def setUp(self):
self.env = Env()
self.v_uri = Uri('http://test.triplepack/#variable')
self.env.assign(self.v_uri, Value(42))
self.template = Template(Name('A'), [Name('x'), Name('y')], [
Property(Name('x'), Value(42)),
Property(Uri('http://example.eg/predicate'), Name('y'))
])
self.expansion = Expansion(Name('e'), Name('A'),
[Value(1), Value(2)], [])
self.template.evaluate(self.env)
def triple_eval(triple):
(s, p, o) = triple
s = s.evaluate(self.env)
p = p.evaluate(self.env)
o = o.evaluate(self.env)
return (s, p, o)
triples = self.expansion.as_triples(self.env)
triples = [triple_eval(triple) for triple in triples]
bindings = self.env._symbol_table
templates = self.env._template_table
self.pack = TriplePack(triples, bindings, templates, [])
def test_expansion_one_arg_with_body(self):
forms = self.parser.parse('e is a a(12345)(x=true)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[Value(12345)],
[Property(Identifier(Name('x')), Value(True))])
self.assertEqual(expect, forms[0])
def test_expansion_one_arg_no_body(self):
forms = self.parser.parse('e is a a(12345)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[Value(12345)],
[])
self.assertEqual(expect, forms[0])
def test_expansion_no_args_no_body(self):
forms = self.parser.parse('e is a a()')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[],
[])
self.assertEqual(expect, forms[0])
def test_triples_get_subjects_2(self):
expansion = Expansion(Identifier(Name('f')), Identifier(Name('A')),
[Value(1), Value(2)], [])
triples = expansion.as_triples(self.env)
triples = [triple_eval(triple, self.env) for triple in triples]
doublePack = TriplePack(self.pack.triples + triples,
self.pack.bindings, self.pack.templates,
self.pack._paths)
self.assertEqual(
doublePack.subjects,
set([
self.expansion.identifier.evaluate(self.env),
expansion.identifier.evaluate(self.env)
]))
def test_expansion_multiple_properties(self):
forms = self.parser.parse('e is a a()(x=true y=false)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[],
[Property(Identifier(Name('x')), Value(True)),
Property(Identifier(Name('y')), Value(False))])
self.assertEqual(expect, forms[0])
def test_expansion_expansion_as_arg(self):
forms = self.parser.parse('e is a a(f is a b(12345))')
f = self.parser.parse('f is a b(12345)')[0]
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[f],
[])
self.assertEqual(expect, forms[0])
def test_empty_template_noargs(self):
script = 'DNASequence()(Other())'
forms = self.parser.parse(script)
expected_template = Template(
Identifier(Name('DNASequence')), [],
[Expansion(None, Identifier(Name('Other')), [], [])])
self.assertCountEqual(forms, [expected_template])
def test_assignment_uri_expansion(self):
script = '<expansion> = e is a t()'
expected = [
Assignment(
Identifier(Uri('expansion')),
Expansion(Identifier(Name('e')), Identifier(Name('t')), [],
[]))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_template_onearg_base(self):
script = 'B(x)(x = 42)\nA(x)(B(x) encoding = <SBOL:IUPACDNA>)'
forms = self.parser.parse(script)
expected_template = Template(Identifier(Name('A')), ['x'], [
Expansion(None, Identifier(Name('B')), [Identifier(Name('x'))],
[]),
Property(Identifier(Name('encoding')),
Identifier(Uri('SBOL:IUPACDNA')))
])
self.assertCountEqual([forms[1]], [expected_template])
class LogicExtensionsTest(unittest.TestCase):
def setUp(self):
self.env = Env()
self.v_uri = Uri('http://test.triplepack/#variable')
self.env.assign(self.v_uri, Value(42))
self.template = Template(Name('A'), [Name('x'), Name('y')], [
Property(Name('x'), Value(42)),
Property(Uri('http://example.eg/predicate'), Name('y'))
])
self.expansion = Expansion(Name('e'), Name('A'),
[Value(1), Value(2)], [])
self.template.evaluate(self.env)
def triple_eval(triple):
(s, p, o) = triple
s = s.evaluate(self.env)
p = p.evaluate(self.env)
o = o.evaluate(self.env)
return (s, p, o)
triples = self.expansion.as_triples(self.env)
triples = [triple_eval(triple) for triple in triples]
bindings = self.env._symbol_table
templates = self.env._template_table
self.pack = TriplePack(triples, bindings, templates, [])
