class ParserLiteralTest(unittest.TestCase):
def setUp(self):
self.parser = Parser()
def tearDown(self):
None
def test_parser_literal_boolean(self):
forms = self.parser.parse('true false')
self.assertEqual(forms, [Value(True, None), Value(False, None)])
def test_parser_literal_double(self):
forms = self.parser.parse('0.12345')
self.assertEqual(forms, [Value(0.12345, None)])
def test_parser_literal_integer(self):
forms = self.parser.parse('12345')
self.assertEqual(forms, [Value(12345, None)])
def test_parser_literal_negative_integer(self):
forms = self.parser.parse('-12345')
self.assertEqual(forms, [Value(-12345, None)])
def test_parser_literal_string(self):
script = '"string with whitespace"'
forms = self.parser.parse(script)
self.assertEqual(forms, [Value("string with whitespace", None)])
class TestIdentifierParsing(unittest.TestCase):
def setUp(self):
self.parser = Parser()
def tearDown(self):
None
def test_identifier_single_part(self):
script = 'n'
expected = [Identifier(Name('n'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_two_parts(self):
script = 'p.n'
expected = [Identifier(Name('p'), Name('n'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_three_parts(self):
script = 'p.n.n1'
expected = [Identifier(Name('p'), Name('n'), Name('n1'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_starts_with_uri(self):
script = '<http://prefix/>.n'
expected = [Identifier(Uri('http://prefix/'), Name('n'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_ends_with_uri(self):
script = 'p.<n>'
expected = [Identifier(Name('p'), Uri('n'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_uri_in_middle(self):
script = 'p.<n>.n1'
expected = [Identifier(Name('p'), Uri('n'), Name('n1'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_uri_only(self):
script = '<http://name.eg/#test>'
expected = [Identifier(Uri('http://name.eg/#test'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_identifier_self_as_prefix(self):
script = 'self.n'
expected = [Identifier(Self(), Name('n'))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_name_self_as_suffix(self):
script = 'p.self'
expected = [Identifier(Name('p'), Self())]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
class TestPropertyClass(unittest.TestCase):
def setUp(self):
self.env = Env()
self.parser = Parser()
def tearDown(self):
None
def test_as_triples_simple(self):
p = Property(Identifier(Name('x')), Identifier(Name('y')))
expected = [(Identifier(Self()), Identifier(Name('x')),
Identifier(Name('y')))]
actually = p.as_triples(self.env)
self.assertEqual(expected, actually)
def test_as_triples_expansion(self):
forms = self.parser.parse('t()(x=1) e is a t()')
t = forms[0]
e = forms[1]
p = Property(Identifier(Name('y')), e)
t.evaluate(self.env)
expected = [(Identifier(Name('e')),
Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')),
Identifier(Name('e')))]
actually = p.as_triples(self.env)
self.assertEqual(expected, actually)
def test_as_triples_self_in_name(self):
p = Property(Identifier(Self()), Value(1))
expected = [(Identifier(Self()), Identifier(Self()), Value(1))]
actually = p.as_triples(self.env)
self.assertEqual(expected, actually)
def produce_tables(version="sbol_2", lib_paths=None):
'''
Method that is independant from the rdf/xml production, simply runs the parsing and evaluation
process on the templates to produce the symbols and template tables.
This process is just the parse_from file method and returns the tables.
'''
if lib_paths is None:
optpaths = [os.path.join(os.getcwd(), "templates")]
else:
optpaths = [lib_paths]
to_run_fn = os.path.join(optpaths[0], "temp.shb")
f = open(to_run_fn, "a")
f.write("use <" + version + ">")
f.close()
parser = Parser(filename=to_run_fn, debug_lvl=1)
with open(to_run_fn, 'r') as in_file:
data = in_file.read()
env = Env(filename=to_run_fn,
serializer="sbolxml",
paths=optpaths,
version=version)
forms = parser.parse(data)
forms = pre_process(forms, version)
env.interpret(forms)
prefixes = [prefix for prefix in env._rdf._g.namespaces()]
os.remove(to_run_fn)
return env._symbol_table, env._template_table, prefixes
class ParserPragmaTest(unittest.TestCase):
def setUp(self):
self.parser = Parser()
def tearDown(self):
None
def test_prefix_pragma_uri(self):
script = "@prefix Prefix = <http://example.eg/>"
expected = [
PrefixPragma('Prefix', Identifier(Uri('http://example.eg/')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_prefix_pragma_name(self):
script = "@prefix Prefix = name"
expected = [PrefixPragma('Prefix', Identifier(Name('name')))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_default_prefix_pragma(self):
script = "@prefix Prefix"
expected = [DefaultPrefixPragma('Prefix')]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_import_pragma_uri(self):
script = "@use <import>"
expected = [ImportPragma(Identifier(Uri('import')))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
script = "use <import>"
expected = [ImportPragma(Identifier(Uri('import')))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_import_pragma_name(self):
script = "@use this.target"
expected = [ImportPragma(Identifier(Name('this'), Name('target')))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
script = "use this.target"
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_extension_pragma(self):
expected = [ExtensionPragma('E', [])]
actually = self.parser.parse('@extension E()')
self.assertEqual(expected, actually)
class ParserAssignmentTest(unittest.TestCase):
def setUp(self):
self.parser = Parser()
self.maxDiff = None
self.logger = logging.getLogger(__name__)
def tearDown(self):
None
def test_assignment_name_string(self):
script = 'Name = "hello"'
expected = [Assignment(Identifier(Name('Name')), Value("hello"))]
actually = self.parser.parse(script)
self.assertCountEqual(expected, actually)
def test_assignment_name_integer(self):
script = 'Name = 12345'
expected = [Assignment(Identifier(Name('Name')), Value(12345))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_name_boolean(self):
script = 'Name = true'
expected = [Assignment(Identifier(Name('Name')), Value(True))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
script = 'Name = false'
