())
self.assertFalse(model.hasUnresolvedImports())
importer.clearImports(model)
self.assertTrue(model.hasUnresolvedImports())
def test_is_resolved_units(self):
from libcellml import Importer, Parser
parser = Parser()
importer = Importer()
model = parser.parseModel(
file_contents("importer/master_units.cellml"))
self.assertEqual(0, parser.issueCount())
importer.resolveImports(model, resource_path("importer/"))
self.assertEqual(0, importer.issueCount())
u = model.units(0)
self.assertTrue(u.isResolved())
def test_add_model(self):
from libcellml import Component, Importer, Model, Parser
parser = Parser()
importer = Importer()
model = parser.parseModel(
file_contents('importer/generic_no_source.cellml'))
sourceModel = Model('source')
sourceModel.addComponent(Component('a'))
sourceModel.addComponent(Component('b'))
sourceModel.addComponent(Component('c'))
sourceModel.addComponent(Component('d'))
# Add a model manually to the library, including the URL that it will replace in future imports.
self.assertTrue(importer.addModel(sourceModel, 'i_dont_exist.cellml'))
self.assertFalse(importer.addModel(sourceModel, 'i_dont_exist.cellml'))
importer.resolveImports(model, '')
self.assertEqual(0, importer.issueCount())
self.assertFalse(model.hasUnresolvedImports())
def test_coverage(self):
from libcellml import Analyser
from libcellml import AnalyserEquation
from libcellml import AnalyserEquationAst
from libcellml import AnalyserExternalVariable
from libcellml import AnalyserModel
from libcellml import AnalyserVariable
from libcellml import Model
from libcellml import Parser
from test_resources import file_contents
# Try to create an analyser equation/model/variable, something that is not allowed.
self.assertRaises(AttributeError, AnalyserEquation)
self.assertRaises(AttributeError, AnalyserModel)
self.assertRaises(AttributeError, AnalyserVariable)
# Analyse a model, so we can then do some coverage.
p = Parser()
m = p.parseModel(file_contents('generator/noble_model_1962/model.cellml'))
a = Analyser()
a.analyseModel(m)
# Ensure coverage for Analyser.
c = m.component(1)
v0 = c.variable(0)
aev = AnalyserExternalVariable(v0)
self.assertTrue(a.addExternalVariable(aev))
self.assertTrue(a.containsExternalVariable(aev))
self.assertTrue(a.containsExternalVariable(m, c.name(), v0.name()))
self.assertEqual(aev.variable().name(), a.externalVariable(0).variable().name())
self.assertEqual(aev.variable().name(), a.externalVariable(m, c.name(), v0.name()).variable().name())
v2 = c.variable(2)
self.assertTrue(a.addExternalVariable(AnalyserExternalVariable(c.variable(1))))
self.assertTrue(a.addExternalVariable(AnalyserExternalVariable(v2)))
self.assertTrue(a.addExternalVariable(AnalyserExternalVariable(c.variable(3))))
self.assertEqual(4, a.externalVariableCount())
self.assertTrue(a.removeExternalVariable(1))
self.assertTrue(a.removeExternalVariable(aev))
self.assertTrue(a.removeExternalVariable(m, c.name(), v2.name()))
a.removeAllExternalVariables()
# Ensure coverage for AnalyserModel.
am = a.model()
self.assertTrue(am.isValid())
self.assertFalse(am.hasExternalVariables())
self.assertIsNotNone(am.voi())
self.assertEqual(4, am.stateCount())
self.assertIsNotNone(am.states())
self.assertIsNotNone(am.state(3))
self.assertEqual(17, am.variableCount())
self.assertIsNotNone(am.variables())
self.assertIsNotNone(am.variable(3))
self.assertEqual(16, am.equationCount())
self.assertIsNotNone(am.equations())
self.assertIsNotNone(am.equation(3))
self.assertFalse(am.needEqFunction())
self.assertFalse(am.needNeqFunction())
self.assertFalse(am.needLtFunction())
self.assertFalse(am.needLeqFunction())
self.assertFalse(am.needGtFunction())
self.assertFalse(am.needGeqFunction())
self.assertFalse(am.needAndFunction())
self.assertFalse(am.needOrFunction())
self.assertFalse(am.needXorFunction())
self.assertFalse(am.needNotFunction())
self.assertFalse(am.needMinFunction())
self.assertFalse(am.needMaxFunction())
self.assertFalse(am.needSecFunction())
self.assertFalse(am.needCscFunction())
self.assertFalse(am.needCotFunction())
self.assertFalse(am.needSechFunction())
self.assertFalse(am.needCschFunction())
self.assertFalse(am.needCothFunction())
self.assertFalse(am.needAsecFunction())
self.assertFalse(am.needAcscFunction())
self.assertFalse(am.needAcotFunction())
self.assertFalse(am.needAsechFunction())
self.assertFalse(am.needAcschFunction())
self.assertFalse(am.needAcothFunction())
self.assertTrue(am.areEquivalentVariables(am.voi().variable(), am.voi().variable()))
