def test_parse_reaction_table_file(self):
path = self.write_model_file('reactions.tsv', '\n'.join([
'id\tname\tequation',
'rxn_1\tReaction 1\t|A| => (2) |B|',
'rxn_2\tSecond reaction\t<=> |C|'
]))
reactions = list(native.parse_reaction_file(path))
self.assertEqual(len(reactions), 2)
self.assertEqual(reactions[0].id, 'rxn_1')
self.assertEqual(reactions[0].name, 'Reaction 1')
self.assertEqual(reactions[0].properties['name'], 'Reaction 1')
self.assertEqual(reactions[0].equation, Reaction(
Reaction.Right, [(Compound('A'), 1)], [(Compound('B'), 2)]))
self.assertEqual(reactions[0].ec, None)
self.assertEqual(reactions[0].genes, None)
self.assertEqual(reactions[0].filemark.filecontext.filepath, path)
self.assertEqual(reactions[0].filemark.line, 2)
self.assertEqual(reactions[1].id, 'rxn_2')
self.assertEqual(reactions[1].name, 'Second reaction')
self.assertEqual(reactions[1].equation, Reaction(
Reaction.Bidir, [], [(Compound('C'), 1)]))
self.assertEqual(reactions[1].filemark.filecontext.filepath, path)
self.assertEqual(reactions[1].filemark.line, 3)
def test_parse_reaction_table_file(self):
path = self.write_model_file(
'reactions.tsv', '\n'.join([
'id\tname\tequation', 'rxn_1\tReaction 1\t|A| => (2) |B|',
'rxn_2\tSecond reaction\t<=> |C|'
]))
reactions = list(native.parse_reaction_file(path))
self.assertEqual(len(reactions), 2)
self.assertEqual(reactions[0].id, 'rxn_1')
self.assertEqual(reactions[0].name, 'Reaction 1')
self.assertEqual(reactions[0].properties['name'], 'Reaction 1')
self.assertEqual(
reactions[0].equation,
Reaction(Direction.Forward, [(Compound('A'), 1)],
[(Compound('B'), 2)]))
self.assertEqual(reactions[0].properties.get('ec'), None)
self.assertEqual(reactions[0].genes, None)
self.assertEqual(reactions[0].filemark.filecontext.filepath, path)
self.assertEqual(reactions[0].filemark.line, 2)
self.assertEqual(reactions[1].id, 'rxn_2')
self.assertEqual(reactions[1].name, 'Second reaction')
self.assertEqual(reactions[1].equation,
Reaction(Direction.Both, [], [(Compound('C'), 1)]))
self.assertEqual(reactions[1].filemark.filecontext.filepath, path)
self.assertEqual(reactions[1].filemark.line, 3)
def test_parse_reaction_yaml_file(self):
path = self.write_model_file(
'reaction.yaml', '\n'.join([
'- id: rxn_1', ' equation: "|A| => |B|"', '- id: rxn_2',
' equation:', ' reversible: no', ' left:',
' - id: B', ' value: 1', ' right:',
' - id: A', ' value: 1'
]))
reactions = list(native.parse_reaction_file(path))
self.assertEqual(len(reactions), 2)
self.assertEqual(reactions[0].id, 'rxn_1')
self.assertEqual(reactions[1].id, 'rxn_2')
def test_parse_reaction_yaml_file(self):
path = self.write_model_file('reaction.yaml', '\n'.join([
'- id: rxn_1',
' equation: "|A| => |B|"',
'- id: rxn_2',
' equation:',
' reversible: no',
' left:',
' - id: B',
' value: 1',
' right:',
' - id: A',
' value: 1'
]))
reactions = list(native.parse_reaction_file(path))
self.assertEqual(len(reactions), 2)
self.assertEqual(reactions[0].id, 'rxn_1')
self.assertEqual(reactions[1].id, 'rxn_2')
