def test_calculate_max_number_activities(self):
# model with activities, archive with results that have add activity in interventions
a1 = mnm_repr.Activity('act1', None, ['a'], [])
a2 = mnm_repr.Activity('act1', None, ['b'], [])
a3 = mnm_repr.Activity('act1', None, ['c'], [])
a4 = mnm_repr.Activity('act1', None, ['d'], [])
base_model = mnm_repr.Model('m1', [], [a1], [])
des1 = exp_repr.ExperimentDescription(
None, [mnm_repr.Add(a2), mnm_repr.Add(a1)])
des2 = exp_repr.ExperimentDescription(None, [mnm_repr.Add(a3)])
des3 = exp_repr.ExperimentDescription(
None, [mnm_repr.Add(a4), mnm_repr.Add(a3)])
res1 = exp_repr.Result('r1', des1, None)
res2 = exp_repr.Result('r2', des2, None)
res3 = exp_repr.Result('r3', des3, None)
exp1 = exp_repr.Experiment('exp1', [res1])
exp2 = exp_repr.Experiment('exp2', [res2])
exp3 = exp_repr.Experiment('exp3', [res3])
arch = Archive()
arch.known_results = [exp1, exp2, exp3]
rev = RevisionModule(arch)
out = rev.calculate_max_number_activities(base_model)
self.assertEqual(out, 4)
def test_apply_multiple_interventions(self):
intervention1 = mnm_repr.Add(self.con1)
intervention2 = mnm_repr.Remove(self.con1)
intervention3 = mnm_repr.Add(self.act1)
intervention4 = mnm_repr.Remove(self.act1)
setup_conds = [self.con2]
interm_activs = [self.act2]
term_conds = [self.con3, self.con4]
model = mnm_repr.Model('ID', setup_conds, interm_activs, term_conds)
model.apply_interventions(
[intervention1, intervention2, intervention3, intervention4])
self.assertEqual(model.setup_conditions, frozenset([self.con2]))
self.assertEqual(model.intermediate_activities, frozenset([self.act2]))
def test_make_derivative_models(self):
rev = RevisionModule('archive')
cond_subst_1 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_subst_2 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
base_model = mnm_repr.Model(
'm1', [cond_subst_1], [],
[]) #model that is compatible with interventions
second_mod = mnm_repr.Model('deriv_m1_0', [cond_subst_1, cond_subst_2],
[], [])
third_mod = mnm_repr.Model('deriv_m1_1', [], [], [])
exd1 = exp_repr.ExperimentDescription(None,
[mnm_repr.Add(cond_subst_2)])
exd2 = exp_repr.ExperimentDescription(None,
[mnm_repr.Remove(cond_subst_1)])
res1 = exp_repr.Result('r1', exd1, True)
res2 = exp_repr.Result('r2', exd2, True)
extracted_results = [res1, res2] #need interventions in description
models_results = rev.make_derivative_models(base_model,
extracted_results)
self.assertEqual(models_results, {
base_model: [],
second_mod: [res1],
third_mod: [res2]
})
def test_apply_intervention_add_activity(self):
intervention = mnm_repr.Add(self.act1)
setup_conds = [self.con1, self.con2]
interm_activs = [self.act2]
term_conds = [self.con3, self.con4]
model = mnm_repr.Model('ID', setup_conds, interm_activs, term_conds)
model.apply_intervention(intervention)
self.assertEqual(model.intermediate_activities,
frozenset([self.act2, self.act1]))
def test_ban_experiment(self):
comp = mnm_repr.Medium()
ent1 = mnm_repr.Metabolite('m1')
cond1 = mnm_repr.PresentEntity(ent1, comp)
inter1 = mnm_repr.Add(cond1)
ent2 = mnm_repr.Metabolite('m2')
cond2 = mnm_repr.PresentEntity(ent2, comp)
inter2 = mnm_repr.Remove(cond2)
exp_description = exp_repr.ExperimentDescription(
exp_repr.DetectionEntity('ent1'), [inter1, inter2])
out = exporter.ban_experiment(exp_description)
# print([out])
self.assertIn('\n:- designed(experiment(detection_entity_exp, ent1))',
out)
self.assertIn(',remove(setup_present(m2, none, c_01))', out)
self.assertIn(',add(setup_present(m1, none, c_01))', out)
def create_revised_models(self, base_model, solution):
interv_add = [
mnm_repr.Add(self.archive.get_matching_element(e_id))
for e_id in solution[0]
]
interv_rem = [
mnm_repr.Remove(self.archive.get_matching_element(e_id))
for e_id in solution[1]
]
covered_res = [
self.archive.get_matching_result(res_id) for res_id in solution[2]
]
ignored_res = [
self.archive.get_matching_result(res_id) for res_id in solution[3]
]
new_model = copy(base_model)
new_model.apply_interventions(interv_rem)
new_model.apply_interventions(interv_add)
new_model.results_covered = frozenset(covered_res)
new_model.ignored_results = frozenset(ignored_res)
return new_model
def generate_all_possible(self, entities, compartments, activities,
setup_conds, import_activities):
# exp types:
self.types = {
DetectionEntity: None,
AdamTwoFactorExperiment: None,
ReconstructionActivity: None,
ReconstructionEnzReaction: None,
ReconstructionTransporterRequired: None,
LocalisationEntity: None,
DetectionActivity: None
}
# compartments for checking localisation:
self.design_compartment = {
'c_02': None,
'c_03': None,
'c_04': None,
'c_05': None,
'c_06': None,
'c_07': None,
'c_08': None,
'c_09': None,
'c_10': None,
'c_11': None,
'c_12': None,
'c_13': None,
'c_14': None,
'c_15': None,
'c_16': None,
'c_17': None,
'c_18': None,
'c_19': None,
'c_20': None,
'c_21': None,
'c_22': None,
'c_23': None,
'c_24': None,
'c_25': None,
'c_26': None,
'c_27': None,
'c_28': None,
'c_29': None,
'c_30': None,
'c_31': None,
'c_32': None,
'c_33': None,
'c_34': None
}
# rest of elements:
self.design_deletable = {}
self.design_available = {}
self.design_activity_rec = {}
self.design_activity_det = {}
self.design_entity_loc = {}
self.design_entity_det = {}
self.intervention_add = {}
self.intervention_remove = {}
#
for act in import_activities:
self.intervention_add[mnm_repr.Add(act)] = 1
#
for st in setup_conds:
# all genes can be removed; metabs can only be removed from medium
if (isinstance(st.entity, mnm_repr.Gene)
or isinstance(st.compartment, Medium)):
self.intervention_remove[mnm_repr.Remove(st)] = None
if isinstance(st.entity, mnm_repr.Gene):
self.design_deletable[st.entity] = None
#
for ent in entities:
if isinstance(ent, mnm_repr.Gene):
continue
else: # Met, Prot, Cplx
self.design_available[ent] = None
self.design_entity_det[ent] = None
if isinstance(ent, mnm_repr.Metabolite):
self.intervention_add[mnm_repr.Add(
mnm_repr.PresentEntity(ent, Medium()))] = None
else: # Prot, Cplx
self.design_entity_loc[ent] = None
#
for act in activities:
# don't test these additional import reactions: they're only to help with experiments
if act in import_activities:
continue
elif isinstance(act, mnm_repr.Growth):
self.design_activity_det[act] = None
else:
self.design_activity_rec[act] = None