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,
)
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')
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)
