def setUp(self) -> None:
self.parser = ConceptParser(namespace_to_pattern={
'hgnc': re.compile(r'\d+'),
'ec-code': re.compile(r'.+'),
})
self.assertEqual({}, self.parser.namespace_to_identifier_to_encoding)
self.assertEqual({}, self.parser.namespace_to_name_to_encoding)
def setUp(self):
super().setUp()
default_namespace = {'X', 'Y', 'W Z'}
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
default_namespace=default_namespace,
)
class TestConceptParserRegex(unittest.TestCase):
"""Tests for regular expression parsing"""
def setUp(self) -> None:
self.parser = ConceptParser(namespace_to_pattern={
'hgnc': re.compile(r'\d+'),
'ec-code': re.compile(r'.+'),
})
self.assertEqual({}, self.parser.namespace_to_identifier_to_encoding)
self.assertEqual({}, self.parser.namespace_to_name_to_encoding)
def test_valid(self):
for curie, namespace, name in [
('hgnc:391', 'hgnc', '391'),
('ec-code:1.1.1.27', 'ec-code', '1.1.1.27'),
]:
with self.subTest(curie=curie):
result = self.parser.parseString(curie)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual(namespace, result['namespace'])
self.assertEqual(name, result['name'])
def test_invalid(self):
"""Test invalid BEL term."""
s = 'hgnc:AKT1'
with self.assertRaises(MissingNamespaceRegexWarning):
result = self.parser.parseString(s)
print(result.asDict())
def test_valid_obo(self):
"""Test parsing an identifier that has a name."""
s = 'hgnc:391 ! AKT1'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertIn('identifier', result)
self.assertEqual('hgnc', result['namespace'])
self.assertEqual('AKT1', result['name'])
self.assertEqual('391', result['identifier'])
def test_invalid_obo(self):
"""Test parsing an OBO-style identifier where the identifier and name are switched."""
s = 'hgnc:AKT1 ! 391'
with self.assertRaises(MissingNamespaceRegexWarning):
result = self.parser.parseString(s)
print(result.asDict())
class TestConceptParserLenient(_ParserMixin):
"""Tests where naked names are allowed."""
def setUp(self):
super().setUp()
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
allow_naked_names=True,
)
def test_valid_1(self):
s = 'A:3'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual('A', result['namespace'])
self.assertEqual('3', result['name'])
def test_valid_2(self):
s = 'A:"3"'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual('A', result['namespace'])
self.assertEqual('3', result['name'])
def test_invalid_1(self):
s = 'C:4'
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_2(self):
s = 'A:4'
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_not_invalid_3(self):
s = 'bare'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual(DIRTY, result['namespace'])
self.assertEqual('bare', result['name'])
def test_not_invalid_4(self):
s = '"quoted"'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual(DIRTY, result['namespace'])
self.assertEqual('quoted', result['name'])
def setUp(self):
identifier_parser = ConceptParser(namespace_to_pattern={
'MOD': re.compile('.*'),
'HGNC': re.compile('.*'),
})
identifier_qualified = identifier_parser.identifier_qualified
self.parser = get_protein_modification_language(identifier_qualified)
def setUp(self):
identifier_parser = ConceptParser()
self.parser = get_gene_modification_language(
concept_fqualified=identifier_parser.identifier_fqualified,
concept_qualified=identifier_parser.identifier_qualified,
)
self.expected = GeneModification('Me')
class TestConceptEnumerated(_ParserMixin):
def setUp(self):
super().setUp()
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term)
def test_valid_1(self):
s = 'A:3'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertEqual('A', result['namespace'])
self.assertEqual('3', result['name'])
def test_valid_2(self):
s = 'A:"3"'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertEqual('A', result['namespace'])
self.assertEqual('3', result['name'])
def test_invalid_1(self):
s = 'C:4'
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_2(self):
s = 'A:4'
with self.assertRaises(Exception):
self.parser.parseString(s)
def test_invalid_3(self):
s = 'bare'
with self.assertRaises(NakedNameWarning):
self.parser.parseString(s)
def test_invalid_4(self):
s = '"quoted"'
with self.assertRaises(NakedNameWarning):
self.parser.parseString(s)
class TestConceptParserDefault(_ParserMixin):
"""Tests where the concept parser allows an enumerated list of unqualified entities."""
def setUp(self):
super().setUp()
default_namespace = {'X', 'Y', 'W Z'}
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
default_namespace=default_namespace,
)
def test_valid_1(self):
s = 'A:3'
result = self.parser.parseString(s)
self.assertIn('namespace', result)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual('A', result['namespace'])
self.assertEqual('3', result['name'])
def test_valid_2(self):
s = 'X'
result = self.parser.parseString(s)
self.assertIn('name', result)
self.assertEqual('X', result['name'])
def test_valid_3(self):
s = '"W Z"'
result = self.parser.parseString(s)
self.assertIn('name', result)
self.assertNotIn('identifier', result)
self.assertEqual('W Z', result['name'])
def test_not_in_defaultNs(self):
s = 'D'
with self.assertRaises(Exception):
self.parser.parseString(s)
def setUp(self):
identifier_parser = ConceptParser(
namespace_to_pattern={'GO': re.compile('.*')})
identifier_qualified = identifier_parser.identifier_qualified
self.parser = get_location_language(identifier_qualified)
def setUp(self):
super().setUp()
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term)
def setUp(self):
super().setUp()
self.parser = ConceptParser(
namespace_to_term_to_encoding=self.namespace_to_term,
allow_naked_names=True,
)
def setUp(self):
identifier_parser = ConceptParser()
identifier_qualified = identifier_parser.identifier_qualified
self.parser = get_protein_modification_language(identifier_qualified)
def setUp(self):
identifier_parser = ConceptParser()
identifier_qualified = identifier_parser.identifier_qualified
self.parser = get_fusion_language(identifier_qualified)