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_expansion(self):
"""Test basic expansion of combinatorial derivations"""
doc = sbol3.Document()
doc.read(os.path.join(TESTFILE_DIR, 'simple_library.nt'))
sbol3.set_namespace('http://sbolstandard.org/testfiles')
roots = list(
sbol_utilities.expand_combinatorial_derivations.
root_combinatorial_derivations(doc))
assert len(
roots) == 1, f'Unexpected roots: {[r.identity for r in roots]}'
derivative_collections = sbol_utilities.expand_combinatorial_derivations.expand_derivations(
roots)
assert not len(doc.validate())
assert len(doc.find('Round_1_order_collection').members) == 24
output_doc = sbol3.Document()
for c in derivative_collections:
copy_toplevel_and_dependencies(output_doc, c)
assert not len(output_doc.validate())
temp_name = tempfile.mkstemp(suffix='.nt')[1]
output_doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(
temp_name, os.path.join(TESTFILE_DIR,
'expanded_simple_library.nt'))
def test_round_trip(self):
# Test the int list property, which is not used by the
# core SBOL 3 data model
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
obj = CustomIdentifiedClass()
self.assertEqual([], obj.foo_int)
obj.foo_int.append(7)
obj.foo_int.append(14)
self.assertEqual([7, 14], obj.foo_int)
tl_name = 'my_obj'
tl = CustomTopClass(tl_name)
tl.children.append(obj)
doc = sbol3.Document()
doc.add(tl)
doc2 = sbol3.Document()
# Round trip the document
with tempfile.TemporaryDirectory() as tmpdirname:
test_file = os.path.join(tmpdirname, 'custom.nt')
doc.write(test_file, sbol3.NTRIPLES)
doc2.read(test_file, sbol3.NTRIPLES)
tl2 = doc2.find(tl_name)
obj2 = tl2.children[0]
# The lists are necessarily unordered because of RDF
# Compare specially
self.assertCountEqual([7, 14], obj2.foo_int)
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_annotation(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
# Create custom annotation
annotation_uri = 'http://example.org/boolean_property'
annotation_value = 'foo'
c = sbol3.Component('c1', sbol3.SBO_DNA)
c.annotation = sbol3.TextProperty(c, annotation_uri,
0, 1, [])
c.annotation = annotation_value
self.assertEqual(annotation_value, c.annotation)
doc = sbol3.Document()
doc.add(c)
doc2 = sbol3.Document()
with tempfile.TemporaryDirectory() as tmpdirname:
test_file = os.path.join(tmpdirname, 'annotation.xml')
doc.write(test_file, sbol3.RDF_XML)
# Roundtrip
doc2.read(test_file, sbol3.RDF_XML)
# Recover annotation
c = doc2.find('c1')
c.annotation = sbol3.TextProperty(c, annotation_uri,
0, 1, [])
self.assertEqual(annotation_value, c.annotation)
def test_migrate(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
test_path = os.path.join(SBOL3_LOCATION, 'multicellular',
'multicellular.ttl')
doc = sbol3.Document()
doc.read(test_path)
orig_len = len(doc)
doc2 = sbol3.Document()
doc2.migrate(doc)
self.assertEqual(orig_len, len(doc2))
self.assertEqual(0, len(doc))
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_read_default_namespace(self):
# This is a modified version of the initial bug report for
# https://github.com/SynBioDex/pySBOL3/issues/337
doc = sbol3.Document()
sbol3.set_namespace('http://foo.org')
doc.add(sbol3.Sequence('bar'))
self.assertEqual(0, len(doc.validate()))
file_format = sbol3.SORTED_NTRIPLES
data = doc.write_string(file_format=file_format)
doc2 = sbol3.Document()
doc2.read_string(data, file_format=file_format) # Successful read
sbol3.set_namespace('http://baz.com/')
doc3 = sbol3.Document()
doc3.read_string(data, file_format=file_format)
def test_two_behaviors(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the behavior and constraints
print('Creating Constraints')
a = paml.Primitive("a")
b = paml.Primitive("b")
# Constrain start of b to follow end of a by [10, 15]
follows_constraint = pamlt.precedes(a, [10, 15], b, units=tyto.OM.hour)
doc.add(a)
# doc.add(follows_constraint)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def main(argv=None):
args = parse_args(argv)
init_logging(args.debug)
doc = sbol3.Document()
doc.read(args.inputfile)
my_visitor = MyVisitor()
doc.accept(my_visitor)
def test_doc_diff(self):
# Invoke sbol_utilities.sbol_diff.doc_diff directly
esl_doc = sbol3.Document()
esl_doc.read(ESL_SBOL_PATH)
sl_doc = sbol3.Document()
sl_doc.read(SL_SBOL_PATH)
actual = sbol_utilities.sbol_diff.doc_diff(esl_doc,
esl_doc,
silent=True)
expected = 0
self.assertEqual(expected, actual)
actual = sbol_utilities.sbol_diff.doc_diff(esl_doc,
sl_doc,
silent=True)
expected = 1
self.assertEqual(expected, actual)
def test_sample_set(self):
