"""
==================================
Metabolism using user-friendly FBA
==================================
"""
import argparse
# vivarium-core imports
import pytest
# vivarium-ecoli imports
from ecoli.experiments.ecoli_master_sim import EcoliSim, CONFIG_DIR_PATH
from ecoli.library.json_state import get_state_from_file
import numpy as np
import pathlib
import datetime
import dill
# disables growth rate control
[docs]
def run_colony(
filename='metabolism_redux_classic',
total_time=1500,
divide=True,
# initial_state_file='wcecoli_t0', # 'met_division_test_state',
progress_bar=True,
log_updates=False,
emitter='timeseries', # 'timeseries',
name='metabolism-redux-classic-rich',
raw_output=False,
save=True,
save_times=[1, 200, 400, 1300],
condition = "with_aa", # basal, with_aa
fixed_media = "minimal_plus_amino_acids" # minimal, minimal_plus_amino_acids
):
# filename = 'default'
sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")
sim.total_time = total_time
sim.divide = divide
sim.progress_bar = progress_bar
sim.log_updates = log_updates
sim.emitter = emitter
# sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
sim.raw_output = raw_output
sim.save = save
sim.save_times = save_times
sim.condition = condition
sim.fixed_media = fixed_media
for seed in [i for i in range(20, 29, 1)]:
sim.seed = seed
sim.build_ecoli()
sim.run()
query = []
folder = f'out/cofactors/rich-{seed}/'
save_sim_output(folder, query, sim, save_model=False)
@pytest.mark.slow
def test_ecoli_with_metabolism_redux(
filename='metabolism_redux',
total_time=4,
divide=False,
progress_bar=True,
log_updates=False,
emitter='timeseries',
):
sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
sim.total_time = total_time
sim.divide = divide
sim.progress_bar = progress_bar
sim.log_updates = log_updates
sim.emitter = emitter
sim.build_ecoli()
# run simulation and add asserts to output
sim.run()
@pytest.mark.slow
def test_ecoli_with_metabolism_redux_div(
filename='metabolism_redux',
total_time=4,
divide=True,
emitter='timeseries',
):
# TODO (Cyrus) - Add test that affirms structure of output query.
sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
sim.total_time = total_time
sim.divide = divide
sim.emitter = emitter
sim.build_ecoli()
sim.run()
query = []
agents = sim.query()['agents'].keys()
for agent in agents:
query.extend([('agents', agent, 'listeners', 'fba_results'),
('agents', agent, 'listeners', 'mass'),
('agents', agent, 'bulk')])
output = sim.query(query)
# test that water is being used (model is running)
assert sum(output['agents'][agent]['listeners']['fba_results']['estimated_exchange_dmdt']['WATER']) != 0
@pytest.mark.slow
def test_ecoli_with_metabolism_classic(
filename='metabolism_redux_classic',
total_time=4,
divide=False,
progress_bar=True,
log_updates=False,
emitter='timeseries',
):
sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
sim.total_time = total_time
sim.divide = divide
sim.progress_bar = progress_bar
sim.log_updates = log_updates
sim.emitter = emitter
sim.build_ecoli()
# run simulation and add asserts to output
sim.run()
# @pytest.mark.slow
# def test_ecoli_with_metabolism_classic_div(
# filename='metabolism_redux_classic',
# total_time=10,
# divide=True,
# emitter='timeseries',
# initial_state_file='met_division_test_state',
# ):
# # TODO (Cyrus) - Add test that affirms structure of output query.
# sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + '.json')
# sim.total_time = total_time
# sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
#
# sim.divide = divide
# sim.emitter = emitter
#
# # this means that sims will not create conflicting random indices
# sim.seed += int(sim.initial_state['agents']['0']['global_time'])
#
# sim.build_ecoli()
#
# sim.run()
#
# # assert division occured
# assert len(sim.query()['agents']) == 3, "Cell did not divide in metabolism division test"
experiment_library = {
'2': run_ecoli_with_metabolism_redux,
'2a': run_ecoli_with_metabolism_redux_classic,
'2b': run_colony,
'3': test_ecoli_with_metabolism_redux,
'3a': test_ecoli_with_metabolism_classic,
'4': test_ecoli_with_metabolism_redux_div,
'5': run_ecoli_with_default_metabolism,
}
[docs]
def save_sim_output(folder, query, sim, save_model=False):
agents = sim.query()['agents'].keys()
for agent in agents:
query = []
query.extend([('agents', agent, 'listeners', 'fba_results'),
('agents', agent, 'listeners', 'mass'),
('agents', agent, 'listeners', 'unique_molecule_counts'),
('agents', agent, 'bulk')])
output = sim.query(query)
pathlib.Path(folder).mkdir(parents=True, exist_ok=True)
np.save(folder + f'{agent}_output.npy', output)
if save_model:
f = open(folder + 'agent_steps.pkl', 'wb')
dill.dump(sim.ecoli_experiment.steps['agents'][agent], f)
f.close()
# run experiments with command line arguments: python ecoli/experiments/metabolism_redux_sim.py -n exp_id
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='user-friendly metabolism')
parser.add_argument('--name', '-n', default=[], nargs='+', help='test ids to run')
args = parser.parse_args()
run_all = not args.name
for name in args.name:
experiment_library[name]()
if run_all:
for name, test in experiment_library.items():
test()