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# -*- coding: utf-8 -*-
"""Tests for node utilities."""
import unittest
from pybel import BELGraph
from pybel.constants import INCREASES
from pybel.dsl import ComplexAbundance as g
from pybel.dsl import CompositeAbundance as c
from pybel.dsl import Protein, Reaction
from pybel.examples.various_example import (
adp,
atp,
glucose,
glucose_6_phosphate,
hk1,
phosphate,
single_reaction_graph,
)
from pybel.struct.node_utils import flatten_list_abundance, reaction_cartesian_expansion
class TestNodeUtils(unittest.TestCase):
"""Test node utilities."""
def test_flatten_complex(self):
"""Test flattening a nested complex."""
p1, p2, p3 = (Protein("N", str(i + 1)) for i in range(3))
pairs = [
# Mainly complexes
(g([p1, p2, p3]), g([p1, p2, p3])), # no nesting
(g([p1, p2, p3]), g([g([p1, p2]), p3])), # one nesting
(g([p1, p2, p3]), g([g([p1]), p2, p3])), # one nesting
(g([p1, p2, p3]), g([g([p1]), g([p2]), p3])), # one nesting
# Mainly composites
(c([p1, p2, p3]), c([p1, p2, p3])), # no nesting
(c([p1, p2, p3]), c([c([p1, p2]), p3])), # one nesting
(c([p1, p2, p3]), c([c([p1]), p2, p3])), # one nesting
(c([p1, p2, p3]), c([c([p1]), c([p2]), p3])), # one nesting
# TODO: mixtures of composites and complexes?
]
for expected, source in pairs:
self.assertEqual(expected, flatten_list_abundance(source))
def test_flatten_reaction(self):
"""Test flattening a reaction."""
single_reaction_graph_copy = single_reaction_graph.copy()
self.assertEqual(single_reaction_graph_copy.number_of_nodes(), 7)
self.assertEqual(single_reaction_graph_copy.number_of_edges(), 7)
reaction_cartesian_expansion(single_reaction_graph_copy)
self.assertEqual(single_reaction_graph_copy.number_of_nodes(), 6)
self.assertEqual(single_reaction_graph_copy.number_of_edges(), 8)
pairs = [
(glucose, INCREASES, glucose_6_phosphate),
(glucose, INCREASES, adp),
(hk1, INCREASES, glucose_6_phosphate),
(hk1, INCREASES, adp),
(atp, INCREASES, glucose_6_phosphate),
(atp, INCREASES, adp),
(phosphate, INCREASES, glucose_6_phosphate),
(phosphate, INCREASES, adp),
]
for source, target, data in single_reaction_graph_copy.edges(data=True):
self.assertIn((source, INCREASES, target), pairs)
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)
# pairs = [
# (glucose, INCREASES, glucose_6_phosphate),
# (glucose, INCREASES, adp),
# (hk1, INCREASES, glucose_6_phosphate),
# (hk1, INCREASES, adp),
# (atp, INCREASES, glucose_6_phosphate),
# (atp, INCREASES, adp),
# (phosphate, INCREASES, glucose_6_phosphate),
# (phosphate, INCREASES, adp),
# ]
#
# for source, target, data in node_increases_reaction_graph.edges(data=True):
# self.assertIn((source, INCREASES, target), pairs)
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)
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