# Test extending an SBOL class to create a new type with all the
# properties of the SBOL type plus whatever other properties the
# programmer defines. The key to doing this properly is to use
# multiple inheritance to extend both the desired SBOL type and
# CustomTopLevel so that the type is properly serialized to RDF.
doc = sbol3.Document()
ss_uri = 'http://example.org/sbol3/ss1'
template_uri = 'http://example.org/sbol3/template1'
ss = SampleSet(identity=ss_uri, template=template_uri)
doc.add(ss)
doc2 = sbol3.Document()
rdf_format = sbol3.TURTLE
output = doc.write_string(rdf_format)
doc2.read_string(output, rdf_format)
def test_round_trip(self):
# See https://github.com/SynBioDex/pySBOL3/issues/156
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
comp1 = sbol3.Component('comp1', sbol3.SBO_DNA)
cd1 = sbol3.CombinatorialDerivation('cd1', comp1)
self.assertEqual(comp1.identity, cd1.template)
doc1 = sbol3.Document()
doc1.add(comp1)
doc1.add(cd1)
doc2 = sbol3.Document()
doc2.read_string(doc1.write_string(sbol3.SORTED_NTRIPLES),
sbol3.SORTED_NTRIPLES)
comp2 = doc2.find(comp1.identity)
self.assertIsInstance(comp2, sbol3.Component)
cd2 = doc2.find(cd1.identity)
self.assertIsInstance(cd2, sbol3.CombinatorialDerivation)
def test_3to2_conversion(self):
"""Test ability to convert from SBOL3 to SBOL2"""
# Get the SBOL3 test document
tmp_sub = copy_to_tmp(package=['BBa_J23101.nt'])
doc3 = sbol3.Document()
doc3.read(os.path.join(tmp_sub, 'BBa_J23101.nt'))
# Convert to SBOL2 and check contents
doc2 = convert3to2(doc3)
assert len(
doc2.componentDefinitions
) == 1, f'Expected 1 CD, but found {len(doc2.componentDefinitions)}'
# TODO: bring this back after resolution of https://github.com/sboltools/sbolgraph/issues/15
#assert len(doc2.activities) == 1, f'Expected 1 Activity, but found {len(doc2.activities)}'
assert len(
doc2.sequences
) == 1, f'Expected 1 Sequence, but found {len(doc2.sequences)}'
assert doc2.componentDefinitions[
0].identity == 'https://synbiohub.org/public/igem/BBa_J23101'
assert doc2.componentDefinitions[0].sequences[
0] == 'https://synbiohub.org/public/igem/BBa_J23101_sequence'
assert doc2.sequences[
0].encoding == 'http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html'
assert doc2.sequences[
0].elements == 'tttacagctagctcagtcctaggtattatgctagc'
def test_activity_bad_inflows(self):
"""Test whether validator can detect error due to excess or missing inflows"""
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
# Create the protocol
print('Creating protocol')
protocol = paml.Protocol('broken')
doc.add(protocol)
# call order backwards, to make an edge from the final to the initial
protocol.order(protocol.final(), protocol.initial())
# access a parameter node and order it backwards too
p = uml.ActivityParameterNode()
protocol.nodes.append(p)
protocol.order(protocol.final(), p)
# Validate the document, which should produce two errors
print('Validating and writing protocol')
v = doc.validate()
assert len(v) == 3, f'Expected 3 validation issues, but found {len(v)}'
expected = [
'https://bbn.com/scratch/broken/ActivityParameterNode1: Too few values for property parameter. Expected 1, found 0',
'https://bbn.com/scratch/broken/InitialNode1: InitialNode must have no incoming edges, but has 1',
'https://bbn.com/scratch/broken/FlowFinalNode1: Node has no incoming edges, so cannot be executed'
]
observed = [str(e) for e in v]
assert observed == expected, f'Unexpected error content: {observed}'
