def test_missing_information(self):
"""Test that entity and abundance functions raise on missing name/identifier."""
with self.assertRaises(ValueError):
entity(namespace='test')
with self.assertRaises(ValueError):
protein(namespace='test')
def test_object_has_translocation(self):
"""p(HGNC: EGF) increases tloc(p(HGNC: VCP), GOCCID: 0005634, GOCCID: 0005737)"""
g = BELGraph()
u_node = protein(name='EFG', namespace='HGNC')
v_node = protein(name='VCP', namespace='HGNC')
u = g.add_node_from_data(u_node)
v = g.add_node_from_data(v_node)
g.add_qualified_edge(
u_node,
v_node,
relation=INCREASES,
citation='10855792',
evidence=
"Although found predominantly in the cytoplasm and, less abundantly, in the nucleus, VCP can be "
"translocated from the nucleus after stimulation with epidermal growth factor.",
annotations={'Species': '9606'},
object_modifier=translocation(from_loc=entity(
namespace='GO', identifier='0005634'),
to_loc=entity(namespace='GO',
identifier='0005737')))
self.assertFalse(is_translocated(g, u))
self.assertFalse(is_degraded(g, u))
self.assertFalse(has_activity(g, u))
self.assertFalse(has_causal_in_edges(g, u))
self.assertTrue(has_causal_out_edges(g, u))
self.assertTrue(is_translocated(g, v))
self.assertFalse(is_degraded(g, v))
self.assertFalse(has_activity(g, v))
self.assertTrue(has_causal_in_edges(g, v))
self.assertFalse(has_causal_out_edges(g, v))
def test_subject_degradation_location(self):
self.assertEqual(self.add_edge(subject_modifier=degradation()),
self.add_edge(subject_modifier=degradation()))
self.assertEqual(
self.add_edge(subject_modifier=degradation(
location=entity(name='somewhere', namespace='GOCC'))),
self.add_edge(subject_modifier=degradation(
location=entity(name='somewhere', namespace='GOCC'))))
self.assertNotEqual(
self.add_edge(subject_modifier=degradation()),
self.add_edge(subject_modifier=degradation(
location=entity(name='somewhere', namespace='GOCC'))))
def _help_test_non_standard_namespace(self, statement):
result = self.parser.parseString(statement)
expected = {
KIND: PMOD,
IDENTIFIER: entity('MOD', 'PhosRes'),
PMOD_CODE: 'Ser',
PMOD_POSITION: 473
}
self.assertEqual(expected, pmod(name='PhosRes', namespace='MOD', code='Ser', position=473))
self.assertEqual(expected, result.asDict())
def test_decreases(self):
"""Test parsing a decreases relation with a reaction.
3.1.3 http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html#Xdecreases
"""
statement = 'pep(p(SFAM:"CAPN Family", location(GOCC:intracellular))) -| reaction(reactants(p(HGNC:CDK5R1)),products(p(HGNC:CDK5)))'
result = self.parser.relation.parseString(statement)
expected_dict = {
SUBJECT: {
MODIFIER: ACTIVITY,
TARGET: {
FUNCTION: PROTEIN,
NAMESPACE: 'SFAM',
NAME: 'CAPN Family',
LOCATION: {
NAMESPACE: 'GOCC',
NAME: 'intracellular'
}
},
EFFECT: {
NAME: 'pep',
NAMESPACE: BEL_DEFAULT_NAMESPACE
},
},
RELATION: 'decreases',
OBJECT: {
FUNCTION: REACTION,
REACTANTS: [{
FUNCTION: PROTEIN,
NAMESPACE: 'HGNC',
NAME: 'CDK5R1'
}],
PRODUCTS: [{
FUNCTION: PROTEIN,
NAMESPACE: 'HGNC',
NAME: 'CDK5'
}]
}
}
self.assertEqual(expected_dict, result.asDict())
sub = protein('SFAM', 'CAPN Family')
self.assert_has_node(sub)
obj_member_1 = protein('HGNC', 'CDK5R1')
self.assert_has_node(obj_member_1)
obj_member_2 = protein('HGNC', 'CDK5')
self.assert_has_node(obj_member_2)
obj = reaction(reactants=[obj_member_1], products=[obj_member_2])
self.assert_has_node(obj)
self.assert_has_edge(obj, obj_member_1, relation=HAS_REACTANT)
self.assert_has_edge(obj, obj_member_2, relation=HAS_PRODUCT)
expected_edge_attributes = {
RELATION: DECREASES,
SUBJECT: {
MODIFIER: ACTIVITY,
EFFECT: {
NAME: 'pep',
NAMESPACE: BEL_DEFAULT_NAMESPACE,
},
LOCATION: {
NAMESPACE: 'GOCC',
NAME: 'intracellular',
}
}
}
self.assertEqual(
expected_edge_attributes[SUBJECT],
activity(name='pep',
location=entity(name='intracellular', namespace='GOCC')))
self.assert_has_edge(sub, obj, **expected_edge_attributes)