expected = [Assignment(Identifier(Name('Name')), Value(False))]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_name_double(self):
script = 'Name = 0.12345'
actually = self.parser.parse(script)
expected = [Assignment(Identifier(Name('Name')), Value(0.12345))]
self.assertEqual(expected, actually)
def test_assignment_name_uri(self):
script = 'Name = <http://uri.org/>'
expected = [
Assignment(Identifier(Name('Name')),
Identifier(Uri('http://uri.org/')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_name_name(self):
script = 'Name = Name'
expected = [
Assignment(Identifier(Name('Name')), Identifier(Name('Name')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_string(self):
script = '<http://uri.org/> = "hello"'
expected = [
Assignment(Identifier(Uri('http://uri.org/')), Value("hello"))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_integer(self):
script = '<http://uri.org/> = 12345'
expected = [
Assignment(Identifier(Uri('http://uri.org/')), Value(12345))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_boolean(self):
script = '<http://uri.org/> = true'
expected = [
Assignment(Identifier(Uri('http://uri.org/')), Value(True))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
script = '<http://uri.org/> = false'
expected = [
Assignment(Identifier(Uri('http://uri.org/')), Value(False))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_double(self):
script = '<http://uri.org/> = 0.12345'
expected = [
Assignment(Identifier(Uri('http://uri.org/')), Value(0.12345))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_uri(self):
script = '<http://uri.org/> = <http://value.org>'
expected = [
Assignment(Identifier(Uri('http://uri.org/')),
Identifier(Uri('http://value.org')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_uri_name(self):
script = '<http://uri.org/> = Name'
expected = [
Assignment(Identifier(Uri('http://uri.org/')),
Identifier(Name('Name')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_self_name(self):
script = 'self.v = Name'
expected = [
Assignment(Identifier(Self(), Name('v')), Identifier(Name('Name')))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
def test_assignment_name_expansion(self):
script = 'expansion = e is a t()'
expected = [
Assignment(
Identifier(Name('expansion')),
Expansion(Identifier(Name('e')), Identifier(Name('t')), [],
[]))
]
actually = self.parser.parse(script)
self.assertEqual(expected, actually)
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)
class ParserExpansionTest(unittest.TestCase):
def setUp(self):
self.parser = Parser()
self.maxDiff = None
def tearDown(self):
None
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_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_multi_args_no_body(self):
forms = self.parser.parse('e is a a(12345, 54321)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[Value(12345),
Value(54321)],
[])
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_expansion_no_args_with_body(self):
forms = self.parser.parse('e is a a()(x=true)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[],
[Property(Identifier(Name('x')), Value(True))])
self.assertEqual(expect, forms[0])
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_multi_args_with_body(self):
forms = self.parser.parse('e is a a(12345, 54321)(x=true)')
expect = Expansion(Identifier(Name('e')),
Identifier(Name('a')),
[Value(12345),
Value(54321)],
[Property(Identifier(Name('x')), Value(True))])
self.assertEqual(expect, forms[0])
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])
class EnvTest(unittest.TestCase):
def setUp(self):
self.env = Env()
self.parser = Parser()
def tearDown(self):
None
def test_prefix_binding(self):
prefix_uri = Uri('http://test.prefix.eg/')
prefix = 'prefix'
self.env.bind_prefix(prefix, prefix_uri)
self.assertTrue('prefix' in [p for (p, n) in self.env._rdf._g.namespaces()])
def test_get_and_set_default_prefix(self):
prefix = 'x'
self.env.bind_prefix(prefix, Uri('http://eg/'))
before = Uri(self.env._rdf._g.identifier.toPython())
self.assertEqual(before, self.env.uri)
self.assertEqual(self.env.prefix, None)
self.env.prefix = prefix
self.env.uri = Uri('http://eg/')
self.assertEqual(Uri('http://eg/'), self.env.uri)
self.assertEqual('x', self.env.prefix)
def test_self_uri_set(self):
uri = Uri('setselfuri')
self.env.self_uri = uri
self.assertEqual(self.env.self_uri, uri)
def test_assignment(self):
uri = Uri('http://test.variable/#x')
value = Value(12345)
self.env.assign(uri, value)
self.assertEqual(self.env._symbol_table.get(uri), value)
def test_lookup(self):
uri = Uri('http://test.variable/#x')
value = Value(12345)
self.env.assign(uri, value)
self.assertEqual(self.env.lookup(uri), value)
def test_template_binding(self):
template = self.parser.parse('t()(x = 1 y = 2)')[0]
uri = template.identifier.evaluate(self.env)
with self.assertRaises(KeyError):
self.env.lookup_template(uri)
self.env.assign_template(uri, template.as_triples(self.env))
self.assertEqual(self.env._template_table.get(uri, False),
template.as_triples(self.env))
def test_template_lookup(self):
template = self.parser.parse('t()(x = 1 y = 2)')[0]
uri = template.identifier.evaluate(self.env)
with self.assertRaises(KeyError):
self.env.lookup_template(uri)
self.env._template_table[uri] = template.as_triples(self.env)
self.assertEqual(self.env.lookup_template(uri),
template.as_triples(self.env))
def test_extension_binding(self):
t = self.parser.parse('t()(@extension E() @extension F())')[0]
uri = t.identifier.evaluate(self.env)
extensions = t.extensions
self.assertFalse(self.env.lookup_extensions(uri))
self.env.assign_extensions(uri, extensions)
self.assertEqual(extensions, self.env._extension_table.get(uri, None))
def test_extension_lookup(self):
t = self.parser.parse('t()(@extension E() @extension F())')[0]
uri = t.identifier.evaluate(self.env)
extensions = t.extensions
self.assertFalse(self.env.lookup_extensions(uri))
self.env._extension_table[uri] = extensions
self.assertEqual(extensions, self.env.lookup_extensions(uri))
class TemplateClassTest(unittest.TestCase):
def setUp(self):
self.env = Env()
self.parser = Parser()
self.maxDiff = None
def tearDown(self):
None
def test_init(self):
'''
Simplest check, does Templates Identifier get added to parts list.
