def test_list_wrapping(self):
# Ensure that at least certain properties handle automatic list
# wrapping and are typed to do so.
# See https://github.com/SynBioDex/pySBOL3/issues/301
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
instance_uri = 'https://example.org/instance'
seq1 = sbol3.Sequence('seq1')
test_loc = sbol3.EntireSequence(seq1)
seq2 = sbol3.Sequence('seq2')
test_source_loc = sbol3.EntireSequence(seq1)
subcomp1 = sbol3.SubComponent(instance_of=instance_uri,
locations=test_loc,
source_locations=test_source_loc)
self.assertEqual([test_loc], subcomp1.locations)
self.assertEqual([test_source_loc], subcomp1.source_locations)
def test_cloning_with_children(self):
# This test does not use `sbol3.set_namespace` as the other
# cloning unit tests do. This is on purpose to verify that
# cloning does not rely on the default namespace.
doc = sbol3.Document()
namespace = 'https://github.com/synbiodex/pysbol3'
c1_identity = posixpath.join(namespace, 'c1')
c2_identity = posixpath.join(namespace, 'c2')
s1_identity = posixpath.join(namespace, 's1')
c1 = sbol3.Component(c1_identity, sbol3.SBO_DNA)
doc.add(c1)
seq1 = sbol3.Sequence(s1_identity)
doc.add(seq1)
c1.sequences.append(seq1)
sc1 = sbol3.SubComponent(c1)
es1 = sbol3.EntireSequence(seq1)
sc1.source_locations.append(es1)
c1.features = [sc1]
c2 = c1.clone(c2_identity)
self.assertEqual(c2_identity, c2.identity)
self.assertIsNone(c2.document)
# Check on the SubComponent
sc2 = c2.features[0]
self.assertIsInstance(sc2, sbol3.SubComponent)
self.assertNotEqual(sc1.identity, sc2.identity)
self.assertTrue(sc2.identity.startswith(c2.identity))
# Ensure that the reference was updated properly
self.assertEqual(c2.identity, sc2.instance_of)
self.assertIsNone(sc2.document)
es2 = sc2.source_locations[0]
self.assertIsInstance(es2, sbol3.EntireSequence)
self.assertNotEqual(es1.identity, es2.identity)
self.assertTrue(es2.identity.startswith(c2.identity))
self.assertEqual(es1.sequence, es2.sequence)
self.assertIsNone(es2.document)
def test_list_wrapping(self):
# Ensure that at least certain properties handle automatic list
# wrapping and are typed to do so.
# See https://github.com/SynBioDex/pySBOL3/issues/301
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
seq = sbol3.Sequence('seq1')
test_loc = sbol3.EntireSequence(seq)
seq_feat1 = sbol3.SequenceFeature(locations=test_loc)
self.assertEqual([test_loc], seq_feat1.locations)
def test_list_wrapping(self):
# Ensure that at least certain properties handle automatic list
# wrapping and are typed to do so.
# See https://github.com/SynBioDex/pySBOL3/issues/301
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
test_type = sbol3.SBO_DNA
seq = sbol3.Sequence('seq1')
test_loc = sbol3.EntireSequence(seq)
lsc = sbol3.LocalSubComponent(types=test_type, locations=test_loc)
self.assertEqual([test_type], lsc.types)
self.assertEqual([test_loc], lsc.locations)
def test_cascade_identity(self):
# Test that updating identity of an owned object cascades
# to child owned objects
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
c1 = sbol3.Component('c1', sbol3.SBO_DNA)
seq = sbol3.Sequence('seq1')
loc = sbol3.EntireSequence(seq)
seq_feature = sbol3.SequenceFeature([loc])
c1.features.append(seq_feature)
self.assertIsNotNone(seq_feature.identity)
# identity should cascade down to the location after it
# is set on the sequence feature
self.assertIsNotNone(loc.identity)
def test_list_wrapping(self):
