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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# python unittest framework
"""Tests for Pathway module."""
import unittest
# modules to be tested
from Bio.Pathway import Reaction
from Bio.Pathway.Rep.Graph import Graph
from Bio.Pathway.Rep.MultiGraph import MultiGraph
class GraphTestCase(unittest.TestCase):
def test_Equals(self):
a = Graph(["a", "b", "c"])
a.add_edge("a", "b", "label1")
a.add_edge("b", "c", "label1")
a.add_edge("b", "a", "label2")
b = Graph(["a", "b", "c"])
self.assertNotEqual(a, b, "equal to similar nodes, no edges")
b.add_edge("a", "b", "label1")
self.assertNotEqual(a, b, "equal to similar nodes, edge subset")
b.add_edge("b", "c", "label1")
b.add_edge("b", "a", "label2")
self.assertEqual(a, b, "not equal to similar")
c = Graph(["a", "b", "c"])
c.add_edge("a", "b", "label2")
c.add_edge("b", "c", "label2")
c.add_edge("b", "a", "label1")
self.assertNotEqual(a, c, "equal to similar with different labels")
self.assertNotEqual(c, Graph(), "equal to empty graph")
self.assertEqual(Graph(), Graph(), "empty graph not equal to self")
def test_Nodes(self):
a = Graph()
self.assertEqual(a.nodes(), [], "default graph not empty")
a.add_node("a")
self.assertEqual(a.nodes(), ["a"], "one node not added")
a.add_node("a")
self.assertEqual(a.nodes(), ["a"], "duplicate node added")
a.add_node("b")
self.assertEqual(sorted(a.nodes()), ["a", "b"], "second node not added")
def test_Edges(self):
a = Graph(["a", "b", "c", "d"])
a.add_edge("a", "b", "label1")
self.assertEqual(a.child_edges("a"), [("b", "label1")])
a.add_edge("b", "a", "label2")
self.assertEqual(a.parent_edges("a"), [("b", "label2")])
a.add_edge("b", "c", "label3")
self.assertEqual(a.parent_edges("c"), [("b", "label3")])
self.assertEqual(sorted(a.children("b")), ["a", "c"], "incorrect children")
self.assertEqual(a.children("d"), [], "incorrect children for singleton")
self.assertEqual(a.parents("a"), ["b"], "incorrect parents")
def test_RemoveNode(self):
a = Graph(["a", "b", "c", "d", "e"])
a.add_edge("a", "e", "label1")
a.add_edge("b", "e", "label1")
a.add_edge("c", "e", "label2")
a.add_edge("d", "e", "label3")
a.add_edge("e", "d", "label4")
a.add_edge("a", "b", "label5")
a.remove_node("e")
b = Graph(["a", "b", "c", "d"])
b.add_edge("a", "b", "label5")
self.assertEqual(a, b) # , "incorrect node removal")
def testAdditionalFunctions(self):
a = Graph(["a", "b", "c"])
a.add_edge("a", "b", "label1")
a.add_edge("b", "c", "label1")
a.add_edge("b", "a", "label2")
self.assertEqual(str(a), "<Graph: 3 node(s), 3 edge(s), 2 unique label(s)>")
self.assertEqual(
repr(a),
"<Graph: ('a': ('b', 'label1'))('b': ('a', 'label2'),('c', 'label1'))('c': )>",
)
self.assertListEqual(a.edges("label1"), [("a", "b"), ("b", "c")])
self.assertListEqual(a.labels(), ["label1", "label2"])
class MultiGraphTestCase(unittest.TestCase):
def test_Equals(self):
a = MultiGraph(["a", "b", "c"])
a.add_edge("a", "b", "label1")
a.add_edge("b", "c", "label1")
a.add_edge("b", "a", "label2")
b = MultiGraph(["a", "b", "c"])
self.assertNotEqual(a, b, "equal to similar nodes, no edges")
b.add_edge("a", "b", "label1")
self.assertNotEqual(a, b, "equal to similar nodes, edge subset")
b.add_edge("b", "c", "label1")
b.add_edge("b", "a", "label2")
self.assertEqual(a, b, "not equal to similar")
c = MultiGraph(["a", "b", "c"])
c.add_edge("a", "b", "label2")
c.add_edge("b", "c", "label2")
c.add_edge("b", "a", "label1")
