def test_flatten_reaction_3(self):
"""Test flattening a graph containing 2 reactions connected to each other."""
two_reactions_graph = BELGraph()
reaction_1 = Reaction(reactants=[glucose, atp], products=hk1)
reaction_2 = Reaction(reactants=glucose_6_phosphate, products=adp)
two_reactions_graph.add_increases(reaction_1,
reaction_2,
citation='X',
evidence='X')
self.assertEqual(two_reactions_graph.number_of_nodes(), 7)
self.assertEqual(two_reactions_graph.number_of_edges(), 6)
reaction_cartesian_expansion(two_reactions_graph)
# TODO Fix so unqualified duplicate edges are not created (it should be the 6 edges below)
self.assertEqual(two_reactions_graph.number_of_nodes(), 5)
self.assertEqual(two_reactions_graph.number_of_edges(), 8)
def test_reaction(self):
"""Add identified reaction."""
graph = BELGraph()
reaction = Reaction(
namespace='rhea',
identifier='44104',
reactants=[
Abundance(namespace='chebi', identifier='17478'),
Abundance(namespace='chebi', identifier='15377'),
Abundance(namespace='chebi', identifier='57540'),
],
products=[
Abundance(namespace='chebi', identifier='29067'),
Abundance(namespace='chebi', identifier='15378'),
Abundance(namespace='chebi', identifier='57945'),
],
)
graph.add_node_from_data(reaction)
self.assertEqual(7, graph.number_of_nodes())
self.assertEqual(6, graph.number_of_edges())
def test_flatten_reaction_2(self):
"""Test flattening a qualified reaction."""
node_increases_reaction_graph = BELGraph()
glycolisis_step_1 = Reaction(reactants=[glucose, hk1, atp],
products=[glucose_6_phosphate, adp, hk1])
node_increases_reaction_graph.add_increases(glucose_6_phosphate,
glycolisis_step_1,
citation='X',
evidence='X')
self.assertEqual(node_increases_reaction_graph.number_of_nodes(), 6)
self.assertEqual(node_increases_reaction_graph.number_of_edges(), 7)
reaction_cartesian_expansion(node_increases_reaction_graph)
self.assertEqual(node_increases_reaction_graph.number_of_nodes(), 5)
# TODO Fix so unqualified duplicate edges are not created (it should be the 8 edges below)
self.assertEqual(node_increases_reaction_graph.number_of_edges(), 12)
def test_reaction(self):
node = Reaction(reactants=[Abundance(namespace='CHEBI', name='A')],
products=[Abundance(namespace='CHEBI', name='B')])
self.assertEqual('rxn(reactants(a(CHEBI:A)), products(a(CHEBI:B)))',
str(node))
Gene('HGNC', 'APP'),
Pathology('MESHD', 'Alzheimer Disease'),
ComplexAbundance([Protein('HGNC', 'F3'), Protein('HGNC', 'F7')]),
Protein('HGNC', 'F3'),
Protein('HGNC', 'F7'),
Protein('HGNC', 'F9'),
Protein('HGNC', 'GSK3B', variants=ProteinModification('Ph', 'Ser', 9)),
Protein('HGNC', 'GSK3B'),
Pathology('MESHD', 'Psoriasis'),
Pathology('MESHD', 'Skin Diseases'),
Reaction(
reactants=[
Abundance('CHEBI', '(3S)-3-hydroxy-3-methylglutaryl-CoA'),
Abundance('CHEBI', 'NADPH'),
Abundance('CHEBI', 'hydron')
],
products=[
Abundance('CHEBI', 'NADP(+)'),
Abundance('CHEBI', 'mevalonate')
]
),
Abundance('CHEBI', '(3S)-3-hydroxy-3-methylglutaryl-CoA'),
Abundance('CHEBI', 'NADPH'),
Abundance('CHEBI', 'hydron'),
Abundance('CHEBI', 'mevalonate'),
Abundance('CHEBI', 'NADP(+)'),
Abundance('CHEBI', 'nitric oxide'),
ComplexAbundance([
Protein('HGNC', 'ITGAV'),
Protein('HGNC', 'ITGB3')
]),
jun = hgnc(name='JUN')
mirna_1 = mirbase(name=n())
mirna_2 = mirbase(name=n())
pathology_1 = Pathology('DO', n())
ap1_complex = ComplexAbundance([fos, jun])
egfr_dimer = ComplexAbundance([egfr, egfr])
yfg_data = hgnc(name='YFG')
e2f4_data = hgnc(name='E2F4')
bound_ap1_e2f4 = ComplexAbundance([ap1_complex, e2f4_data])
superoxide = chebi(name='superoxide')
hydrogen_peroxide = chebi(name='hydrogen peroxide')
oxygen = chebi(name='oxygen')
superoxide_decomposition = Reaction(reactants=[superoxide],
products=[hydrogen_peroxide, oxygen])
def assert_unqualified_edge(test_case, u: BaseEntity, v: BaseEntity,
rel: str) -> None:
"""Assert there's only one edge and get the data for it"""
test_case.assertIn(u, test_case.graph)
test_case.assertIn(v, test_case.graph[u])
edges = list(test_case.graph[u][v].values())
test_case.assertEqual(1, len(edges))
data = edges[0]
test_case.assertEqual(rel, data[RELATION])
class TestNetworkCache(BelReconstitutionMixin, FleetingTemporaryCacheMixin):
def test_get_network_missing(self):
def test_reaction_has_contents(self):
"""Test that the construction of reaction doesn't have empty lists."""
with self.assertRaises(ReactionEmptyException):
Reaction([], [])