def test_invalid_create(self):
start = 0
end = 10
r = sbol3.Range(sbol3.PYSBOL3_MISSING, start, end)
report = r.validate()
self.assertIsNotNone(report)
self.assertEqual(1, len(report.errors))
# end must be > 0, and end must be > start
start = 1
end = 0
r = sbol3.Range(sbol3.PYSBOL3_MISSING, start, end)
report = r.validate()
self.assertIsNotNone(report)
self.assertEqual(2, len(report.errors))
# end must be >= start
start = 10
end = 9
r = sbol3.Range(sbol3.PYSBOL3_MISSING, start, end)
report = r.validate()
self.assertIsNotNone(report)
self.assertEqual(1, len(report.errors))
start = 7
end = 7
r = sbol3.Range(sbol3.PYSBOL3_MISSING, start, end)
self.assertEqual(start, r.start)
self.assertEqual(end, r.end)
report = r.validate()
self.assertIsNotNone(report)
self.assertEqual(0, len(report.errors))
def compute_sequence(component: sbol3.Component) -> sbol3.Sequence:
"""Compute the sequence of a component and add this information into the Component in place
:param component: Component whose sequence is to be computed
:return: Sequence that has been computed
"""
sorted, circular = order_subcomponents(component)
# make the blank sequence
sequence = sbol3.Sequence(
component.display_id + "_sequence",
encoding='https://identifiers.org/edam:format_1207'
) # ### BUG: pySBOL #185
sequence.elements = '' # Should be in keywords, except pySBOL3 #208
# for each component in turn, add it and set its location
for i in range(len(sorted)):
subc = sorted[i].instance_of.lookup()
assert len(subc.sequences) == 1
subseq = subc.sequences[0].lookup()
assert sequence.encoding == subseq.encoding
sorted[i].locations.append(
sbol3.Range(sequence,
len(sequence.elements) + 1,
len(sequence.elements) + len(subseq.elements)))
sequence.elements += subseq.elements
# when all have been handled, the sequence is fully realized
component.document.add(sequence)
component.sequences.append(sequence)
return sequence
def test_creation(self):
start = 1
end = 10
r = sbol3.Range(sbol3.PYSBOL3_MISSING, start, end)
self.assertIsNotNone(r)
self.assertEqual(start, r.start)
self.assertEqual(end, r.end)
self.assertEqual(sbol3.SBOL_RANGE, r.type_uri)
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_keyword_args(self):
# Test that all arguments, both required and optional, can be
# specified by keyword
seq_uri = 'https://example.com/pysbol3/seq1'
start = 7
end = 14
range_uri = 'https://example.com/pysbol3/r1'
r1 = sbol3.Range(sequence=seq_uri,
end=end,
start=start,
identity=range_uri)
self.assertEqual(seq_uri, r1.sequence)
self.assertEqual(start, r1.start)
self.assertEqual(end, r1.end)
self.assertEqual(range_uri, r1.identity)
display_id = range_uri[range_uri.rindex('/') + 1:]
self.assertEqual(display_id, r1.display_id)
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_type_constraint(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
c = sbol3.Component('foo', sbol3.SBO_DNA)
with self.assertRaises(TypeError):
c.features = [sbol3.Range('https://example.com/fake', 1, 2)]
self.assertEqual(c.features.type_constraint, sbol3.Feature)