# Ensure that at least certain properties handle automatic list
# wrapping and are typed to do so.
# See https://github.com/SynBioDex/pySBOL3/issues/301
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
seq = sbol3.Sequence('seq1')
test_loc = sbol3.EntireSequence(seq)
variable_uri = 'https://example.org/variable'
var_coll_uri = 'https://example.org/collection'
var_feat1 = sbol3.VariableFeature(cardinality=sbol3.SBOL_ZERO_OR_MORE,
variable=variable_uri,
variant_collections=var_coll_uri)
self.assertEqual([var_coll_uri], var_feat1.variant_collections)
def test_overwrite_identity(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
c1 = sbol3.Component('c1', sbol3.SBO_DNA)
seq = sbol3.Sequence('seq1')
loc = sbol3.EntireSequence(seq)
seq_feature = sbol3.SequenceFeature([loc])
c1.features.append(seq_feature)
self.assertIsNotNone(seq_feature.identity)
# identity should cascade down to the location after it
# is set on the sequence feature
self.assertIsNotNone(loc.identity)
old_sf_identity = seq_feature.identity
old_loc_identity = loc.identity
c2 = sbol3.Component('c2', sbol3.SBO_DNA)
# Try adding the same object to a different parent
# This should cause an error because the object is
# still parented by c1.
# See https://github.com/SynBioDex/pySBOL3/issues/178
with self.assertRaises(ValueError):
c2.features.append(seq_feature)
self.assertEqual(old_loc_identity, loc.identity)
self.assertEqual(old_sf_identity, seq_feature.identity)
def test_create(self):
es1 = sbol3.EntireSequence(sbol3.PYSBOL3_MISSING)
locations = [es1]
sf = sbol3.SequenceFeature(locations)
self.assertEqual(locations, sf.locations)
def test_identified_constructors(self):
# I don't remember why I wanted this test.
# Test all of the Identified constructors.
args_map = {
'Association': ['https://example.com/fake'],
'ComponentReference':
['https://example.com/fake', 'https://example.com/fake'],
'Constraint': [
'https://example.com/restriction',
'https://example.com/subject', 'https://example.com/object'
],
'CustomIdentified': ['https://example.com/fake'],
'Cut': ['https://example.com/fake', 1],
'EntireSequence': ['https://example.com/fake'],
'ExternallyDefined': [['https://example.com/fake'],
'https://example.com/fake'],
'Interaction': [['https://example.com/fake']],
'LocalSubComponent': [['https://example.com/fake']],
'Measure': [1.0, OM_KILOGRAM],
'Participation': [[sbol3.SBO_INHIBITOR],
'https://example.com/fake'],
'Range': ['https://example.com/fake', 1, 2],
'SequenceFeature':
[[sbol3.EntireSequence('https://example.com/fake')]],
'SubComponent': ['https://example.com/fake'],
'Usage': ['https://example.com/fake'],
'VariableFeature':
[sbol3.SBOL_ONE_OR_MORE, 'https://example.com/fake']
}
skip_list = [sbol3.Identified, sbol3.Feature, sbol3.Location]
abstract_list = [
sbol3.CustomIdentified, sbol3.TopLevel, sbol3.CustomTopLevel
]
for name in dir(sbol3):
item = getattr(sbol3, name)
if not isinstance(item, type):
continue
if issubclass(item, sbol3.TopLevel):
if item not in abstract_list:
self.assertTrue(hasattr(item, 'accept'),
f'{str(item)} has no accept attribute')
continue
if not issubclass(item, sbol3.Identified):
continue
if item in skip_list:
continue
arg_list = []
if name in args_map:
arg_list = args_map[name]
try:
item(*arg_list)
except TypeError as e:
self.fail('Unable to construct sbol3.%s: %s' % (name, e))
except sbol3.ValidationError as e:
self.fail('Constructed invalid sbol3.%s: %s' % (name, e))
if item in abstract_list:
# Skip over abstract classes when checking for the
# accept method
continue
self.assertTrue(hasattr(item, 'accept'),
f'{str(item)} has no accept attribute')
def test_creation(self):
# EntireSequence has no properties, so there isn't much to test here
es = sbol3.EntireSequence(sbol3.PYSBOL3_MISSING)
self.assertIsNotNone(es)
self.assertEqual(sbol3.SBOL_ENTIRE_SEQUENCE, es.type_uri)