def test_timed_small_protocol(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the Protocol
print('Creating Protocol')
protocol = paml.Protocol('test_protocol')
# Protocol starts at time zero
start = pamlt.startTime(protocol, 0, units=tyto.OM.hour)
# Protocol lasts 10 - 15 hours
duration = pamlt.duration(protocol, [10, 15], units=tyto.OM.hour)
time_constraints = pamlt.TimeConstraints("small_protocol_constraints",
constraints=pamlt.And(
[start, duration]),
protocols=[protocol])
doc.add(protocol)
doc.add(time_constraints)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
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_expressions(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the Expressions
print('Creating Protocol')
# expression e1: 60s * duration(a1)
a1 = paml.Primitive("a1")
d1 = uml.Duration(observation=uml.DurationObservation(event=[a1]))
m1 = pamlt.TimeMeasure(expr=sbol3.Measure(60, tyto.OM.second))
e1 = uml.Expression(symbol="*", is_ordered=False, operand=[m1, d1])
#doc.add(e1)
# expression lt1: e1 < e2
e2 = pamlt.TimeMeasure(expr=sbol3.Measure(120, tyto.OM.second))
lt1 = uml.Expression(symbol="<", is_ordered=True, operand=[e1, e2])
#doc.add(lt1)
# c1: Not(lt1)
c1 = pamlt.Not(constrained_elements=lt1)
# doc.add(c1)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_single_behavior(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the behavior and constraints
print('Creating Constraints')
a = paml.Primitive("a")
# Constrain start time of a to [0, 10]
start_a = pamlt.startTime(a, [0, 10], units=tyto.OM.hour)
# Constrain end time of a to [10, 15]
end_a = pamlt.endTime(a, [10, 15], units=tyto.OM.hour)
# Constrain duration of a to [1, 5]
duration_a = pamlt.duration(a, [1, 5], units=tyto.OM.hour)
constraint = pamlt.And([start_a, end_a, duration_a])
time_constraints = pamlt.TimeConstraints("small_protocol_constraints",
constraints=[constraint])
doc.add(a)
doc.add(time_constraints)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_ordered_behavior_parameters(self):
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
parameter1 = uml.OrderedPropertyValue(
index=0,
property_value=uml.Parameter(
direction="in",
default_value=uml.LiteralInteger(value=0),
is_unique=True,
is_ordered=True,
lower_value=uml.LiteralInteger(value=0),
upper_value=uml.LiteralInteger(value=10)))
parameter2 = uml.OrderedPropertyValue(
index=1,
property_value=uml.Parameter(
direction="in",
default_value=uml.LiteralInteger(value=0),
is_unique=True,
is_ordered=True,
lower_value=uml.LiteralInteger(value=0),
upper_value=uml.LiteralInteger(value=10)))
behavior = uml.Behavior("b", parameters=[parameter1, parameter2])
assert parameter1 in behavior.parameters and parameter2 in behavior.parameters
doc.add(behavior)
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_guess_format(self):
doc = sbol3.Document()
# Expect ValueError because '.foo' file extension is unknown
with self.assertRaises(ValueError):
doc.read('test.foo')
# Expect ValueError because '.foo' file extension is unknown
with self.assertRaises(ValueError):
doc.write('test.foo')
def test_read(self):
identity = 'https://github.com/synbiodex/pysbol3/experiment1'
nt_data = f'<{identity}> <{rdflib.RDF.type}> <{sbol3.SBOL_EXPERIMENT}> .'
doc = sbol3.Document()
doc.read_string(nt_data, 'ttl')
experiment = doc.find(identity)
self.assertIsNotNone(experiment)
self.assertIsInstance(experiment, sbol3.Collection)
def run_round_trip_file(self, test_path, file_format):
"""Runs a round trip test on the file at the given path.