def test_and_true_true(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
conjunction = And(true, true)
triples = list(self.pack.triples)
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_and_true_false(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = And(true, false)
triples = list(self.pack.triples)
with self.assertRaises(ExtensionError):
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_and_false_true(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = And(false, true)
triples = list(self.pack.triples)
with self.assertRaises(ExtensionError):
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_and_false_false(self):
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = And(false, false)
triples = list(self.pack.triples)
with self.assertRaises(ExtensionError):
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_or_true_true(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
conjunction = Or(true, true)
triples = list(self.pack.triples)
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_or_true_false(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = Or(true, false)
triples = list(self.pack.triples)
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_or_false_true(self):
true = AtLeastOne(Uri('http://example.eg/predicate', None))
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = Or(false, true)
triples = list(self.pack.triples)
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_or_false_false(self):
false = AtLeastOne(Uri('http://test.eg/#notthere', None))
conjunction = Or(false, false)
triples = list(self.pack.triples)
with self.assertRaises(ExtensionError):
conjunction.run(self.pack)
self.assertEqual(triples, self.pack.triples)
class CardinalityExtensionsTest(unittest.TestCase):
def setUp(self):
self.env = Env()
self.v_uri = Uri('http://test.triplepack/#variable', None)
self.env.assign(self.v_uri, Value(42, None))
self.template = Template(Name('A'), [Name('x'), Name('y')], [
Property(Name('x'), Value(42)),
Property(Uri('http://example.eg/predicate'), Name('y'))
])
self.expansion = Expansion(Name('e'), Name('A'),
[Value(1), Value(2)], [])
self.template.evaluate(self.env)
def triple_eval(triple):
(s, p, o) = triple
s = s.evaluate(self.env)
p = p.evaluate(self.env)
o = o.evaluate(self.env)
return (s, p, o)
triples = self.expansion.as_triples(self.env)
triples = [triple_eval(triple) for triple in triples]
bindings = self.env._symbol_table
templates = self.env._template_table
self.pack = TriplePack(triples, bindings, templates, [])
def test_at_least_one(self):
triples = list(self.pack.triples)
with self.assertRaises(CardinalityError):
ext = AtLeastOne(Uri('http://test.eg/#notthere'))
ext.run(self.pack)
ext = AtLeastOne(Uri('http://example.eg/predicate'))
ext.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_exactly_one_fails(self):
with self.assertRaises(CardinalityError):
ext = ExactlyOne(Uri('http://test.eg/#notthere'))
ext.run(self.pack)
with self.assertRaises(CardinalityError):
ext = ExactlyOne(Uri('http://example.eg/predicate'))
add = self.pack.search(
(None, Uri('http://example.eg/predicate'), None))[0]
self.pack.add(add)
ext.run(self.pack)
def test_exactly_one_succeeds(self):
triples = list(self.pack.triples)
ext = ExactlyOne(Uri('http://example.eg/predicate'))
ext.run(self.pack)
self.assertEqual(triples, self.pack.triples)
def test_exactly_N_fails(self):
with self.assertRaises(CardinalityError):
ext = ExactlyN(Uri('http://example.eg/predicate'), 2)
ext.run(self.pack)
with self.assertRaises(CardinalityError):
ext = ExactlyN(Uri('http://example.eg/predicate'), 2)
add = self.pack.search(
(None, Uri('http://example.eg/predicate'), None))[0]
self.pack.add(add)
self.pack.add(add)
ext.run(self.pack)
def test_exactly_N_succeeds(self):
with self.assertRaises(CardinalityError):
ext = ExactlyN(Uri('http://example.eg/predicate'), 2)
ext.run(self.pack)
ext = ExactlyN(Uri('http://example.eg/predicate'), 2)
add = self.pack.search(
(None, Uri('http://example.eg/predicate'), None))[0]
self.pack.add(add)
ext.run(self.pack)