class LiveUtilityTestCase(unittest.TestCase):
level = 9
def setUp(self):
self.utility = CellMLAPIUtility()
def tearDown(self):
pass
def test_1000_utf8_byte_order_mark_http(self):
url = 'http://models.cellml.org/w/dcowan/Sulman_et_al_2008/' \
'@@rawfile/4b3391441d19e5fab999246f36facd26b86bb3b4/' \
'Ekb-Oxford_Changed.cellml'
model = self.utility.loadModel(url)
self.assertEqual(model.cmetaId,
'ekaterinburg_rat')
def setUp(self):
self.utility = CellMLAPIUtility()
self.opener = StreamURLOpener()
self.opener.approved_protocol.append('file')
class UtilityTestCase(unittest.TestCase):
def setUp(self):
self.utility = CellMLAPIUtility()
self.opener = StreamURLOpener()
self.opener.approved_protocol.append('file')
def tearDown(self):
pass
def assertComponentName(self, componentSet, name):
comp = componentSet.getComponent(name)
self.assertEqual(comp.name, name)
def test_0000_basic(self):
self.assert_(self.utility.cellml_bootstrap)
def test_0010_model_load_file_fail(self):
model_path = get_path('beeler_reuter_1977-api-test.cellml')
# default loader will not allow file://
self.assertRaises(UnapprovedProtocolError,
self.utility.loadModel, model_path)
def test_0011_notopener(self):
opener = object()
# please fail
self.assertRaises(AssertionError, self.utility.loadModel,
'fail', opener)
def test_0100_model_load_standard(self):
model_path = get_path('beeler_reuter_1977-api-test.cellml')
model = self.utility.loadModel(model_path, self.opener)
self.assertEqual(model.cmetaId,
'beeler_reuter_mammalian_ventricle_1977')
def test_0110_model_load_imported(self):
model_path = get_path('subdir1', 'subdir2', 'toplevel.xml')
tl = self.utility.loadModel(model_path, self.opener)
v1 = tl.imports.iterateImports().nextImport().importedModel
v2 = v1.imports.iterateImports().nextImport().importedModel
self.assertComponentName(tl.modelComponents, 'toplevel_component')
self.assertComponentName(v1.modelComponents, 'level1_component')
self.assertComponentName(v2.modelComponents, 'level2_component')
def test_0111_model_load_imported(self):
model_path = get_path('subdir1', 'subdir2', 'toplevel.xml')
fd = urllib2.urlopen(model_path)
doc = etree.parse(fd)
fd.close()
# add the above as xmlbase into new file in temporary location
doc.getroot().set('{http://www.w3.org/XML/1998/namespace}base',
model_path)
stream = StringIO(etree.tostring(doc))
# use the custom utility with the modified loader
tl = self.utility.loadModel(stream, self.opener)
v1 = tl.imports.iterateImports().nextImport().importedModel
v2 = v1.imports.iterateImports().nextImport().importedModel
self.assertComponentName(tl.modelComponents, 'toplevel_component')
self.assertComponentName(v1.modelComponents, 'level1_component')
self.assertComponentName(v2.modelComponents, 'level2_component')
def test_0112_model_load_multiple_import(self):
model_path = get_path('multiimport.xml')
fd = urllib2.urlopen(model_path)
doc = etree.parse(fd)
fd.close()
# add the above as xmlbase into new file in temporary location
doc.getroot().set('{http://www.w3.org/XML/1998/namespace}base',
model_path)
stream = StringIO(etree.tostring(doc))
# use the custom utility with the modified loader
tl = self.utility.loadModel(stream, self.opener)
isi = tl.imports.iterateImports()
v1 = isi.nextImport().importedModel
v2 = isi.nextImport().importedModel
self.assertComponentName(tl.modelComponents, 'component1')
self.assertComponentName(tl.modelComponents, 'component2')
self.assertComponentName(v1.modelComponents, 'level1_component')
self.assertComponentName(v2.modelComponents, 'level2_component')
def test_0200_model_load_broken(self):
model_path = get_path('broken_xml.cellml')
self.assertRaises(ValueError,
self.utility.loadModel, model_path, self.opener)
lastmsg = self.utility.model_loader.lastErrorMessage
self.assertEqual(lastmsg, 'badxml/3/0//')
def test_0300_unicode(self):
model_path = get_path('unicode_valid.cellml')
model = self.utility.loadModel(model_path, self.opener)
self.assertEqual(model.cmetaId, 'unicode_valid')
def test_0301_ascii(self):
model_path = get_path('unicode_invalid.cellml')
model = self.utility.loadModel(model_path, self.opener)
# still loads because lxml will fail and then fallback to latin1
# which covers the entire range of bytes.
self.assertEqual(model.cmetaId, 'unicode_invalid')
def test_1000_extractMaths(self):
model_path = get_path('beeler_reuter_1977-api-test.cellml')
model = self.utility.loadModel(model_path, self.opener)
maths = self.utility.extractMaths(model)
self.assertEqual(len(maths), 12)
# tuple of (cmetaId or name, list of equations)
self.assertEqual(len(maths[1]), 2)
# number of equations
self.assertEqual(len(maths[1][1]), 1)
self.assertEqual(maths[1][0], 'membrane')
self.assert_(maths[1][1][0].startswith(
'<math xmlns="http://www.w3.org/1998/Math/MathML"'))
def test_2000_exportCeleds(self):
model_path = get_path('beeler_reuter_1977.cellml')
model = self.utility.loadModel(model_path, self.opener)
code = self.utility.exportCeleds(model)
# at least the language files we care about.
self.assertTrue('Python' in code.keys())
self.assertTrue('C' in code.keys())
self.assertTrue('F77' in code.keys())
self.assertTrue('MATLAB' in code.keys())
self.assertTrue(code['Python'].startswith('# '))
self.assertTrue('i_Na in component sodium_current (uA_per_mm2)'
in code['Python'])
self.assertTrue('-84.624'
in code['Python'])
def test_3000_validateModel_clean(self):
model_path = get_path('beeler_reuter_1977.cellml')
model = self.utility.loadModel(model_path, self.opener)
results = self.utility.validateModel(model)
self.assertEqual(len(results), 0)
def test_3001_validateModel_unclean(self):
model_path = get_path('beeler_reuter_1977-api-test.cellml')
model = self.utility.loadModel(model_path, self.opener)
results = self.utility.validateModel(model)
# Original model does not validate.
self.assertNotEqual(len(results), 0)
# Would test for the right strings to show up, but wording and
# such may change, so test just the first bits of our wording.
self.assertEqual(results[0][:5], 'Line ')
def setUp(self):
self.utility = CellMLAPIUtility()