'''
template = Template(Identifier(Name('x')), [], [])
self.assertEqual(template.identifier.parts[0], Name('x'))
def test_as_triples_empty(self):
'''
Tests if triples list is empty when no parser call.
'''
template = Template(Identifier(Name('x')), [], [])
self.assertCountEqual(template.as_triples(self.env), [])
def test_as_triples_simple_triple(self):
'''
Tests if triples list is not empty when parser call.
'''
template = self.parser.parse('t()(x = z)')[0]
expect = [(Identifier(Self()), Identifier(Name('x')), Identifier(Name('z')))]
self.assertCountEqual(template.as_triples(self.env), expect)
def test_as_triples_simple_triple_with_self(self):
'''
Tests if triples list is not empty when parser call with self.
'''
template = self.parser.parse('t()(x = self)')[0]
expect = [(Identifier(Self()), Identifier(Name('x')), Identifier(Self()))]
self.assertCountEqual(template.as_triples(self.env), expect)
def test_as_triples_multiple_properties(self):
'''
Tests if triples list is not empty when parser call with multiple properties.
'''
template = self.parser.parse('t()(x = y z = 12345)')[0]
expect = [(Identifier(Self()), Identifier(Name('x')), Identifier(Name('y'))),
(Identifier(Self()), Identifier(Name('z')), Value(12345))]
self.assertCountEqual(template.as_triples(self.env), expect)
def test_as_triples_with_base(self):
'''
Test for correctness when a base and specialised template are defined
'''
forms = self.parser.parse('a()(x = 1) b()(a() y = 2)')
base = forms[0]
specialised = forms[1]
base.evaluate(self.env)
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')), Value(2))]
self.assertCountEqual(specialised.as_triples(self.env), expect)
def test_as_triples_with_base_chain(self):
'''
Test for correctness when a base and multiple/chained specialised templates are defined
# Calls Expansion() ??
'''
forms = self.parser.parse('a()(x = 1)' +
'b()(a() y = 2)' +
'c()(b() z = 3)')
a = forms[0]
b = forms[1]
c = forms[2]
a.evaluate(self.env)
b.evaluate(self.env)
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')), Value(3))]
self.assertCountEqual(c.as_triples(self.env), expect)
def test_as_triples_with_base_with_self(self):
'''
Test for correctness when a base and specialised templates are defined
and base has self as property.
'''
forms = self.parser.parse('a()(x = self) b()(a() y = 2)')
base = forms[0]
specialised = forms[1]
base.evaluate(self.env)
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Identifier(Self())),
(Identifier(Self()), Identifier(Name('y')), Value(2))]
self.assertCountEqual(specialised.as_triples(self.env), expect)
def test_as_triples_params(self):
'''
Test for correctness when a template is defined with param and set to property
'''
forms = self.parser.parse('a(x)(property = x)')
a = forms[0]
expect = [(Identifier(Self()), Identifier(Name('property')), Identifier(Parameter('x',0)))]
for index,triple in enumerate(a.as_triples(self.env)):
for tuple_index,element in enumerate(triple):
self.assertEqual(element,expect[index][tuple_index])
self.assertCountEqual(a.as_triples(self.env), expect)
def test_as_triples_with_base_with_params(self):
'''
Test for correctness when a template is defined and property is set to value.
'''
forms = self.parser.parse('a(x)(x = 12345) b(y)(a(y))')
a = forms[0]
b = forms[1]
template_name = a.identifier.evaluate(self.env)
self.env.assign_template(template_name, a.as_triples(self.env))
expect = [(Identifier(Self()), Identifier(Parameter('y', 0)), Value(12345))]
self.assertCountEqual(expect, b.as_triples(self.env))
def test_as_triples_with_base_with_args(self):
'''
Test for correctness when a template is defined and property is set to value.