# Ensure coverage for AnalyserVariable.
av = am.variable(3)
self.assertEqual(AnalyserVariable.Type.CONSTANT, av.type())
self.assertEqual(3, av.index())
self.assertIsNotNone(av.initialisingVariable())
self.assertIsNotNone(av.variable())
self.assertIsNone(av.equation())
# Ensure coverage for AnalyserEquation.
ae = am.equation(3)
self.assertEqual(AnalyserEquation.Type.RATE, ae.type())
self.assertIsNotNone(ae.ast())
self.assertIsNotNone(ae.dependencies())
self.assertTrue(ae.isStateRateBased())
self.assertIsNotNone(ae.variable())
# Ensure coverage for AnalyserEquationAst.
aea = ae.ast()
self.assertEqual(AnalyserEquationAst.Type.ASSIGNMENT, aea.type())
self.assertEqual('', aea.value())
self.assertIsNone(aea.variable())
self.assertIsNone(aea.parent())
self.assertIsNotNone(aea.leftChild())
self.assertIsNotNone(aea.rightChild())
aea.setType(AnalyserEquationAst.Type.EQ)
aea.setValue(AnalyserTestCase.VALUE)
aea.setVariable(av.variable())
aea.setParent(aea)
aea.setLeftChild(None)
aea.setRightChild(None)
self.assertEqual(AnalyserEquationAst.Type.EQ, aea.type())
self.assertEqual(AnalyserTestCase.VALUE, aea.value())
self.assertIsNotNone(aea.variable())
self.assertIsNotNone(aea.parent())
self.assertIsNone(aea.leftChild())
self.assertIsNone(aea.rightChild())
def test_assign_by_type(self):
from libcellml import Annotator, Parser, Variable, CellmlElementType
from libcellml import UnitsItem, VariablePair
annotator = Annotator()
parser = Parser()
model_string = file_contents("annotator/no_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
c = model.component(0)
self.assertEqual("", model.id())
annotator.assignId(model)
self.assertEqual("b4da55", model.id())
self.assertEqual("", model.encapsulationId())
annotator.assignId(model, CellmlElementType.ENCAPSULATION)
self.assertEqual("b4da56", model.encapsulationId())
self.assertEqual("", c.id())
annotator.assignId(c)
self.assertEqual("b4da57", c.id())
self.assertEqual("", c.encapsulationId())
annotator.assignId(c, CellmlElementType.COMPONENT_REF)
self.assertEqual("b4da58", c.encapsulationId())
c2v1 = model.component("component2").variable("variable1")
c3v1 = model.component("component3").variable("variable1")
self.assertEqual("", Variable.equivalenceConnectionId(c2v1, c3v1))
annotator.assignId(VariablePair(c2v1, c3v1), CellmlElementType.CONNECTION)
self.assertEqual("b4da59", Variable.equivalenceConnectionId(c2v1, c3v1))
self.assertEqual("", Variable.equivalenceMappingId(c2v1, c3v1))
annotator.assignId(VariablePair(c2v1, c3v1))
self.assertEqual("b4da5a", Variable.equivalenceMappingId(c2v1, c3v1))
c3v2 = model.component("component3").variable("variable2")
self.assertEqual("", c3v2.id())
annotator.assignId(c3v2)
self.assertEqual("b4da5b", c3v2.id())
u = model.units(1)
self.assertEqual("", u.id())
annotator.assignId(u)
self.assertEqual("b4da5c", u.id())
r = model.component("component2").reset(0)
self.assertEqual("", r.id())
annotator.assignId(r)
self.assertEqual("b4da5d", r.id())
self.assertEqual("", r.testValueId())
annotator.assignId(r, CellmlElementType.TEST_VALUE)
self.assertEqual("b4da5e", r.testValueId())
self.assertEqual("", r.resetValueId())
annotator.assignId(r, CellmlElementType.RESET_VALUE)
self.assertEqual("b4da5f", r.resetValueId())
i = model.component("component1").importSource()
self.assertEqual("", i.id())
annotator.assignId(i)
self.assertEqual("b4da60", i.id())
self.assertEqual("", u.unitId(0))
annotator.assignId(UnitsItem(u, 0))
self.assertEqual("b4da61", u.unitId(0))
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())
def test_list_duplicate_ids(self):
from libcellml import Annotator, CellmlElementType, Parser
model_string = file_contents("annotator/lots_of_duplicate_ids.cellml")
parser = Parser()
annotator = Annotator()
model = parser.parseModel(model_string)
annotator.setModel(model)
id_list = annotator.duplicateIds()
expected_ids = ('duplicateId1', 'duplicateId2', 'duplicateId3',
'duplicateId4')
self.assertEqual(expected_ids, id_list)
