def test_documentation(self):
# Tests parsing a <documentation> tag from the cellml temp doc ns
path = os.path.join(DIR, 'documentation.cellml')
expected = '\n'.join([
'Article title',
'',
'Michael',
'Clerx',
'',
'University of Oxford',
'',
'Model Status',
'This model is fake.',
'',
'This is a paragraph.',
'',
'schematic diagram',
'',
'A schematic diagram describing the model.',
'',
'Here\'s some extra documentation.',
])
m = v1.parse_file(path)
self.assertEqual(m.meta['documentation'], expected)
def parse_in_file(self, xml):
"""
Inserts the given ``xml`` into a <model> element, writes it to a
temporary file, parses it, and returns the result.
"""
with TemporaryDirectory() as d:
path = d.path('test.cellml')
with open(path, 'w') as f:
f.write(self.wrap(xml))
return v1.parse_file(path)
def test_write_file(self):
# Tests write_file
m1 = cellml.Model('ernie')
with TemporaryDirectory() as d:
path = d.path('test.cellml')
cellml.write_file(path, m1)
m2 = cellml.parse_file(path)
self.assertEqual(m2.name(), 'ernie')
self.assertEqual(len(m2), 0)
def test_cmeta_ids(self):
# Test cmeta ids are parsed
# Test parsing cmeta id
path = os.path.join(DIR, 'br-1977.cellml')
model = v1.parse_file(path)
self.assertEqual(model.cmeta_id(), 'beeler_reuter_1977')
# Invalid cmeta id
self.assertBad('<component cmeta:id="" name="c" />',
'non-empty string')
# Duplicate cmeta id
self.assertBad(
'<component cmeta:id="x" name="c" />'
'<component cmeta:id="x" name="d" />', 'Duplicate cmeta:id')
def test_evaluated_derivatives(self):
# Test parsing a simple model; compare RHS derivatives to known ones
# Load myokit model
org_model = myokit.load_model('example')
org_states = [x.qname() for x in org_model.states()]
org_values = org_model.evaluate_derivatives()
# Load exported version
path = os.path.join(DIR, 'lr-1991-exported-1.cellml')
cm = v1.parse_file(path)
new_model = cm.myokit_model()
new_states = [x.qname() for x in new_model.states()]
new_values = new_model.evaluate_derivatives()
# Compare each state (loop unrolled for easier debugging)
org_i = 0
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 1
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 2
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 3
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 4
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 5
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 6
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
org_i = 7
new_i = new_states.index(org_states[org_i])
self.assertEqual(org_values[org_i], new_values[new_i])