And specialised template contains arg
'''
forms = self.parser.parse('a(x)(x = 12345) b()(a(12345))')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
expect = [(Identifier(Self()), Value(12345), Value(12345))]
self.assertCountEqual(expect, b.as_triples(self.env))
def test_as_triples_multiple_base_args_and_parameters(self):
forms = self.parser.parse('a(x, y)(x = y)' +
'b(x, y)(a(x, "string") z=y)' +
'c(x, y)(b(1, 2) x=y)')
a = forms[0]
b = forms[1]
c = forms[2]
a.evaluate(self.env)
b.evaluate(self.env)
expect = [(Identifier(Self()), Value(1), Value("string")),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Parameter('x', 0)), Identifier(Parameter('y', 0)))]
self.assertCountEqual(expect, c.as_triples(self.env))
@unittest.skip("There is no longer a current_self")
def test_current_self_preserved(self):
forms = self.parser.parse('a(x, y, z)(self=self)')
a = forms[0]
previous_self = self.env.uri
a.as_triples(self.env)
new_self = self.env.current_self
self.assertEqual(previous_self, new_self)
def test_as_triples_with_expansion_in_property(self):
forms = self.parser.parse('a()(x = 1) b()(y = e is a a())')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
expect = [(Identifier(Name('e')), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')), Identifier(Name('e')))]
self.assertCountEqual(expect, b.as_triples(self.env))
def test_as_triples_with_expansion_in_property_with_self(self):
forms = self.parser.parse('a()(x = 1) b()(self.y = e is a a())')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
expect = [(Identifier(Name('e')), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Self(), Name('y')), Identifier(Name('e')))]
self.assertCountEqual(expect, b.as_triples(self.env))
def test_as_triples_with_expansion_in_property_with_self_as_name(self):
forms = self.parser.parse('a()(x = 1) b()(y = self.e is a a())')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
expect = [(Identifier(Self(), Name('e')), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')), Identifier(Self(), Name('e')))]
self.assertCountEqual(expect, b.as_triples(self.env))
def test_as_triples_with_base_with_self_named_expansion(self):
forms = self.parser.parse('s()(z=self) t()(x=self.e is a s())')
s = forms[0]
t = forms[1]
s.evaluate(self.env)
e = Identifier(Self(), Name('e'))
expect_s = [(Identifier(Self()), Identifier(Name('z')), Identifier(Self()))]
self.assertCountEqual(expect_s, s.as_triples(self.env))
expect_t = [(e, Identifier(Name('z')).evaluate(self.env), e),
(Identifier(Self()), Identifier(Name('x')), e)]
self.assertCountEqual(expect_t, t.as_triples(self.env))
def test_as_triples_with_expansion_as_argument(self):
forms = self.parser.parse('r()(y=1) s(exp)(x=exp)' +
't()(s(e is a r()))')
r = forms[0]
s = forms[1]
t = forms[2]
r.evaluate(self.env)
s.evaluate(self.env)
e = self.parser.parse('e is a r()')[0]
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), e)]
self.assertCountEqual(expect, t.as_triples(self.env))
def test_evaluate_stores_triples(self):
forms = self.parser.parse('t()(x=1 y=2)')
t = forms[0]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_of_base(self):
forms = self.parser.parse('s()(z=3)t()(x=1 y=2 s())')
s = forms[0]
t = forms[1]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value(3))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_of_bases(self):
forms = self.parser.parse('q()(a=4) s()(z=3)t()(x=1 y=2 s() q())')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value(3)),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), Value(4))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_of_chained_bases(self):
forms = self.parser.parse('q()(a=4) s()(z=3 q())t()(x=1 y=2 s())')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value(3)),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), Value(4))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_parameterised_bases(self):
forms = self.parser.parse('q(p)(a=p)' +
's(t)(z=t q("s"))' +
't()(x=1 y=2 s("t"))')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value("t")),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), Value("s"))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_forward_parameterised_bases(self):
forms = self.parser.parse('q(p)(a=p)' +
's(t)(z=t q(t))' +
't()(x=1 y=2 s("t"))')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), Value("t")),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), Value("t"))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_unevaluated_parameter(self):
forms = self.parser.parse('q(p)(a=p)' +
's(t)(z=t q(t))' +
't(t)(x=1 y=2 s(t))')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
param = Identifier(Parameter('t', 0))
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), param),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), param)]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_unevaluated_parameters(self):
forms = self.parser.parse('q(p)(a=p)' +
's(u,v)(z=u q(v))' +
't(a,b)(x=1 y=2 s(a,b))')
q = forms[0]
s = forms[1]
t = forms[2]
with self.assertRaises(KeyError):
self.env.lookup_template(t.identifier.evaluate(self.env))
q.evaluate(self.env)
s.evaluate(self.env)
t.evaluate(self.env)
a = Identifier(Parameter('a', 0))