# Get the collections by duplicated id.
c2v1 = model.component("component2").variable("variable1")
c2v2 = model.component("component2").variable("variable2")
c3v1 = model.component("component2").component("component3").variable(
"variable1")
c3v2 = model.component("component2").component("component3").variable(
"variable2")
c4v1 = model.component("component4").variable("variable1")
c4v2 = model.component("component4").variable("variable2")
expected_items = {
"duplicateId1": (
(CellmlElementType.UNITS, model.units("units2")),
(CellmlElementType.IMPORT, model.importSource(0)),
(CellmlElementType.MAP_VARIABLES, (c4v1, c2v1)),
(CellmlElementType.COMPONENT, model.component("component2")),
(CellmlElementType.CONNECTION, (c2v1, c3v1)),
(CellmlElementType.TEST_VALUE,
model.component("component2").reset(0)),
(CellmlElementType.COMPONENT_REF,
model.component("component2").component("component3")),
(CellmlElementType.VARIABLE,
model.component("component2").component(
"component3").variable("variable2")),
),
"duplicateId2": (
(CellmlElementType.MODEL, model),
(CellmlElementType.UNITS, model.units("units1")),
(CellmlElementType.UNITS, model.units("blob")),
(CellmlElementType.CONNECTION, (c4v2, c2v2)),
(CellmlElementType.VARIABLE, c4v2),
(CellmlElementType.COMPONENT_REF,
model.component("component2")),
(CellmlElementType.RESET,
model.component("component2").reset(0)),
(CellmlElementType.VARIABLE, c3v1),
),
"duplicateId3": (
(CellmlElementType.IMPORT, model.importSource(1)),
(CellmlElementType.UNITS, model.units("units3")),
(CellmlElementType.VARIABLE, c4v1),
(CellmlElementType.VARIABLE, c2v2),
(CellmlElementType.MAP_VARIABLES, (c2v2, c4v2)),
(CellmlElementType.COMPONENT,
model.component("component2").component("component3")),
(CellmlElementType.ENCAPSULATION, model),
),
"duplicateId4": (
(CellmlElementType.UNIT, ((model.units("units2"), 0))),
(CellmlElementType.COMPONENT, model.component("component1")),
(CellmlElementType.COMPONENT, model.component("component4")),
(CellmlElementType.MAP_VARIABLES, (c2v1, c3v1)),
(CellmlElementType.VARIABLE, c2v1),
(CellmlElementType.MAP_VARIABLES, (c2v2, c4v2)),
(CellmlElementType.RESET_VALUE,
model.component("component2").reset(0)),
)
}
for id in expected_ids:
items_with_id = annotator.items(id)
count = 0
for item in items_with_id:
self.assertEqual(item[0], expected_items[id][count][0])
