def test_dunder_uri(self):
# See issue #319
# The __uri__ method to convert an object to a URI
# was returning a str, not a URIRef
sa = sbol2.SequenceAnnotation('test_sa')
comp = sbol2.Component('test_comp')
sa.component = comp
expected = rdflib.URIRef(comp.identity)
self.assertEqual(expected,
sa.properties[sbol2.SBOL_COMPONENT_PROPERTY][0])
def test_containers(self):
# Note: Alphabetical Order
x = sbol.Activity()
x = sbol.CombinatorialDerivation()
x = sbol.Component()
x = sbol.ComponentDefinition()
x = sbol.Document()
x = sbol.Interaction()
x = sbol.Module()
x = sbol.ModuleDefinition()
x = sbol.Participation()
x = sbol.SequenceAnnotation()
def test_add_remove_role(self):
c = sbol2.Component('c1')
self.assertEqual([], c.roles)
c.addRole(sbol2.SO_PROMOTER)
self.assertEqual([sbol2.SO_PROMOTER], c.roles)
c.addRole(sbol2.SO_MISC)
self.assertEqual([sbol2.SO_PROMOTER, sbol2.SO_MISC], c.roles)
c.addRole(sbol2.SO_CDS)
self.assertEqual([sbol2.SO_PROMOTER, sbol2.SO_MISC, sbol2.SO_CDS],
c.roles)
c.removeRole(1)
self.assertEqual([sbol2.SO_PROMOTER, sbol2.SO_CDS], c.roles)
def test_recursive_add(self):
# Make sure that when an object gets added to a document
# all of its child objects also get added.
cd = sbol2.ComponentDefinition('cd')
comp = sbol2.Component('cd_c')
cd.components.add(comp)
# Use of cd.sequence is dubious because the sequence attribute
# isn't really there in SBOL 2.3. But it's the test case that
# found the bug with recursive addition of objects, so we use it.
seq = sbol2.Sequence('cd_seq')
cd.sequence = seq
doc = sbol2.Document()
doc.addComponentDefinition(cd)
# The cd and sequence should be in the document
# The component is not top level, so doesn't get added
self.assertEqual(2, len(doc))
def test_role(self):
c = sbol2.Component('c1')
self.assertTrue(hasattr(c, 'identity'))
self.assertEqual(None, c.roleIntegration)
self.assertEqual([], c.roles)
c.roles = [sbol2.SO_PROMOTER]
# The SBOL 2.3.0 spec says that if a component has roles then
# it MUST have a roleIntegration. There is a validator that should
# set roleIntegration if not set
self.assertNotEqual(None, c.roleIntegration)
self.assertEqual(sbol2.SBOL_ROLE_INTEGRATION_MERGE, c.roleIntegration)
c.roleIntegration = sbol2.SBOL_ROLE_INTEGRATION_OVERRIDE
c.roles = []
# It is ok to have a roleIntegration even if there are no roles
self.assertEqual(sbol2.SBOL_ROLE_INTEGRATION_OVERRIDE,
c.roleIntegration)
def test_delete_downstream(self):
doc = sbol2.Document()
gene = sbol2.ComponentDefinition("BB0001")
promoter = sbol2.ComponentDefinition("R0010")
rbs = sbol2.ComponentDefinition("B0032")
cds = sbol2.ComponentDefinition("E0040")
terminator = sbol2.ComponentDefinition("B0012")
doc.addComponentDefinition([gene, promoter, rbs, cds, terminator])
gene.assemblePrimaryStructure([promoter, rbs, cds, terminator])
primary_structure_components = gene.getPrimaryStructureComponents()
c_promoter = primary_structure_components[0]
c_rbs = primary_structure_components[1]
c_cds = primary_structure_components[2]
c_terminator = primary_structure_components[3]
gene.deleteDownstreamComponent(c_rbs)
primary_structure = gene.getPrimaryStructure()
primary_structure = [cd.identity for cd in primary_structure]
valid_primary_structure = [
promoter.identity, rbs.identity, terminator.identity
]
self.assertEqual(primary_structure, valid_primary_structure)
# Test deletion when the target Component is the last Component
gene.deleteDownstreamComponent(c_rbs)
primary_structure = gene.getPrimaryStructure()
primary_structure = [cd.identity for cd in primary_structure]
valid_primary_structure = [promoter.identity, rbs.identity]
self.assertEqual(primary_structure, valid_primary_structure)
# Test failure when user tries to delete Component upstream of the first
# Component
with self.assertRaises(ValueError):
gene.deleteDownstreamComponent(c_cds)
# Test failure when the user supplies a Component that isn't part of the
# primary structure
with self.assertRaises(ValueError):
gene.deleteDownstreamComponent(sbol2.Component())