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_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_recursive_validation(self):
# Test that the owned object, in this case the Range,
# is also validated when the SequenceFeature is validated.
seq_uri = 'https://github.com/synbiodex/pysbol3/sequence'
start = 10
end = 1
r = sbol3.Range(seq_uri, start, end)
report = r.validate()
# end < start is a validation error
self.assertEqual(1, len(report.errors))
sf = sbol3.SequenceFeature([r])
report = sf.validate()
# We should find the validation issue in the owned
# object (the range).
self.assertEqual(1, len(report.errors))
def test_validate(self):
# Test the document level validation
# This should validate all the objects in the document
# and return a report containing all errors and warnings.
doc = sbol3.Document()
c1 = sbol3.Component('https://github.com/synbiodex/pysbol3/c1',
sbol3.SBO_DNA)
doc.add(c1)
s1 = sbol3.Sequence('https://github.com/synbiodex/pysbol3/s1')
doc.add(s1)
start = 10
end = 1
r = sbol3.Range(s1, start, end)
sf = sbol3.SequenceFeature([r])
c1.features.append(sf)
report = doc.validate()
# We should find the validation issue in the Range
self.assertEqual(1, len(report))
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_validation(self):
locations = []
sf = sbol3.SequenceFeature(locations)
report = sf.validate()
self.assertIsNotNone(report)
self.assertEqual(1, len(report.errors))
def test_create(self):
es1 = sbol3.EntireSequence(sbol3.PYSBOL3_MISSING)
locations = [es1]
sf = sbol3.SequenceFeature(locations)
self.assertEqual(locations, sf.locations)
