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# -*- coding: utf-8 -*-
"""Tests for graph operations."""
import unittest
from pybel import BELGraph
from pybel.dsl import protein
from pybel.struct.operations import (
left_full_join,
left_node_intersection_join,
left_outer_join,
node_intersection,
union,
)
from pybel.testing.utils import n
p1, p2, p3, p4, p5, p6, p7, p8 = (protein(namespace="HGNC", name=n()) for _ in range(8))
class TestLeftFullJoin(unittest.TestCase):
"""Tests the variants of the left full join, including the exhaustive vs. hash algorithms and calling by function
or magic functions"""
def setUp(self):
"""Set up tests for the left full join with two example graphs."""
g = BELGraph()
g.add_increases(p1, p2, citation="PMID1", evidence="Evidence 1")
h = BELGraph()
h.add_increases(p1, p2, citation="PMID1", evidence="Evidence 1")
h.add_increases(p1, p2, citation="PMID2", evidence="Evidence 2")
h.add_increases(p1, p3, citation="PMID1", evidence="Evidence 3")
self.g = g
self.h = h
self._help_check_initial_g(self.g)
self._help_check_initial_h(self.h)
def _help_check_initial_g(self, graph: BELGraph):
"""Test the initial G graph."""
self.assertEqual(2, graph.number_of_nodes(), msg="initial graph G had wrong number of nodes")
self.assertEqual(1, graph.number_of_edges(), msg="initial graph G had wrong number of edges")
def _help_check_initial_h(self, graph: BELGraph):
"""Test the initial H graph."""
self.assertEqual(3, graph.number_of_nodes(), msg="initial graph H had wrong number of nodes")
self.assertEqual(3, graph.number_of_edges(), msg="initial graph H had wrong number of edges")
def _help_check_result(self, j: BELGraph):
"""Help check the result of left joining H into G.
:param j: The resulting graph from G += H
"""
self.assertEqual(3, j.number_of_nodes())
self.assertEqual(
3,
j.number_of_edges(),
msg="G edges:\n{}".format("\n".join(map(str, j.edges(data=True)))),
)
def test_function(self):
"""Test full joining two networks using the function."""
left_full_join(self.g, self.h)
self._help_check_result(self.g)
self._help_check_initial_h(self.h)
def test_full_join_with_isolated_nodes(self):
"""Test what happens when there are isolated nodes."""
a = BELGraph()
a.add_increases(p1, p2, citation=n(), evidence=n())
a.add_node_from_data(p4)
b = BELGraph()
b.add_increases(p2, p3, citation=n(), evidence=n())
b.add_node_from_data(p5)
left_full_join(a, b)
for node in p1, p2, p3, p4, p5:
self.assertIn(node, a)
def test_in_place_operator_failure(self):
"""Test that using the wrong type with the in-place addition operator raises an error."""
with self.assertRaises(TypeError):
self.g += None
def test_in_place_operator(self):
"""Test full joining two networks using the BELGraph in-place addition operator."""
self.g += self.h
self._help_check_result(self.g)
self._help_check_initial_h(self.h)
def test_operator_failure(self):
"""Test that using the wrong type with the addition operator raises an error."""
with self.assertRaises(TypeError):
self.g + None
def test_operator(self):
"""Test full joining two networks using the BELGraph addition operator."""
j = self.g + self.h
self._help_check_result(j)
self._help_check_initial_g(self.g)
self._help_check_initial_h(self.h)
def test_union_failure(self):
"""Test that the union of no graphs raises a value error."""
with self.assertRaises(ValueError):
union([])
def test_union_trivial(self):
"""Test that the union of a single graph returns that graph."""
res = union([self.g])
self.assertEqual(self.g, res)
def test_union(self):
"""Test that the union of a pair of graphs is the same as the full join."""