b = Identifier(Parameter('b', 1))
found = self.env.lookup_template(t.identifier.evaluate(self.env))
expect = [(Identifier(Self()), Identifier(Name('x')).evaluate(self.env), Value(1)),
(Identifier(Self()), Identifier(Name('y')).evaluate(self.env), Value(2)),
(Identifier(Self()), Identifier(Name('z')).evaluate(self.env), a),
(Identifier(Self()), Identifier(Name('a')).evaluate(self.env), b)]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_expansion_as_property(self):
forms = self.parser.parse('a(x)(p=x)' +
'b()(q = e is a a(2))')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
b.evaluate(self.env)
env = self.env
me = Identifier(Self())
found = env.lookup_template(b.identifier.evaluate(env))
expect = [(Identifier(Name('e')).evaluate(env), Identifier(Name('p')).evaluate(env), Value(2)),
(me, Identifier(Name('q')).evaluate(env), Identifier(Name('e')).evaluate(env))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_expansion_in_body(self):
forms = self.parser.parse('a(x)(p=x)' +
'b()(e is a a(2))')
a = forms[0]
b = forms[1]
a.evaluate(self.env)
b.evaluate(self.env)
env = self.env
found = env.lookup_template(b.identifier.evaluate(env))
expect = [(Identifier(Name('e')).evaluate(env), Identifier(Name('p')).evaluate(env), Value(2))]
self.assertCountEqual(found, expect)
def test_evaluate_stores_triples_with_expansion_in_argument(self):
forms = self.parser.parse('a(x)(p=x)' +
'b(x)(e=x)' +
'c()(b(f is a a(2)))')
a = forms[0]
b = forms[1]
c = forms[2]
a.evaluate(self.env)
b.evaluate(self.env)
c.evaluate(self.env)
env = self.env
me = Identifier(Self())
found = env.lookup_template(c.identifier.evaluate(env))
expect = [(me, Identifier(Name('e')).evaluate(env), Identifier(Name('f')).evaluate(env))]
self.assertCountEqual(found, expect)
expect = [(Identifier(Name('f')).evaluate(env), Identifier(Name('p')).evaluate(env), Value(2))]
self.assertCountEqual(self.env._rdf.triples, expect)
def test_evaluate_stores_triples_with_expansions(self):
forms = self.parser.parse('a(x)(e=x)' +
'b(y)(p=y)' +
'c()(a(f is a b(1))' +
' q = g is a b(2)' +
' h is a b(3))')
a = forms[0]
b = forms[1]
c = forms[2]
a.evaluate(self.env)
b.evaluate(self.env)
c.evaluate(self.env)
me = Identifier(Self())
env = self.env
f = Identifier(Name('f')).evaluate(env)
g = Identifier(Name('g')).evaluate(env)
h = Identifier(Name('h')).evaluate(env)
found = env.lookup_template(c.identifier.evaluate(env))
expect = [(me, Identifier(Name('e')).evaluate(env), f),
(g, Identifier(Name('p')).evaluate(env), Value(2)),
(me, Identifier(Name('q')).evaluate(env), g),
(h, Identifier(Name('p')).evaluate(env), Value(3))]
self.assertCountEqual(found, expect)
expect = [(f, Identifier(Name('p')).evaluate(env), Value(1))]
self.assertCountEqual(self.env._rdf.triples, expect)
def test_init_extensions(self):
forms = self.parser.parse('t()(@extension E() @extension F())')
t = forms[0]
expect = [ExtensionPragma('E', []), ExtensionPragma('F', [])]
self.assertCountEqual(t.collect_extensions(self.env), expect)
def test_evaluate_stores_extensions(self):
forms = self.parser.parse('t()(@extension E() @extension F())')
t = forms[0]
t.evaluate(self.env)
found = self.env.lookup_extensions(t.identifier.evaluate(self.env))
self.assertCountEqual(found, [ExtensionPragma(
'E', []), ExtensionPragma('F', [])])
def test_evaluate_stores_base_extensions(self):
forms = self.parser.parse(
's()(@extension F()) t()(s() @extension E())')
s = forms[0]
t = forms[1]
s.evaluate(self.env)
t.evaluate(self.env)
found = self.env.lookup_extensions(t.identifier.evaluate(self.env))
expect = [ExtensionPragma('F', []), ExtensionPragma('E', [])]
self.assertCountEqual(found, expect)
def test_evaluate_extension_arguments(self):
forms = self.parser.parse('t()(@extension E(12345))')
t = forms[0]
t.evaluate(self.env)
found = self.env.lookup_extensions(t.identifier.evaluate(self.env))
self.assertCountEqual(found, [ExtensionPragma('E', [Value(12345)])])
def test_evaluate_extension_arguments_name(self):
forms = self.parser.parse('t()(@extension E(argument))')
t = forms[0]
t.evaluate(self.env)
found = self.env.lookup_extensions(t.identifier.evaluate(self.env))
expect = [ExtensionPragma('E', [Identifier(Name('argument')).evaluate(self.env)])]
self.assertCountEqual(found, expect)
def test_evaluate_extension_self_name(self):
forms = self.parser.parse('t()(@extension E(self.argument))')
t = forms[0]
self.env.current_self = Name(Self())
t.evaluate(self.env)
found = self.env.lookup_extensions(t.identifier.evaluate(self.env))
expect = [ExtensionPragma('E', [Identifier(Self(), Name('argument'))])]
self.assertCountEqual(found, expect)
def test_evaluate_to_template_name(self):
forms = self.parser.parse('t()(x=1 y=2)')
t = forms[0]
self.assertEqual(t.identifier.evaluate(self.env), t.evaluate(self.env))
def test_extension_parameters(self):
forms = self.parser.parse('t(a)(@extension AtLeastOne(a))')
t = forms[0]
t.evaluate(self.env)
atleastone = self.env.lookup_extensions(t.identifier.evaluate(self.env))[0]
arg = Identifier(t.parameters[1])
self.assertEqual(arg, atleastone.args[0])
def test_extension_parameters_multiple(self):
forms = self.parser.parse('t(a, b)(@extension AtLeastOne(a, b))')
t = forms[0]
t.evaluate(self.env)
