def test_set_solute_moles_should_fail(self):
solute = message_helpers.build_compound(name='Solute')
solvent = message_helpers.build_compound(name='Solvent')
with self.assertRaisesRegex(ValueError, 'defined volume'):
message_helpers.set_solute_moles(solute, [solvent], '10 mM')
solute = message_helpers.build_compound(name='Solute', amount='1 mol')
solvent = message_helpers.build_compound(name='Solvent', amount='1 L')
with self.assertRaisesRegex(ValueError, 'overwrite'):
message_helpers.set_solute_moles(solute, [solvent], '10 mM')
def test_set_solute_moles(self):
solute = message_helpers.build_compound(name='Solute')
solvent2 = message_helpers.build_compound(name='Solvent',
amount='100 mL')
message_helpers.set_solute_moles(solute, [solvent2], '1 molar')
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='MILLIMOLE', value=100))
solvent3 = message_helpers.build_compound(name='Solvent',
amount='75 uL')
message_helpers.set_solute_moles(solute, [solvent3],
'3 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=225))
solvent4 = message_helpers.build_compound(name='Solvent',
amount='0.2 uL')
message_helpers.set_solute_moles(solute, [solvent4],
'30 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=6))
solvent5 = message_helpers.build_compound(name='Solvent',
amount='0.8 uL')
message_helpers.set_solute_moles(solute, [solvent4, solvent5],
'30 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=30))
def resolve_input(input_string):
"""Resolve a text-based description of an input in one of the following
formats:
(1) [AMOUNT] of [NAME]
(2) [AMOUNT] of [CONCENTRATION] [SOLUTE] in [SOLVENT]
Args:
input_string: String describing the input.
Returns:
ReactionInput message.
Raises:
ValueError: if the string cannot be parsed properly.
"""
reaction_input = reaction_pb2.ReactionInput()
if ' of ' not in input_string:
raise ValueError('String does not match template!')
amount_string, description = input_string.split(' of ')
if ' in ' not in description:
component_name = description
component = reaction_input.components.add()
component.CopyFrom(
message_helpers.build_compound(name=component_name.strip(),
amount=amount_string))
resolve_names(reaction_input)
return reaction_input
pattern = re.compile(r'(\d+.?\d*)\s?(\w+)\s(.+)\sin\s(.+)')
match = pattern.fullmatch(description.strip())
if not match:
raise ValueError('String did not match template!')
conc_value, conc_units, solute_name, solvent_name = match.groups()
solute = reaction_input.components.add()
solvent = reaction_input.components.add()
solute.CopyFrom(message_helpers.build_compound(name=solute_name.strip()))
solvent.CopyFrom(
message_helpers.build_compound(name=solvent_name.strip(),
amount=amount_string))
if solvent.amount.WhichOneof('kind') != 'volume':
raise ValueError('Total amount of solution must be a volume!')
solvent.amount.volume_includes_solutes = True
message_helpers.set_solute_moles(solute, [solvent],
f'{conc_value} {conc_units}')
resolve_names(reaction_input)
return reaction_input