j = union([self.g, self.h])
self._help_check_result(j)
self._help_check_initial_g(self.g)
self._help_check_initial_h(self.h)
class TestLeftFullOuterJoin(unittest.TestCase):
def setUp(self):
g = BELGraph()
g.add_edge(p1, p2)
h = BELGraph()
h.add_edge(p1, p3)
h.add_edge(p1, p4)
h.add_edge(p5, p6)
h.add_node(p7)
self.g = g
self.h = h
def _help_check_initial_g(self, g):
self.assertEqual(2, g.number_of_nodes())
self.assertEqual({p1, p2}, set(g))
self.assertEqual(1, g.number_of_edges())
self.assertEqual({(p1, p2)}, set(g.edges()))
def _help_check_initial_h(self, h):
self.assertEqual(6, h.number_of_nodes())
self.assertEqual({p1, p3, p4, p5, p6, p7}, set(h))
self.assertEqual(3, h.number_of_edges())
self.assertEqual({(p1, p3), (p1, p4), (p5, p6)}, set(h.edges()))
def _help_check_result(self, j):
"""After H has been full outer joined into G, this is what it should be"""
self.assertEqual(4, j.number_of_nodes())
self.assertEqual({p1, p2, p3, p4}, set(j))
self.assertEqual(3, j.number_of_edges())
self.assertEqual({(p1, p2), (p1, p3), (p1, p4)}, set(j.edges()))
def test_in_place_type_failure(self):
with self.assertRaises(TypeError):
self.g &= None
def test_type_failure(self):
with self.assertRaises(TypeError):
self.g & None
def test_magic(self):
# left_outer_join(g, h)
self.g &= self.h
self._help_check_initial_h(self.h)
self._help_check_result(self.g)
def test_operator(self):
# left_outer_join(g, h)
j = self.g & self.h
self._help_check_initial_h(self.h)
self._help_check_initial_g(self.g)
self._help_check_result(j)
def test_left_outer_join(self):
left_outer_join(self.g, self.h)
self._help_check_initial_h(self.h)
self._help_check_result(self.g)
def test_left_outer_exhaustive_join(self):
self.g &= self.h
left_outer_join(self.g, self.h)
self._help_check_initial_h(self.h)
self._help_check_result(self.g)
class TestInnerJoin(unittest.TestCase):
"""Tests various graph merging procedures"""
def setUp(self):
g = BELGraph()
g.add_edge(p1, p2)
g.add_edge(p1, p3)
g.add_edge(p8, p3)
h = BELGraph()
h.add_edge(p1, p3)
h.add_edge(p1, p4)
h.add_edge(p5, p6)
h.add_node(p7)
self.g = g
self.h = h
def _help_check_initialize_g(self, graph):
self.assertEqual(4, graph.number_of_nodes())
self.assertEqual(3, graph.number_of_edges())
def _help_check_initialize_h(self, graph):
self.assertEqual(6, graph.number_of_nodes())
self.assertEqual({p1, p3, p4, p5, p6, p7}, set(graph))
self.assertEqual(3, graph.number_of_edges())
self.assertEqual({(p1, p3), (p1, p4), (p5, p6)}, set(graph.edges()))
def test_initialize(self):
self._help_check_initialize_g(self.g)
self._help_check_initialize_h(self.h)
def _help_check_join(self, j):
self.assertEqual(2, j.number_of_nodes())
self.assertEqual({p1, p3}, set(j))
self.assertEqual(1, j.number_of_edges())
self.assertEqual(
{
(p1, p3),
},
set(j.edges()),
)
def test_in_place_type_failure(self):
with self.assertRaises(TypeError):
self.g ^ None
def test_type_failure(self):
with self.assertRaises(TypeError):
self.g ^= None
def test_magic(self):
j = self.g ^ self.h
self._help_check_join(j)
self._help_check_initialize_h(self.h)
self._help_check_initialize_g(self.g)
def test_left_node_intersection_join(self):
j = left_node_intersection_join(self.g, self.h)
self._help_check_join(j)
self._help_check_initialize_h(self.h)
self._help_check_initialize_g(self.g)
def test_node_intersection(self):
j = node_intersection([self.h, self.g])
self._help_check_join(j)
self._help_check_initialize_h(self.h)
self._help_check_initialize_g(self.g)
def test_intersection_failure(self):
with self.assertRaises(ValueError):
node_intersection([])
def test_intersection_trivial(self):
res = node_intersection([self.g])
self.assertEqual(self.g, res)
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