atleastone = self.env.lookup_extensions(t.identifier.evaluate(self.env))[0]
args = [Identifier(p) for p in t.parameters[1:]]
self.assertCountEqual(args, atleastone.args)
def test_bodied_expansion_in_template(self):
forms = self.parser.parse('s()(a = 1)' +
't()(self.e is a s()(b = 2))')
s = forms[0]
t = forms[1]
s.evaluate(self.env)
expect = [(Identifier(Self(), Name('e')),
Identifier(Name('a')).evaluate(self.env),
Value(1)),
(Identifier(Self(), Name('e')),
Identifier(Name('b')),
Value(2))]
self.assertCountEqual(expect, t.as_triples(self.env))
def test_bodied_expansion_in_template_property(self):
forms = self.parser.parse('s()(a = 1)' +
't()(x = self.e is a s()(b = 2))')
s = forms[0]
t = forms[1]
s.evaluate(self.env)
expect = [(Identifier(Self(), Name('e')),
Identifier(Name('a')).evaluate(self.env),
Value(1)),
(Identifier(Self(), Name('e')),
Identifier(Name('b')),
Value(2)),
(Identifier(Self()),
Identifier(Name('x')),
Identifier(Self(), Name('e')))]
self.assertCountEqual(expect, t.as_triples(self.env))
def test_as_triples_multiple_inheritance(self):
forms = self.parser.parse('s()(a=123)' +
't()(b=456)' +
'u()(s() t())')
s = forms[0]
t = forms[1]
u = forms[2]
s.evaluate(self.env)
t.evaluate(self.env)
expect = [(Identifier(Self()),
Identifier(Name('a')).evaluate(self.env),
Value(123)),
(Identifier(Self()),
Identifier(Name('b')).evaluate(self.env),
Value(456))]
self.assertEqual(expect, u.as_triples(self.env))
def test_as_triples_nested_multiple_inheritance(self):
forms = self.parser.parse('s()(a=123)' +
't()(s() b=456)' +
'u()(s() t() c=789)' +
'v()(s() t() u())')
s = forms[0]
t = forms[1]
u = forms[2]
v = forms[3]
s.evaluate(self.env)
t.evaluate(self.env)
u.evaluate(self.env)
a = (Identifier(Self()), Identifier(Name('a')).evaluate(self.env), Value(123))
b = (Identifier(Self()), Identifier(Name('b')).evaluate(self.env), Value(456))
c = (Identifier(Self()), Identifier(Name('c')).evaluate(self.env), Value(789))
expect = [a, a, b, a, a, b, c]
self.assertEqual(expect, v.as_triples(self.env))
def parse_from_file(filepath,
serializer='sbolxml',
optpaths=[],
out=None,
extensions=[],
debug_lvl=1,
version="sbol_2",
no_validation=None):
if version == "sbol_3" and serializer == "sbolxml":
serializer = "rdfxml"
if len(optpaths) == 0:
optpaths.append("templates")
parser = Parser(filename=filepath, debug_lvl=debug_lvl)
with open(filepath, 'r', encoding="utf8") as in_file:
data = in_file.read()
env = Env(filename=filepath,
serializer=serializer,
paths=optpaths,
extensions=extensions,
version=version)
forms = parser.parse(data)
forms = pre_process(forms, version)
env.interpret(forms)
sbol = str(env)
ret_code = ""
if not no_validation:
if version == "sbol_3":
ret_code = "No Validation Currently for SBOL3"
print(ret_code)
errors = []
else:
errors = []
response = validate_sbol(sbol)
try:
if response['valid']:
print('SBOL validator success.')
ret_code = "SBOL validator success."
else:
print("SBOL validator failure.")
for e in response['errors']:
print(e)
errors = response['errors']
ret_code = "SBOL validator failure."
except TypeError:
errors = ["Unable to Validate output."]
else:
ret_code = "No Validation."
errors = ["No Validation."]
if out is None:
print(sbol)
else:
with open(out, 'w') as o:
o.write(sbol)
return {ret_code: errors}
class TriplePackTest(unittest.TestCase):
def setUp(self):
self.env = Env()
self.parser = Parser()
self.vuri = self.parser.parse(
'<http://test.triplepack/#variable>')[0].parts[0]
self.env.assign(self.vuri, Value(42))
self.template = self.parser.parse(
('A(x, y)(x = 42 '
'<http://example.eg/predicate> = y)'))[0]
self.expansion = self.parser.parse('e is a A(1, 2)')[0]
self.template.evaluate(self.env)
triples = self.expansion.as_triples(self.env)
triples = [triple_eval(triple, self.env) for triple in triples]
bindings = self.env._symbol_table
templates = self.env._template_table
self.pack = TriplePack(triples, bindings, templates, self.env._paths)
def test_triples_init(self):
exp_uri = Identifier(Name('e')).evaluate(self.env)
triples = [(exp_uri, Value(1), Value(42)),
(exp_uri, Uri('http://example.eg/predicate'), Value(2))]
self.assertCountEqual(self.pack.triples, triples)
self.assertCountEqual(self.pack.bindings, self.env._symbol_table)
self.assertCountEqual(self.pack.templates, self.env._template_table)
def test_triples_lookup(self):
self.assertEqual(self.pack.lookup(self.vuri), Value(42))
self.assertEqual(self.pack.lookup(Uri('http://triplepack.org/#not')),
None)
def test_triples_lookup_template(self):
self.assertCountEqual(
self.pack.lookup_template(
self.template.identifier.evaluate(self.env)),
self.template.as_triples(self.env))
self.assertCountEqual(
self.pack.lookup_template(Uri('http://triplepack.org/#not')), None)
def test_triples_get_subjects_1(self):
self.assertEqual(self.pack.subjects,
set([self.expansion.identifier.evaluate(self.env)]))
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_triples_get_subjects_empty(self):
emptyPack = TriplePack([], {}, {}, [])
self.assertEqual(emptyPack.subjects, set())
def test_triples_get_predicates(self):
self.assertEqual(self.pack.predicates,
set([Value(1),
Uri('http://example.eg/predicate')]))
def test_triples_get_predicates_empty(self):