# SWIG copies the pointers so can't expect a comparison to be true. Not sure how to
# compare these ...
# self.assertEqual(item[1], expected_items[id][count][1])
count = count + 1
def test_auto_id_individual(self):
from libcellml import Annotator, CellmlElementType, Parser, Variable
from libcellml import Unit, VariablePair
annotator = Annotator()
parser = Parser()
model_string = file_contents("annotator/no_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
self.assertEqual(
"b4da55",
annotator.assignId(model.component(0),
CellmlElementType.COMPONENT))
self.assertEqual("b4da55", model.component(0).id())
self.assertEqual(
"b4da56",
annotator.assignId(model.component("component2"),
CellmlElementType.COMPONENT_REF))
self.assertEqual("b4da56",
model.component("component2").encapsulationId())
self.assertEqual(
"b4da57",
annotator.assignId(
VariablePair(
model.component("component2").variable("variable1"),
model.component("component2").variable(
"variable1").equivalentVariable(0)),
CellmlElementType.CONNECTION))
self.assertEqual(
"b4da57",
Variable.equivalenceConnectionId(
model.component("component2").variable("variable1"),
model.component("component2").variable(
"variable1").equivalentVariable(0)))
self.assertEqual("b4da58", annotator.assignId(model.importSource(0)))
self.assertEqual("b4da58", model.importSource(0).id())
self.assertEqual(
"b4da59",
annotator.assignId(
VariablePair(
model.component("component2").variable("variable2"),
model.component("component2").variable(
"variable2").equivalentVariable(0)),
CellmlElementType.MAP_VARIABLES))
self.assertEqual(
"b4da59",
Variable.equivalenceMappingId(
model.component("component2").variable("variable2"),
model.component("component2").variable(
"variable2").equivalentVariable(0)))
self.assertEqual("b4da5a",
annotator.assignId(model, CellmlElementType.MODEL))
self.assertEqual("b4da5a", model.id())
self.assertEqual(
"b4da5b",
annotator.assignId(
model.component("component2").reset(0),
CellmlElementType.RESET))
self.assertEqual("b4da5b", model.component("component2").reset(0).id())
self.assertEqual(
"b4da5c",
annotator.assignId(
model.component("component2").reset(0),
CellmlElementType.RESET_VALUE))
self.assertEqual("b4da5c",
model.component("component2").reset(0).resetValueId())
self.assertEqual(
"b4da5d",
annotator.assignId(
model.component("component2").reset(0),
CellmlElementType.TEST_VALUE))
self.assertEqual("b4da5d",
model.component("component2").reset(0).testValueId())
self.assertEqual("b4da5e", annotator.assignId(Unit(model.units(1), 0)))
self.assertEqual("b4da5e", model.units(1).unitId(0))
self.assertEqual("b4da5f", annotator.assignId(model.units(1)))
self.assertEqual("b4da5f", model.units(1).id())
self.assertEqual("b4da60",
annotator.assignId(model.component(1).variable(0)))
self.assertEqual("b4da60", model.component(1).variable(0).id())
self.assertEqual(
"b4da61", annotator.assignId(model,
CellmlElementType.ENCAPSULATION))
self.assertEqual("b4da61", model.encapsulationId())
def test_type_based_retrieval(self):
from libcellml import Annotator, Model, Parser
annotator = Annotator()
model = Model()
parser = Parser()
model_string = file_contents("annotator/unique_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
v1v1 = (model.component("component2").variable("variable1"),
model.component("component2").component("component3").variable(
"variable1"))
v2v2 = (model.component("component2").variable("variable2"),
model.component("component2").component("component3").variable(
"variable2"))
self.assertEqual(model.name(), annotator.model("model_1").name())
self.assertEqual(model.name(),
annotator.encapsulation("encapsulation_1").name())
self.assertEqual(
model.component("component1").name(),
annotator.component("component_1").name())
self.assertEqual(
model.component("component2").name(),
annotator.component("component_2").name())
self.assertEqual(
model.component("component2").name(),
annotator.component("component_ref_1").name())
self.assertEqual(
model.component("component2").component("component3").name(),
annotator.component("component_3").name())
self.assertEqual(
model.component("component2").component("component3").name(),
annotator.componentRef("component_ref_2").name())
self.assertEqual(
model.component("component1").importSource().url(),
annotator.importSource("import_1").url())
self.assertEqual(
model.units("units1").name(),
annotator.units("units_1").name())
self.assertEqual(
model.units("units1").importSource().url(),
annotator.importSource("import_2").url())
self.assertEqual(
