def test_namespace_name_persistience(self, mock_get):
"""Test that a namespace defined by a URL can't be overwritten by a definition by another URL."""
s = NAMESPACE_URL_FMT.format(HGNC_KEYWORD, HGNC_URL)
self.parser.parseString(s)
help_check_hgnc(self, self.parser.namespace_to_term_to_encoding)
s = NAMESPACE_URL_FMT.format(HGNC_KEYWORD, 'XXXXX')
with self.assertRaises(RedefinedNamespaceError):
self.parser.parseString(s)
help_check_hgnc(self, self.parser.namespace_to_term_to_encoding)
def test_control_compound(self, mock_get):
text_location = 'TextLocation'
lines = [
ANNOTATION_URL_FMT.format(MESH_DISEASES_KEYWORD,
MESH_DISEASES_URL),
NAMESPACE_URL_FMT.format(HGNC_KEYWORD, HGNC_URL),
'DEFINE ANNOTATION TextLocation AS LIST {"Abstract","Results","Legend","Review"}'
]
self.parser.parse_lines(lines)
self.assertIn(MESH_DISEASES_KEYWORD, self.parser.annotation_to_term)
self.assertIn(HGNC_KEYWORD, self.parser.namespace_to_term_to_encoding)
self._help_test_local_annotation(text_location)
def test_parse_namespace_url_file(self, mock):
"""Tests parsing a namespace by file URL"""
s = NAMESPACE_URL_FMT.format('TESTNS1', test_ns_1)
self.parser.parseString(s)
expected_values = {
'TestValue1': {'O'},
'TestValue2': {'O'},
'TestValue3': {'O'},
'TestValue4': {'O'},
'TestValue5': {'O'}
}
self.assertIn('TESTNS1', self.parser.namespace_to_term)
for k, values in expected_values.items():
self.assertIn(k, self.parser.namespace_to_term['TESTNS1'])
self.assertEqual(set(values),
set(self.parser.namespace_to_term['TESTNS1'][k]))
def test_squiggly_filepath(self):
line = NAMESPACE_URL_FMT.format(HGNC_KEYWORD, LOCAL_TEST_PATH)
self.parser.parseString(line)
help_check_hgnc(self, self.parser.namespace_to_term_to_encoding)
def test_namespace_nocache(self):
"""Checks namespace is loaded into parser but not cached"""
s = NAMESPACE_URL_FMT.format('TESTNS3', test_ns_nocache_path)
self.parser.parseString(s)
self.assertIn('TESTNS3', self.parser.namespace_to_term)
self.assertEqual(0, len(self.manager.list_namespaces()))
def test_squiggly_filepath(self):
line = NAMESPACE_URL_FMT.format(
HGNC_KEYWORD,
"~/dev/pybel/src/pybel/testing/resources/belns/hgnc-names.belns")
self.parser.parseString(line)
help_check_hgnc(self, self.parser.namespace_to_term)