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_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_inheritance(self):
import libcellml
from libcellml import Importer
# Test inheritance.
x = Importer()
self.assertIsInstance(x, libcellml.logger.Logger)
# Test access to inherited methods.
self.assertIsNone(x.issue(0))
self.assertIsNone(x.issue(-1))
self.assertEqual(x.issueCount(), 0)
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_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_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_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_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_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())
who_am_i = annotator.item('whoAmIAndWhereDidIComeFrom')
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))
# (You can verify this for yourself by printing your model to the terminal again if you like.)
# Now the problem we have is that we need to connect to variables inside imported components,
# but these don't exist in our model yet: the import sources that we created in Steps 4 and 5
# are simply a recipe they don't actually create anything.
print_model(model)
# In order to connect to variables in imported components, we can create dummy variables inside them.
# These will be overwritten when the imports are resolved and the model flattened, at which time
# the imported variables will replace the dummy ones. As with other steps, we have a choice here.
# We can manually create variables or clone existing ones into the destination components we have
# already created or we can make use of the Importer class to help us manage these. We're going to
# do the latter now.
# 10.a
# Create an Importer item.
importer = Importer()
# end 10.a
# Resolving imports for a model triggers the importer to go searching for all of the
# information required by this model's imports, even through multiple generations of import layers.
# It also instantiates each of those requirements into the importer's own library.
# You could use the Model.hasUnresolvedImports() function to test whether the operation was
# successful or not expecting it to be true before resolution, and false afterwards.
# 10.b
# Pass the model and the path to the GateModel.cellml file into the Importer.resolveImports
# function.
importer.resolveImports(model, '')
# 10.c
# Check the Importer for issues and print any found to the terminal - we do not expect any at this stage.
who_am_i = annotator.item('whoAmIAndWhereDidIComeFrom')
print('The type of item with ID "whoAmIAndWhereDidIComeFrom" is {}'.format(
get_cellml_element_type_from_enum(who_am_i[0])))
# 5.b
# Cast it into a CellML item of the appropriate type.
units = who_am_i[1]
# 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, '')
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))
# (You can verify this for yourself by printing your model to the terminal again if you like.)
# Now the problem we have is that we need to connect to variables inside imported components,
# but these don't exist in our model yet: the import sources that we created in Steps 4 and 5
# are simply a recipe they don't actually create anything.
print_model(model)
# In order to connect to variables in imported components, we can create dummy variables inside them.
# These will be overwritten when the imports are resolved and the model flattened, at which time
# the imported variables will replace the dummy ones. As with other steps, we have a choice here.
# We can manually create variables or clone existing ones into the destination components we have
# already created or we can make use of the Importer class to help us manage these. We're going to
# do the latter now.
# 10.a
# Create an Importer item.
importer = Importer()
# end 10.a
# Resolving imports for a model triggers the importer to go searching for all of the
# information required by this model's imports, even through multiple generations of import layers.
# It also instantiates each of those requirements into the importer's own library.
# You could use the Model.hasUnresolvedImports() function to test whether the operation was
# successful or not expecting it to be true before resolution, and false afterwards.
# 10.b
# Pass the model and the path to the GateModel.cellml file into the Importer.resolveImports
# function.
importer.resolveImports(model, import_path)
# 10.c
# Check the Importer for issues and print any found to the terminal - we do not expect any at this stage.
print(' STEP 4: Resolve the imports ')
print('----------------------------------------------------------')
# It's important to remember that the imports are merely instructions for how
# components or units items should be located: only their syntax is checked by the
# validator, not that the files exist or contain the required information. To debug
# the imported aspects of the model, we need to use an Importer class.
# To resolve the imports, we need a path to a base location against which any
# relative file addresses can be resolved. For this tutorial, if you've downloaded
# the files into the same directory as the code, so simply using an empty string is sufficient.
# If they're another directory, make sure to end your path with a slash, '/'.
# Use the function importer.resolveImports(model, path).
# 4.a
# Create an Importer instance and use it to resolve the model.
importer = Importer()
importer.resolveImports(model, '')
# 4.b
# Similarly to the validator, the importer will log any issues it encounters.
# Retrieve these and print to the terminal (you can do this manually or using the
# convenience function as before).
print_issues(importer)
# end 4.b
# Importer error[0]:
# Description: Import of component 'importedGateH' from 'GateModel.cellml' requires
# component named 'i_dont_exist' which cannot be found.
# We need to change the import reference for the component to be 'gateEquations' instead
# of 'i_dont_exist'. You can either retrieve the component using its name or directly
print('-----------------------------')
import_path = os.path.dirname(model_file)
# It's important to remember that the imports are merely instructions for how
# components or units items should be located: only their syntax is checked by the
# validator, not that the files exist or contain the required information. To debug
# the imported aspects of the model, we need to use an Importer class.
# To resolve the imports, we need a path to a base location against which any
# relative file addresses can be resolved. For this tutorial, if you've downloaded
# the files into the same directory as the code, so simply using an empty string is sufficient.
# If they're another directory, make sure to end your path with a slash, '/'.
# Use the function importer.resolveImports(model, path).
# 4.a
# Create an Importer instance and use it to resolve the model.
importer = Importer()
importer.resolveImports(model, import_path)
# 4.b
# Similarly to the validator, the importer will log any issues it encounters.
# Retrieve these and print to the terminal (you can do this manually or using the
# convenience function as before).
print_issues(importer)
# end 4.b
# Importer error[1]:
# Description: Import of component 'importedGateH' from 'GateModel.cellml' requires
# component named 'i_dont_exist' which cannot be found.
# We need to change the import reference for the component to be 'gateEquations' instead
# of 'i_dont_exist'. You can either retrieve the component using its name or directly
def test_create_destroy(self):
from libcellml import Importer
x = Importer()
del x
def test_imports(self):
from libcellml import Model, Importer, ImportSource, Units
m = Model()
u = Units()
im = Importer()
u.setImportSource(ImportSource())
m.addUnits(u)
self.assertTrue(m.hasImports())
self.assertEqual(0, im.importSourceCount())
i = ImportSource()
i.setUrl('actual_url')
im.addImportSource(i)
self.assertEqual(1, im.importSourceCount())
i1 = im.importSource(0)
self.assertTrue(im.hasImportSource(i))
im.removeImportSource(0)
i2 = ImportSource()
self.assertEqual(0, im.importSourceCount())
im.addImportSource(i2)
self.assertEqual(1, im.importSourceCount())
im.removeAllImportSources()
self.assertEqual(0, im.importSourceCount())
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.
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.
model = parser.parseModel(content)
# 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('----------------------------------------------------------')
# Use the parser to deserialise the contents of the string you've read and return the model.
model = parser.parseModel(read_file.read())
# 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('----------------------------------------------------------')
# 2.a
# Create an Importer instance and use it to resolve the imports in your model.
importer = Importer()
importer.resolveImports(model, '')
# 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('----------------------------------------------------------')
