def test_compile_autoconstruct_sequence(self):
# Ensure that autoconstruction of Sequence URIs works correctly with
# different configuration options
root_id = 'root'
sub_id = 'sub'
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, True)
doc = sbol2.Document()
root = doc.componentDefinitions.create(root_id)
sub = doc.componentDefinitions.create(sub_id)
root.compile([sub])
expected_identity = sbol2.getHomespace(
) + '/Sequence/' + root_id + '/1'
self.assertEqual(root.sequence.identity, expected_identity)
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, False)
doc = sbol2.Document()
root = doc.componentDefinitions.create(root_id)
sub = doc.componentDefinitions.create(sub_id)
root.compile([sub])
expected_identity = sbol2.getHomespace() + '/' + root_id + '_seq/1'
self.assertEqual(root.sequence.identity, expected_identity)
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
sbol2.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, True)
def test_import_into_typed_namespace_from_nontyped_namespace(self):
# Copy an sbol-typed URI to a non-typed, sbol-compliant URI
sbol.setHomespace('http://examples.org')
sbol.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, False)
sbol.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
doc = sbol.Document()
comp = sbol.ComponentDefinition('cd')
seq = sbol.Sequence('seq')
comp.sequences = seq.identity
doc.addComponentDefinition(comp)
doc.addSequence(seq)
# Import the object into the new namespace
sbol.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, True)
old_homespace = sbol.getHomespace()
sbol.setHomespace('http://acme.com')
comp_copy = comp.copy(None, old_homespace)
# Verify new namespace was correctly substituted and type token was successfully
# added
self.assertEqual(comp_copy.identity,
'http://acme.com/ComponentDefinition/cd/1')
self.assertEqual(comp_copy.persistentIdentity,
'http://acme.com/ComponentDefinition/cd')
self.assertEqual(comp_copy.sequences[0],
'http://acme.com/Sequence/seq/1')
# Verify wasDerivedFrom relationship
self.assertEqual(comp_copy.wasDerivedFrom[0], comp.identity)
def test_import_object_into_new_namespace(self):
# When copying an object into a new namespace, confirm that it's URI is copied
# into the new namespace. Also confirm that any ReferencedObject attributes
# whose values point to an object in the old namespace are also copied into the
# new namespace
sbol.setHomespace('http://examples.org')
sbol.Config.setOption(sbol2.ConfigOptions.SBOL_COMPLIANT_URIS, True)
sbol.Config.setOption(sbol2.ConfigOptions.SBOL_TYPED_URIS, False)
doc = sbol.Document()
comp = sbol.ComponentDefinition('cd')
seq = sbol.Sequence('seq')
doc.addComponentDefinition(comp)
doc.addSequence(seq)
comp.sequences = seq.identity
# Import from old homespace into new homespace
old_homespace = sbol.getHomespace()
sbol.setHomespace('http://acme.com')
comp_copy = comp.copy(None, old_homespace)
# Verify new namespace was correctly substituted
self.assertEqual(comp_copy.identity, 'http://acme.com/cd/1')
self.assertEqual(comp_copy.persistentIdentity, 'http://acme.com/cd')
self.assertEqual(comp_copy.sequences[0], 'http://acme.com/seq/1')
# Verify wasDerivedFrom relationship
self.assertEqual(comp_copy.wasDerivedFrom[0], comp.identity)
# Ensure these are equal under the covers
self.assertEqual(type(comp.properties[sbol.SBOL_SEQUENCE_PROPERTY][0]),
rdflib.URIRef)
self.assertEqual(type(comp.properties[sbol.SBOL_SEQUENCE_PROPERTY][0]),
type(comp_copy.properties[sbol.SBOL_SEQUENCE_PROPERTY][0]))
def test_replace_namespace(self):
sbol.setHomespace('http://wallacecorporation.com')
old_namespace = 'http://tyrellcorporation.com'
old_uri = rdflib.URIRef(old_namespace + '/foo')
new_uri = sbol.identified.replace_namespace(old_uri, old_namespace,
sbol.SBOL_COMPONENT_DEFINITION)
self.assertEqual(type(new_uri), rdflib.URIRef)
self.assertEqual(new_uri, rdflib.URIRef(sbol.getHomespace() + '/foo'))
def init_tutorial(self):
# Set the default namespace (e.g. "http://my_namespace.org")
namespace = "http://my_namespace.org"
homespace = sbol2.setHomespace(namespace)
# Test homespace
self.assertIsNone(homespace)
self.assertEqual(sbol2.getHomespace(), namespace)
# Create a new SBOL document
doc = sbol2.Document()
# Test empty document
self.assertIsInstance(doc, sbol2.Document)
self.assertEqual(len(doc), 0)
return doc
# import sbol3
import sbol2
# doc = sbol3.Document()
# colec = sbol3.Collection('FinalProducts', name='FinalProducts')
# doc.add(colec)
# # print(sbol3.get_namespace())
# sbol_objs = doc.objects
# sbol_objs_names = [x.name for x in sbol_objs]
# if 'FinalProducts' not in sbol_objs_names:
# colec = sbol3.Collection('FinalProducts', name='FinalProducts')
# # colec.members.append('test')
# doc.add(colec)
# else:
# colec = sbol_objs[sbol_objs_names.index('FinalProducts')]
# colec.members.append('this')
sbol2.CombinatorialDerivation()
sbol2.ComponentDefinition()
sbol2.getHomespace()
sbol2.URIRef
default=True,
help=
'Default submits DNA parts to SynBioHub staging server. Set to False to submit to SynBioHub production server.'
)
args = arg_parser.parse_args()
path_to_build_request = args.build_request_excel
SBH_USER = args.sbh_username
SBH_PASSWORD = args.sbh_password
spoof_bool = args.spoof
# Load and parse build request
build_excel = pd.ExcelFile(path_to_build_request)
build_request = pd.read_excel(build_excel,
'Design',
index_col=0,
header=None)
ontology_terms = pd.read_excel(build_excel, 'Ontology Terms', index_col=0)
# create parts Document
parts_doc = make_parts_doc(build_request)
# connect to SBH server and set Homespace
sbh_server = sbh_login(SBH_USER, SBH_PASSWORD, spoof_bool, parts_doc)
# parse build request and add parts to parts Document
parse_parts_to_sbh(build_request, ontology_terms, parts_doc)
# submit parts Document to SBH server
sbh_server.submit(parts_doc, sbol.getHomespace(), 1)