self.assertNotEqual(a, c, "equal to similar with different labels")
self.assertNotEqual(c, MultiGraph(), "equal to empty graph")
self.assertEqual(MultiGraph(), MultiGraph(), "empty graph not equal to self")
def test_Nodes(self):
a = MultiGraph()
self.assertEqual(a.nodes(), [], "default graph not empty")
a.add_node("a")
self.assertEqual(a.nodes(), ["a"], "one node not added")
a.add_node("a")
self.assertEqual(a.nodes(), ["a"], "duplicate node added")
a.add_node("b")
self.assertEqual(sorted(a.nodes()), ["a", "b"], "second node not added")
def test_Edges(self):
a = MultiGraph(["a", "b", "c", "d"])
a.add_edge("a", "b", "label1")
self.assertEqual(a.child_edges("a"), [("b", "label1")])
a.add_edge("a", "b", "label2")
self.assertEqual(sorted(a.child_edges("a")), [("b", "label1"), ("b", "label2")])
a.add_edge("b", "a", "label2")
self.assertEqual(a.parent_edges("a"), [("b", "label2")])
a.add_edge("b", "c", "label3")
self.assertEqual(a.parent_edges("c"), [("b", "label3")])
children = a.children("b")
children.sort()
self.assertEqual(children, ["a", "c"], "incorrect children")
self.assertEqual(a.children("d"), [], "incorrect children for singleton")
self.assertEqual(a.parents("a"), ["b"], "incorrect parents")
def test_RemoveNode(self):
a = MultiGraph(["a", "b", "c", "d", "e"])
a.add_edge("a", "e", "label1")
self.assertEqual(
repr(a), "<MultiGraph: ('a': ('e', 'label1'))('b': )('c': )('d': )('e': )>"
)
a.add_edge("b", "e", "label1")
a.add_edge("c", "e", "label2")
a.add_edge("d", "e", "label3")
a.add_edge("e", "d", "label4")
a.add_edge("a", "b", "label5")
self.assertEqual(
repr(a),
"<MultiGraph: ('a': ('b', 'label5'),('e', 'label1'))('b': ('e', 'label1'))('c': ('e', 'label2'))('d': ('e', 'label3'))('e': ('d', 'label4'))>",
)
a.remove_node("e")
self.assertEqual(
repr(a), "<MultiGraph: ('a': ('b', 'label5'))('b': )('c': )('d': )>"
)
b = MultiGraph(["a", "b", "c", "d"])
b.add_edge("a", "b", "label5")
self.assertEqual(
repr(b), "<MultiGraph: ('a': ('b', 'label5'))('b': )('c': )('d': )>"
)
self.assertEqual(repr(a), repr(b))
self.assertEqual(a, b) # , "incorrect node removal")
def testAdditionalFunctions(self):
a = MultiGraph(["a", "b", "c"])
a.add_edge("a", "b", "label1")
a.add_edge("b", "c", "label1")
a.add_edge("b", "a", "label2")
self.assertEqual(
str(a), "<MultiGraph: 3 node(s), 3 edge(s), 2 unique label(s)>"
)
self.assertListEqual(a.edges("label1"), [("a", "b"), ("b", "c")])
self.assertListEqual(a.labels(), ["label1", "label2"])
class ReactionTestCase(unittest.TestCase):
def setUp(self):
self.r_empty = Reaction()
self.r_prod = Reaction({"a": 1})
self.r_dest = Reaction({"a": -1})
self.r_1 = Reaction({"a": -1, "b": 1})
self.r_1i = Reaction({"a": -1, "b": 1, "c": 0})
self.r_2 = Reaction({"b": -1, "c": 1})
self.r_3 = Reaction({"a": -1, "d": 2})
self.r_4 = Reaction({"c": -1, "d": -1, "a": 1, "e": 2})
def test_eq(self):
self.assertEqual(self.r_1, self.r_1i) # , "not equal to similar")
self.assertNotEqual(self.r_3, self.r_4) # , "equal to different")
def test_rev(self):
self.assertEqual(
self.r_empty.reverse(), self.r_empty, "empty reversed not empty"
)
self.assertEqual(
self.r_prod.reverse(), self.r_dest, "reversed reaction not equal to similar"
)
self.assertEqual(
self.r_4.reverse(),
Reaction({"c": 1, "d": 1, "a": -1, "e": -2}),
"reversed reaction not equal to similar",
)
self.assertEqual(
self.r_3.reverse().reverse(), self.r_3, "double reversal not identity"
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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