emptyPack = TriplePack([], {}, {}, [])
self.assertEqual(emptyPack.predicates, set())
def test_triples_get_objects(self):
self.assertEqual(self.pack.objects, set([Value(2), Value(42)]))
def test_triples_get_objects_empty(self):
emptyPack = TriplePack([], {}, {}, [])
self.assertEqual(emptyPack.objects, set())
def test_triples_get_triples_by_subject(self):
expected_result = [(Identifier(Name('e')).evaluate(self.env), Value(1),
Value(42)),
(Identifier(Name('e')).evaluate(self.env),
Uri('http://example.eg/predicate'), Value(2))]
self.assertEqual(
self.pack.search(
(Identifier(Name('e')).evaluate(self.env), None, None)),
expected_result)
self.assertEqual(
self.pack.search(
(Identifier(Name('f')).evaluate(self.env), None, None)), [])
def test_triples_get_triples_by_predicate(self):
self.assertEqual(
self.pack.search((None, Value(1), None)),
[(Identifier(Name('e')).evaluate(self.env), Value(1), Value(42))])
self.assertEqual(
self.pack.search((None, Uri('http://example.eg/predicate'), None)),
[(Identifier(Name('e')).evaluate(
self.env), Uri('http://example.eg/predicate'), Value(2))])
self.assertEqual(self.pack.search((None, Value(3), None)), [])
def test_triples_get_triples_by_object(self):
self.assertEqual(
self.pack.search((None, None, Value(42))),
[(Identifier(Name('e')).evaluate(self.env), Value(1), Value(42))])
self.assertEqual(self.pack.search(
(None, None, Value(2))), [(Identifier(Name('e')).evaluate(
self.env), Uri('http://example.eg/predicate'), Value(2))])
self.assertEqual(self.pack.search((None, None, Value(3))), [])
def test_triples_get_triples_exact(self):
self.assertEqual(
self.pack.search((Identifier(Name('e')).evaluate(self.env),
Value(1), Value(42))),
[(Identifier(Name('e')).evaluate(self.env), Value(1), Value(42))])
self.assertEqual(
self.pack.search((Value(1), Value(2, None), Value(3, None))), [])
def test_triples_get_triples_subject_predicate(self):
self.assertEqual(
self.pack.search(
(Identifier(Name('e')).evaluate(self.env), Value(1,
None), None)),
[(Identifier(Name('e')).evaluate(self.env), Value(
1, None), Value(42, None))])
self.assertEqual(
self.pack.search((Identifier(Name('f')).evaluate(self.env),
Value(1, None), None)), [])
self.assertEqual(
self.pack.search((Identifier(Name('e')).evaluate(self.env),
Value(2, None), None)), [])
def test_triples_get_triples_subject_object(self):
self.assertEqual(
self.pack.search((Identifier(Name('e')).evaluate(self.env), None,
Value(42, None))),
[(Identifier(Name('e')).evaluate(self.env), Value(
1, None), Value(42, None))])
self.assertEqual(
self.pack.search((Identifier(Name('f')).evaluate(self.env), None,
Value(42, None))), [])
self.assertEqual(
self.pack.search((Identifier(Name('e')).evaluate(self.env), None,
Value(41, None))), [])
def test_triples_get_triples_predicate_object(self):
self.assertEqual(
self.pack.search((None, Value(1, None), Value(42, None))),
[(Identifier(Name('e')).evaluate(self.env), Value(
1, None), Value(42, None))])
self.assertEqual(
self.pack.search((None, Value(2, None), Value(42, None))), [])
self.assertEqual(
self.pack.search((None, Value(1, None), Value(41, None))), [])
def test_triples_subject_has_property(self):
self.assertTrue(
self.pack.has(
Identifier(Name('e')).evaluate(self.env), Value(1, None)))
self.assertFalse(
self.pack.has(
Identifier(Name('e')).evaluate(self.env), Value(2, None)))
self.assertFalse(
self.pack.has(
Identifier(Name('f')).evaluate(self.env), Value(1, None)))
def test_triples_subject_has_unique_property(self):
self.assertTrue(
self.pack.has_unique(
Identifier(Name('e')).evaluate(self.env), Value(1, None)))
self.assertFalse(
self.pack.has_unique(
Identifier(Name('e')).evaluate(self.env), Value(2, None)))
self.assertFalse(
self.pack.has_unique(
Identifier(Name('f')).evaluate(self.env), Value(1, None)))
duplicatePack = TriplePack(
self.pack.triples + [(Identifier(Name('e')).evaluate(
self.env), Value(1, None), Value(42, None))],
self.pack.bindings, self.pack.templates, self.pack._paths)
self.assertFalse(
duplicatePack.has_unique(
Identifier(Name('e')).evaluate(self.env), Value(1, None)))
def test_triples_get_values_for(self):
self.assertEqual(
self.pack.value(
Identifier(Name('e')).evaluate(self.env), Value(1, None)),
Value(42, None))
self.assertEqual(
self.pack.value(
Identifier(Name('e')).evaluate(self.env), Value(2, None)),
None)
self.assertEqual(
self.pack.value(
Identifier(Name('f')).evaluate(self.env), Value(1, None)),
None)
duplicatePack = TriplePack(
self.pack.triples + [(Identifier(Name('e')).evaluate(
self.env), Value(1, None), Value(41, None))],
self.pack.bindings, self.pack.templates, self.pack._paths)
self.assertEqual(
duplicatePack.value(
Identifier(Name('e')).evaluate(self.env), Value(1, None)),
[Value(42, None), Value(41, None)])
def test_triples_add(self):
self.assertFalse(
self.pack.has(
Identifier(Name('e')).evaluate(self.env), Value('fake', None)))
self.pack.add((Identifier(Name('e')).evaluate(self.env),
Value('fake', None), Value('added', None)))
self.assertTrue(
self.pack.has(
Identifier(Name('e')).evaluate(self.env), Value('fake', None)))
self.assertEqual(
self.pack.value(
Identifier(Name('e')).evaluate(self.env), Value('fake', None)),
