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_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_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_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_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_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_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_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_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())
# 1.d
# Print the parsed model to the terminal for viewing.
print_model(model, False)
# end 1
print('----------------------------------------------------------')
print(' STEP 2: Resolve the imports and flatten ')
print('----------------------------------------------------------')
import_path = os.path.dirname(model_file)
# 2.a
# Create an Importer instance and use it to resolve the imports in your model.
importer = Importer()
importer.resolveImports(model, import_path)
# 2.b
# Check that the importer has not raised any issues.
print_issues(importer)
# 2.c
# Use the importer to create a flattened version of the model.
flatModel = importer.flattenModel(model)
# end 2
print('----------------------------------------------------------')
print(' STEP 3: Validate and analyse the flattened model ')
print('----------------------------------------------------------')
from libcellml import Analyser, Importer, Model, Parser, Printer, Validator
if __name__ == '__main__':
# STEP 1
# Parse an existing CellML model from a file.
read_file = open('debugAnalysisExample.cellml', 'r')
parser = Parser()
model = parser.parseModel(read_file.read())
# STEP 2
# Resolve any imports and flatten the model for analysis.
importer = Importer()
# Resolve the imports.
importer.resolveImports(model, '')
# Check for issues.
print('The importer found {} issues.'.format(importer.issueCount()))
for i in range(0, importer.issueCount()):
issue = importer.issue(i)
print(issue.description())
# Flatten the model.
model = importer.flattenModel(model)
# STEP 3
# Create an Validator instance and pass the model to it for processing.
validator = Validator()
validator.validateModel(model)
# Print any issues to the terminal.
print('The type of item with ID "whoAmIAndWhereDidIComeFrom" is {}'.format(
cellmlElementTypeAsString(who_am_i.type())))
# 5.b
# Cast it into a CellML item of the appropriate type.
units = who_am_i.units()
# 5.c
# Use the Component.isImport() function to verify that it is imported.
assert (units.isImport())
# 5.d
# Create an Importer instance and use it to resolve this model's imports.
# Check that it has not raised any issues.
importer = Importer()
importer.resolveImports(model, os.path.dirname(model_file))
print_issues(importer)
# 5.e
# Retrieve all the information needed to locate any annotations on the
# original item:
# - the URL from which it was imported and
# - the id of the item in the original model.
# Print these to the terminal.
url = units.importSource().url()
reference = units.importReference()
imported_id = units.importSource().model().units(reference).id()
print('The units with id "whoAmIAndWhereDidIComeFrom" came from:')
print(' - url: {}'.format(url))
print(' - id: {}'.format(imported_id))
from libcellml import Analyser, Importer, Model, Parser, Printer, Validator
if __name__ == '__main__':
# STEP 1
# Parse an existing CellML model from a file.
read_file = open('resources/importExample1.cellml', 'r')
parser = Parser()
original_model = parser.parseModel(read_file.read())
# STEP 2
# Create an Importer to resolve the imports in the model.
importer = Importer()
# Resolve the imports.
importer.resolveImports(original_model, 'resources/')
# Check for issues.
print('The importer found {} issues.'.format(importer.issueCount()))
for i in range(0,importer.issueCount()):
print(importer.issue(i).description())
print()
# STEP 3
# The analysis tools - the Validator and Analyser - will read only the submitted
# model they do not look into any of the imported items, so they can't check them.
# In order to retain the import structure but be able to use the diagnostic tools,
# we can create a flattened copy of the model for testing. This can be used to
# identify mistakes in the unflattened model too.
# Create a Validator and Analyser and submit the original, unflattened model.
# We don't expect either of these to report any issues.