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)
# 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 validator found {} issues.'.format(validator.issueCount()))
for i in range(0, validator.issueCount()):
issue = validator.issue(i)
print(issue.description())
# 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
# from the issue. Use the Component.setImportReference() function to fix the issue.
# 4.c
# Fix the issues reported by the importer. This needs to be an iterative process as
# more files become available to the importer.
issue0 = importer.issue(0)
issue0.component().setImportReference('gateEquations')
# end 4.c
# The second issue reported is a circular dependency. This is contained in files that
# haven't (yet) been seen at all by you, the user. It's included here to highlight the
# fact that the Importer class opens and instantates all required dependencies, and that
# some of those dependencies may have problems of their own.
# Issue [1] is a WARNING:
# description: Cyclic dependencies were found when attempting to resolve components in model 'CircularReferences'. The dependency loop is:
# - component 'importedGateH' is imported from 'i_dont_exist' in 'GateModel.cellml'
# - component 'importedGateM' is imported from 'gateEquations' in 'GateModel.cellml'
# - component 'controller' is imported from 'controller' in 'CircularControllerReference.cellml'
# - component 'controller' is imported from 'controller2' in 'CircularControllerReference2.cellml'
# - component 'controller2' is imported from 'controller' in 'CircularControllerReference.cellml' and
# 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.
validator = Validator()
validator.validateModel(original_model)
print('Investigating the original model:')