Value('added', None))
def test_triples_set(self):
self.assertEqual(
self.pack.value(
Identifier(Name('e')).evaluate(self.env), Value(1, None)),
Value(42, None))
self.pack.set(
Identifier(Name('e')).evaluate(self.env), Value(1, None),
Value('set', None))
self.assertTrue(
self.pack.has_unique(
Identifier(Name('e')).evaluate(self.env), Value(1, None)))
self.assertEqual(
self.pack.value(
Identifier(Name('e')).evaluate(self.env), Value(1, None)),
Value('set', None))
self.pack.set(
Identifier(Name('e')).evaluate(self.env), Value('fake', None),
Value('set', None))
self.assertTrue(
self.pack.has(
Identifier(Name('e')).evaluate(self.env), Value('fake', None)))
class ParserTemplateTest(unittest.TestCase):
def setUp(self):
self.parser = Parser()
self.maxDiff = None
self.logger = logging.getLogger(__name__)
def tearDown(self):
None
def test_template_noargs_nobase(self):
script = 'DNASequence()(encoding = <SBOL:IUPACDNA>)'
forms = self.parser.parse(script)
expected_template = Template(Identifier(Name('DNASequence')), [], [
Property(Identifier(Name('encoding')),
Identifier(Uri('SBOL:IUPACDNA')))
])
self.assertCountEqual(forms, [expected_template])
def test_empty_template_noargs_nobase(self):
script = 'DNASequence()'
forms = self.parser.parse(script)
expected_template = Template(Identifier(Name('DNASequence')), [], [])
self.assertCountEqual(forms, [expected_template])
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_empty_template_args(self):
script = 'DNASequence(x, y, z)(Other(x))'
forms = self.parser.parse(script)
expected_template = Template(Identifier(
Name('DNASequence')), ['x', 'y', 'z'], [
Expansion(None, Identifier(Name('Other')),
[Identifier(Name('x'))], [])
])
self.assertCountEqual(forms, [expected_template])
def test_empty_template_args_nobase(self):
script = 'DNASequence(x, y, z)'
forms = self.parser.parse(script)
expected_template = Template(Identifier(Name('DNASequence')),
['x', 'y', 'z'], [])
self.assertCountEqual(forms, [expected_template])
def test_template_onearg_nobase(self):
script = 'DNASequence(x)(encoding = <SBOL:IUPACDNA>)'
forms = self.parser.parse(script)
expected_template = Template(Identifier(Name('DNASequence')), ['x'], [
Property(Identifier(Name('encoding')),
Identifier(Uri('SBOL:IUPACDNA')))
])
self.assertCountEqual(forms, [expected_template])
def test_template_multiargs_nobase(self):
script = 'DNASequence(x, y, z)(encoding = <SBOL:IUPACDNA>)'
forms = self.parser.parse(script)
expected_template = Template(Identifier(
Name('DNASequence')), ['x', 'y', 'z'], [
Property(Identifier(Name('encoding')),
Identifier(Uri('SBOL:IUPACDNA')))
])
self.assertCountEqual(forms, [expected_template])
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])
def test_expansion_in_property(self):
script = 'A()(x = e is a B())'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B()')[0]
expected_template = Template(Identifier(Name('A')), [],
[Property(Identifier(Name('x')), e)])
self.assertEqual(expected_template, forms[0])
def test_expansion_in_property_with_body(self):
script = 'A()(x = e is a B()(y = 12345))'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B()(y = 12345)')[0]
expected_template = Template(Identifier(Name('A')), [],
[Property(Identifier(Name('x')), e)])
self.assertEqual(expected_template, forms[0])
def test_expansion_in_body_with_body(self):
script = 'A()(e is a B()(y = 12345))'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B()(y = 12345)')[0]
expected_template = Template(Identifier(Name('A')), [], [e])
self.assertEqual(expected_template, forms[0])
def test_expansion_in_body(self):
script = 'A()(e is a B())'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B()')[0]
expected_template = Template(Identifier(Name('A')), [], [e])
self.assertEqual(expected_template, forms[0])
def test_expansion_in_property_with_args(self):
script = 'A()(x = e is a B(12345))'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B(12345)')[0]
expected_template = Template(Identifier(Name('A')), [],
[Property(Identifier(Name('x')), e)])
self.assertEqual(expected_template, forms[0])
def test_expansion_in_body_with_args(self):
script = 'A()(e is a B(12345))'
forms = self.parser.parse(script)
e = self.parser.parse('e is a B(12345)')[0]
expected_template = Template(Identifier(Name('A')), [], [e])
self.assertEqual(expected_template, forms[0])
def test_extension_in_body(self):
script = 'A()(@extension ExtensionName())'
forms = self.parser.parse(script)
a = forms[0]
expected_template = Template(Identifier(Name('A')), [],
[ExtensionPragma('ExtensionName', [])])
self.assertEqual(expected_template, a)
def test_extension_in_body_with_arg(self):
script = 'A()(@extension ExtensionName(12345))'
forms = self.parser.parse(script)
a = forms[0]
expected_template = Template(Identifier(
Name('A')), [], [ExtensionPragma('ExtensionName', [Value(12345)])])
self.assertEqual(expected_template, a)
def test_extension_in_body_with_multi_args(self):
script = 'A()(@extension ExtensionName(12345, 67890))'
forms = self.parser.parse(script)
a = forms[0]
expected_template = Template(
Identifier(Name('A')), [],
[ExtensionPragma('ExtensionName',
[Value(12345), Value(67890)])])
self.assertEqual(expected_template, a)
