def test_copy_stability(self):
# Test the stability of naming of objects across copies.
# See https://github.com/SynBioDex/pySBOL3/issues/231
#
# Strategy: create an object with 10+ children of the same
# type. Add to a document and serialize the document. Load the
# serialized document. Copy the object to a new document.
# Serialize the new document. Compare the serializations. If we
# use sorted ntriples, the serializations should be the same.
# This will demonstrate that we maintain names properly despite
# the inherently unordered nature of SBOL.
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
c1 = sbol3.Component('c1', types=[sbol3.SBO_DNA])
# Create a double-digit number of children to test sort of 10, 11, 1, etc.
for i in range(12):
instance_of_uri = f'https://example.com/instance/i{i}'
c1.features.append(sbol3.SubComponent(instance_of=instance_of_uri))
doc1 = sbol3.Document()
doc1.add(c1)
# Serialize to string
doc1_string = doc1.write_string(sbol3.SORTED_NTRIPLES)
self.assertIsNotNone(doc1_string)
# Load the serialized document into a new document
tmp_doc = sbol3.Document()
tmp_doc.read_string(doc1_string, sbol3.SORTED_NTRIPLES)
# Locate the top level to copy
tmp_c1 = tmp_doc.find('c1')
self.assertIsNotNone(tmp_c1)
self.assertIsInstance(tmp_c1, sbol3.TopLevel)
# Copy the top level into a new document
doc2 = sbol3.Document()
sbol3.copy([tmp_c1], into_document=doc2)
doc2_string = doc2.write_string(sbol3.SORTED_NTRIPLES)
# Verify that the serializations are identical
self.assertEqual(doc1_string, doc2_string)
def test_copy(self):
namespace = 'https://github.com/synbiodex/pysbol3'
sbol3.set_namespace(namespace)
test_path = os.path.join(SBOL3_LOCATION, 'multicellular',
'multicellular.ttl')
doc = sbol3.Document()
doc.read(test_path)
copies1 = sbol3.copy(doc)
self.assertEqual(len(doc), len(copies1))
document_checker = self.make_document_checker(None)
for obj in copies1:
obj.traverse(document_checker)
# Verify that the copies get the new namespace
copies2 = sbol3.copy(doc, into_namespace=namespace)
document_checker = self.make_document_checker(None)
namespace_checker = self.make_namespace_checker(namespace)
for obj in copies2:
obj.traverse(document_checker)
obj.traverse(namespace_checker)
# Verify new namespace AND new document
namespace3 = 'https://github.com/synbiodex/pysbol3/copytest'
doc3 = sbol3.Document()
copies3 = sbol3.copy(doc,
into_namespace=namespace3,
into_document=doc3)
document_checker = self.make_document_checker(doc3)
namespace_checker = self.make_namespace_checker(namespace3)
for obj in copies3:
obj.traverse(document_checker)
obj.traverse(namespace_checker)
def test_shacl_closure_with_toplevels(self):
# SBOL closure semantics should allow properties to reference
# a TopLevel object not contained in the Document
# This is the test case in https://github.com/SynBioDex/pySBOL3/issues/348
doc = sbol3.Document()
doc.read(os.path.join(TEST_DIR, 'resources', 'package.nt'))
self.assertEqual(len(doc.validate()), 0)
minidoc = sbol3.Document()
c = doc.find('https://synbiohub.org/public/igem/BBa_I20270')
self.assertIsInstance(c, sbol3.TopLevel)
sbol3.copy([c], into_document=minidoc)
# this assertion failed before the fix to the shacl rules
self.assertEqual(len(minidoc.validate()), 0)
def test_copy_properties(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
root = sbol3.Component('root', sbol3.SBO_DNA)
root.name = 'foo'
objects = sbol3.copy([root])
root_copy = objects[0]
self.assertEqual(root_copy.name, 'foo')
def test_copy(self):
# See https://github.com/SynBioDex/pySBOL3/issues/176 reopened
# Copying a tree of objects to a new document left the document
# pointer of the child objects unset. This caused "lookup" to
# fail.
dest_doc = sbol3.Document()
def check_document(i: sbol3.Identified):
# Verify that the object has a document, and that it is the
# expected document.
self.assertIsNotNone(i.document)
self.assertEqual(dest_doc, i.document)
test_path = os.path.join(SBOL3_LOCATION, 'multicellular',
'multicellular.nt')
doc = sbol3.Document()
doc.read(test_path)
sbol3.copy(doc, into_document=dest_doc)
self.assertEqual(len(doc), len(dest_doc))
for obj in dest_doc.objects:
obj.traverse(check_document)
def test_copy_child_objects(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
doc = sbol3.Document()
root = sbol3.Component('root', sbol3.SBO_DNA)
sub1 = sbol3.Component('sub1', sbol3.SBO_DNA)
sub2 = sbol3.Component('sub2', sbol3.SBO_DNA)
sc1 = sbol3.SubComponent(sub1)
sc2 = sbol3.SubComponent(sub2)
root.features.append(sc1)
root.features.append(sc2)
doc.add(root)
doc.add(sub1)
doc.add(sub2)
doc2 = sbol3.Document()
objects = sbol3.copy([root], into_document=doc2)
root_copy = objects[0]
self.assertIn(root_copy, doc2.objects)
self.assertEqual([sc.identity for sc in root.features],
[sc.identity for sc in root_copy.features])