Path can be relative or absolute.
"""
filename = os.path.basename(test_path)
test2_path = os.path.join(self.temp_out_dir, filename)
# Read the document, then write it back to disk
doc = sbol3.Document()
doc.read(test_path, file_format)
skip_list = self.skip_validation
basename = os.path.basename(test_path)
if os.path.splitext(basename)[0] not in skip_list:
# Validate files that are not in the skip list
report = doc.validate()
if report:
for item in report:
print(item)
self.fail(f'got {len(report)} validation errors')
doc.write(test2_path, file_format)
# Read the newly written document and compare results
doc2 = sbol3.Document()
doc2.read(test2_path, file_format)
# TODO: what about Document.compare()?
# self.assertTrue(doc.compare(doc2))
# Now compare the graphs in RDF
g1 = rdflib.Graph()
g1.parse(test_path, format=file_format)
iso1 = rdflib.compare.to_isomorphic(g1)
g2 = rdflib.Graph()
g2.parse(test2_path, format=file_format)
iso2 = rdflib.compare.to_isomorphic(g2)
rdf_diff = rdflib.compare.graph_diff(iso1, iso2)
if rdf_diff[1] or rdf_diff[2]:
self.logger.warning('Detected %d different RDF triples in %s' %
(len(rdf_diff[1]) + len(rdf_diff[2]), test_path))
if not self.logger.isEnabledFor(logging.DEBUG):
self.logger.warning('Set environment variable %s to see details',
DEBUG_ENV_VAR)
for stmt in rdf_diff[1]:
self.logger.debug('Only in original: %r', stmt)
for stmt in rdf_diff[2]:
self.logger.debug('Only in loaded: %r', stmt)
self.fail('Differences in RDF detected')
def test_find_all2(self):
file = os.path.join(SBOL3_LOCATION, 'multicellular',
'multicellular.nt')
doc = sbol3.Document()
doc.read(file)
# Find all instances of Participation
found = doc.find_all(lambda obj: isinstance(obj, sbol3.Participation))
self.assertEqual(11, len(found))
def test_read_with_default_namespace(self):
# Test reading a file when the default namespace is set
# See https://github.com/SynBioDex/pySBOL3/issues/337
sbol3.set_namespace('http://example.com')
test_path = os.path.join(SBOL3_LOCATION, 'toggle_switch',
'toggle_switch.ttl')
doc = sbol3.Document()
doc.read(test_path)
def test_read(self):
identity = 'https://github.com/synbiodex/pysbol3/collection1'
nt_data = f'<{identity}> <{rdflib.RDF.type}> <{sbol3.SBOL_COLLECTION}> .'
doc = sbol3.Document()
doc.read_string(nt_data, 'ttl')
collection = doc.find(identity)
self.assertIsNotNone(collection)
self.assertIsInstance(collection, sbol3.Collection)
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()
root_copy = root.copy(target_doc=doc2)
self.assertEqual([sc.identity for sc in root.features],
[sc.identity for sc in root_copy.features])
def test_add_multiple(self):
# Ensure that duplicate identities cannot be added to the document.
# See https://github.com/SynBioDex/pySBOL3/issues/39
document = sbol3.Document()
experiment1 = sbol3.Experiment(identity=sbol3.SBOL3_NS)
document.add(experiment1)
experiment2 = sbol3.Experiment(identity=sbol3.SBOL3_NS)
with self.assertRaises(ValueError):
document.add(experiment2)
def test_variable_feature_shacl(self):
# See https://github.com/SynBioDex/sbol-shacl/issues/4
# This file should be valid. Ensure we are handling
# VariableFeature in the SHACL rules
test_file = os.path.join(TEST_RESOURCE_DIR, 'simple_library.nt')
doc = sbol3.Document()
doc.read(test_file)
report = doc.validate()
self.assertEqual(0, len(report))
def test_read_ntriples(self):
# Initial test of Document.read
filename = 'model.nt'
test_path = os.path.join(SBOL3_LOCATION, 'entity', 'model', filename)
doc = sbol3.Document()
doc.read(test_path)
with tempfile.TemporaryDirectory() as tmpdirname:
test_file = os.path.join(tmpdirname, filename)
doc.write(test_file, sbol3.NTRIPLES)
