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# Copyright 2001 by Tarjei Mikkelsen. 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
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')
l = sorted(a.nodes())
self.assertEqual(l, ['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')]) # , "incorrect child edges")
a.add_edge('b', 'a', 'label2')
self.assertEqual(a.parent_edges('a'), [('b', 'label2')]) # , "incorrect parent edges")
a.add_edge('b', 'c', 'label3')
self.assertEqual(a.parent_edges('c'), [('b', 'label3')]) # , "incorrect parent edges")
l = sorted(a.children('b'))
self.assertEqual(l, ['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")
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')
l = sorted(a.nodes())
self.assertEqual(l, ['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')]) # , "incorrect child edges")
a.add_edge('a', 'b', 'label2')
l = sorted(a.child_edges('a'))
self.assertEqual(l, [('b', 'label1'), ('b', 'label2')]) # , "incorrect child edges")
a.add_edge('b', 'a', 'label2')
self.assertEqual(a.parent_edges('a'), [('b', 'label2')]) # , "incorrect parent edges")
a.add_edge('b', 'c', 'label3')
self.assertEqual(a.parent_edges('c'), [('b', 'label3')]) # , "incorrect parent edges")
l = a.children('b')
l.sort()
self.assertEqual(l, ['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")
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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