class TestMetabolicDatabase(unittest.TestCase):
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> 2 A'))
self.database.set_reaction('rxn_2', parse_reaction('A <=> B'))
self.database.set_reaction('rxn_3', parse_reaction('A => D[e]'))
self.database.set_reaction('rxn_4', parse_reaction('A + 2 B => C'))
self.database.set_reaction('rxn_5', parse_reaction('C => 3 D[e]'))
self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
def test_reactions(self):
self.assertEqual(
set(self.database.reactions),
{'rxn_1', 'rxn_2', 'rxn_3', 'rxn_4', 'rxn_5', 'rxn_6'})
def test_compounds(self):
self.assertEqual(
set(self.database.compounds),
{Compound('A'),
Compound('B'),
Compound('C'),
Compound('D', 'e')})
def test_compartments(self):
self.assertEqual(set(self.database.compartments), {None, 'e'})
def test_has_reaction_existing(self):
self.assertTrue(self.database.has_reaction('rxn_3'))
def test_has_reaction_not_existing(self):
self.assertFalse(self.database.has_reaction('rxn_7'))
def test_is_reversible_is_true(self):
self.assertTrue(self.database.is_reversible('rxn_2'))
def test_is_reversible_is_false(self):
self.assertFalse(self.database.is_reversible('rxn_5'))
def test_get_reaction_values(self):
self.assertEqual(list(self.database.get_reaction_values('rxn_4')),
[(Compound('A'), -1), (Compound('B'), -2),
(Compound('C'), 1)])
def test_get_compound_reactions(self):
self.assertEqual(
set(self.database.get_compound_reactions(Compound('A'))),
{'rxn_1', 'rxn_2', 'rxn_3', 'rxn_4'})
def test_reversible(self):
self.assertEqual(set(self.database.reversible), {'rxn_2'})
def test_get_reaction(self):
reaction = parse_reaction('A + (2) B => C')
self.assertEqual(self.database.get_reaction('rxn_4'), reaction)
def test_set_reaction_with_zero_coefficient(self):
reaction = Reaction(Direction.Both, [(Compound('A'), 1),
(Compound('B'), 0)],
[(Compound('C'), 1)])
self.database.set_reaction('rxn_new', reaction)
self.assertNotIn('rxn_new',
self.database.get_compound_reactions(Compound('B')))
def test_matrix_get_item(self):
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_1'], 2)
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_2'], -1)
self.assertEqual(self.database.matrix[Compound('B'), 'rxn_2'], 1)
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_4'], -1)
self.assertEqual(self.database.matrix[Compound('B'), 'rxn_4'], -2)
self.assertEqual(self.database.matrix[Compound('C'), 'rxn_4'], 1)
self.assertEqual(self.database.matrix[Compound('C'), 'rxn_5'], -1)
self.assertEqual(self.database.matrix[Compound('D', 'e'), 'rxn_5'], 3)
def test_matrix_get_item_invalid_key(self):
with self.assertRaises(KeyError):
a = self.database.matrix[Compound('A'), 'rxn_5']
with self.assertRaises(KeyError):
b = self.database.matrix['rxn_1']
def test_matrix_set_item_is_invalid(self):
with self.assertRaises(TypeError):
self.database.matrix[Compound('A'), 'rxn_1'] = 4
def test_matrix_iter(self):
matrix_keys = {(Compound('A'), 'rxn_1'), (Compound('A'), 'rxn_2'),
(Compound('B'), 'rxn_2'), (Compound('A'), 'rxn_3'),
(Compound('D', 'e'), 'rxn_3'), (Compound('A'), 'rxn_4'),
(Compound('B'), 'rxn_4'), (Compound('C'), 'rxn_4'),
(Compound('C'), 'rxn_5'), (Compound('D', 'e'), 'rxn_5'),
(Compound('D', 'e'), 'rxn_6')}
self.assertEqual(set(iter(self.database.matrix)), matrix_keys)
def test_matrix_len(self):
self.assertEqual(len(self.database.matrix), 11)
class TestMetabolicDatabase(unittest.TestCase):
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
def test_reactions(self):
self.assertEqual(
set(self.database.reactions),
{'rxn_1', 'rxn_2', 'rxn_3', 'rxn_4', 'rxn_5', 'rxn_6'})
def test_compounds(self):
self.assertEqual(
set(self.database.compounds),
{Compound('A'), Compound('B'), Compound('C'), Compound('D', 'e')})
def test_compartments(self):
self.assertEqual(set(self.database.compartments), {None, 'e'})
def test_has_reaction_existing(self):
self.assertTrue(self.database.has_reaction('rxn_3'))
def test_has_reaction_not_existing(self):
self.assertFalse(self.database.has_reaction('rxn_7'))
def test_is_reversible_is_true(self):
self.assertTrue(self.database.is_reversible('rxn_2'))
def test_is_reversible_is_false(self):
self.assertFalse(self.database.is_reversible('rxn_5'))
def test_get_reaction_values(self):
self.assertEqual(set(self.database.get_reaction_values('rxn_2')),
{ (Compound('A'), -1), (Compound('B'), 1) })
def test_get_compound_reactions(self):
self.assertEqual(set(self.database.get_compound_reactions(Compound('A'))),
{ 'rxn_1', 'rxn_2', 'rxn_3', 'rxn_4' })
def test_reversible(self):
self.assertEqual(set(self.database.reversible), { 'rxn_2' })
def test_get_reaction(self):
reaction = parse_reaction('|A| => |D[e]|')
self.assertEqual(self.database.get_reaction('rxn_3'), reaction)
def test_set_reaction_with_zero_coefficient(self):
reaction = Reaction(
Direction.Both, [(Compound('A'), 1), (Compound('B'), 0)],
[(Compound('C'), 1)])
self.database.set_reaction('rxn_new', reaction)
self.assertNotIn('rxn_new', self.database.get_compound_reactions(Compound('B')))
def test_matrix_get_item(self):
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_1'], 2)
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_2'], -1)
self.assertEqual(self.database.matrix[Compound('B'), 'rxn_2'], 1)
self.assertEqual(self.database.matrix[Compound('A'), 'rxn_4'], -1)
self.assertEqual(self.database.matrix[Compound('C'), 'rxn_4'], 1)
self.assertEqual(self.database.matrix[Compound('C'), 'rxn_5'], -1)
self.assertEqual(self.database.matrix[Compound('D', 'e'), 'rxn_5'], 1)
def test_matrix_get_item_invalid_key(self):
with self.assertRaises(KeyError):
a = self.database.matrix[Compound('A'), 'rxn_5']
with self.assertRaises(KeyError):
b = self.database.matrix['rxn_1']
def test_matrix_set_item_is_invalid(self):
with self.assertRaises(TypeError):
self.database.matrix[Compound('A'), 'rxn_1'] = 4
def test_matrix_iter(self):
matrix_keys = { (Compound('A'), 'rxn_1'),
(Compound('A'), 'rxn_2'),
(Compound('B'), 'rxn_2'),
(Compound('A'), 'rxn_3'),
(Compound('D', 'e'), 'rxn_3'),
(Compound('A'), 'rxn_4'),
(Compound('C'), 'rxn_4'),
(Compound('C'), 'rxn_5'),
(Compound('D', 'e'), 'rxn_5'),
(Compound('D', 'e'), 'rxn_6') }
self.assertEqual(set(iter(self.database.matrix)), matrix_keys)
def test_matrix_len(self):
self.assertEqual(len(self.database.matrix), 10)
