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_annotation_name_persistience_2(self):
"""Tests that an annotation defined by a list can't be overwritten by a definition by URL"""
s = 'DEFINE ANNOTATION TextLocation AS LIST {"Abstract","Results","Legend","Review"}'
self.parser.parseString(s)
self._help_test_local_annotation('TextLocation')
s = ANNOTATION_URL_FMT.format('TextLocation', MESH_DISEASES_URL)
with self.assertRaises(RedefinedAnnotationError):
self.parser.parseString(s)
self._help_test_local_annotation('TextLocation')
self.assertIn('Abstract',
self.parser.annotation_to_local['TextLocation'])
def test_annotation_name_persistience_1(self, mock_get):
"""Test that an annotation defined by a URL can't be overwritten by a definition by a list."""
s = ANNOTATION_URL_FMT.format(MESH_DISEASES_KEYWORD, MESH_DISEASES_URL)
self.parser.parseString(s)
self.assertIn(MESH_DISEASES_KEYWORD, self.parser.annotation_to_term)
s = 'DEFINE ANNOTATION {} AS LIST {{"A","B","C"}}'.format(
MESH_DISEASES_KEYWORD)
with self.assertRaises(RedefinedAnnotationError):
self.parser.parseString(s)
self.assertIn(MESH_DISEASES_KEYWORD, self.parser.annotation_to_term)
self.assertNotIn('A',
self.parser.annotation_to_term[MESH_DISEASES_KEYWORD])
self.assertIn('46, XX Disorders of Sex Development',
self.parser.annotation_to_term[MESH_DISEASES_KEYWORD])
def test_parse_annotation_url_file(self):
"""Tests parsing an annotation by file URL"""
keyword = 'TESTAN1'
url = Path(test_an_1).as_uri()
line = ANNOTATION_URL_FMT.format(keyword, url)
self.parser.parseString(line)
expected_values = {
'TestAnnot1': 'O',
'TestAnnot2': 'O',
'TestAnnot3': 'O',
'TestAnnot4': 'O',
'TestAnnot5': 'O'
}
self.assertEqual(set(expected_values),
self.parser.manager.get_annotation_entry_names(url))
def test_parse_annotation_url_file(self):
"""Tests parsing an annotation by file URL"""
keyword = 'TESTAN1'
url = Path(test_an_1).as_uri()
line = ANNOTATION_URL_FMT.format(keyword, url)
self.parser.parseString(line)
self.parser.ensure_resources()
expected_values = {
'TestAnnot1': 'O',
'TestAnnot2': 'O',
'TestAnnot3': 'O',
'TestAnnot4': 'O',
'TestAnnot5': 'O'
}
annotation = self.parser.manager.get_namespace_by_url(url)
self.assertIsNotNone(annotation)
self.assertEqual(set(expected_values),
{e.name
for e in annotation.entries})