model.units("units2").name(),
annotator.units("units_2").name())
self.assertEqual(
model.units("units2").name(),
annotator.unit("unit_1").units().name())
self.assertEqual(0, annotator.unit("unit_1").index())
self.assertEqual(
model.component("component2").variable("variable1").name(),
annotator.variable("variable_1").name())
self.assertEqual(
model.component("component2").variable("variable2").name(),
annotator.variable("variable_2").name())
self.assertEqual(
model.component("component2").reset(0).variable().name(),
annotator.reset("reset_1").variable().name())
self.assertEqual(
model.component("component2").reset(0).testVariable().name(),
annotator.reset("reset_1").testVariable().name())
self.assertEqual(
model.component("component2").reset(0).testValue(),
annotator.testValue("test_value_1").testValue())
self.assertEqual(
model.component("component2").reset(0).resetValue(),
annotator.resetValue("reset_value_1").resetValue())
self.assertEqual(
model.component("component2").component("component3").variable(
"variable1").name(),
annotator.variable("variable_3").name())
self.assertEqual(
model.component("component2").component("component3").variable(
"variable2").name(),
annotator.variable("variable_4").name())
self.assertEqual(
v1v1[0].name(),
annotator.connection("connection_1").variable1().name())
self.assertEqual(
v1v1[1].name(),
annotator.connection("connection_1").variable2().name())
self.assertEqual(
v1v1[0].name(),
annotator.mapVariables("map_variables_1").variable1().name())
self.assertEqual(
v1v1[1].name(),
annotator.mapVariables("map_variables_1").variable2().name())
self.assertEqual(
v2v2[0].name(),
annotator.mapVariables("map_variables_2").variable1().name())
self.assertEqual(
v2v2[1].name(),
annotator.mapVariables("map_variables_2").variable2().name())
self.assertIsNone(annotator.model("i_dont_exist"))
self.assertIsNone(annotator.component("i_dont_exist"))
self.assertIsNone(annotator.variable("i_dont_exist"))
self.assertIsNone(annotator.units("i_dont_exist"))
self.assertIsNone(annotator.unit("i_dont_exist"))
self.assertIsNone(annotator.reset("i_dont_exist"))
self.assertIsNone(annotator.resetValue("i_dont_exist"))
self.assertIsNone(annotator.testValue("i_dont_exist"))
self.assertIsNone(annotator.componentRef("i_dont_exist"))
self.assertIsNone(annotator.connection("i_dont_exist"))
self.assertIsNone(annotator.importSource("i_dont_exist"))
def test_assign_by_type(self):
from libcellml import Annotator, Parser, Variable
from libcellml import Unit, VariablePair
annotator = Annotator()
parser = Parser()
model_string = file_contents("annotator/no_ids.cellml")
model = parser.parseModel(model_string)
annotator.setModel(model)
c = model.component(0)
self.assertEqual("", model.id())
annotator.assignModelId(model)
self.assertEqual("b4da55", model.id())
self.assertEqual("", model.encapsulationId())
annotator.assignEncapsulationId(model)
self.assertEqual("b4da56", model.encapsulationId())
self.assertEqual("", c.id())
annotator.assignComponentId(c)
self.assertEqual("b4da57", c.id())
self.assertEqual("", c.encapsulationId())
annotator.assignComponentRefId(c)
self.assertEqual("b4da58", c.encapsulationId())
c2v1 = model.component("component2").variable("variable1")
c3v1 = model.component("component3").variable("variable1")
self.assertEqual("", Variable.equivalenceConnectionId(c2v1, c3v1))
annotator.assignConnectionId(VariablePair(c2v1, c3v1))
self.assertEqual("b4da59",
Variable.equivalenceConnectionId(c2v1, c3v1))
self.assertEqual("", Variable.equivalenceMappingId(c2v1, c3v1))
annotator.assignMapVariablesId(VariablePair(c2v1, c3v1))
self.assertEqual("b4da5a", Variable.equivalenceMappingId(c2v1, c3v1))
c3v2 = model.component("component3").variable("variable2")
self.assertEqual("", c3v2.id())
annotator.assignVariableId(c3v2)
self.assertEqual("b4da5b", c3v2.id())
u = model.units(1)
self.assertEqual("", u.id())
annotator.assignUnitsId(u)
self.assertEqual("b4da5c", u.id())
r = model.component("component2").reset(0)
self.assertEqual("", r.id())
annotator.assignResetId(r)
self.assertEqual("b4da5d", r.id())
self.assertEqual("", r.testValueId())
annotator.assignTestValueId(r)
self.assertEqual("b4da5e", r.testValueId())
self.assertEqual("", r.resetValueId())
annotator.assignResetValueId(r)
self.assertEqual("b4da5f", r.resetValueId())
i = model.importSource(0)
self.assertEqual("", i.id())
annotator.assignImportSourceId(i)
self.assertEqual("b4da60", i.id())
self.assertEqual("", u.unitId(0))
annotator.assignUnitId(Unit(u, 0))
self.assertEqual("b4da61", u.unitId(0))
