def prepare_input_for_exp_design(self): exported = [] exported.extend(exporter.hide_show_statements()) # export hide/show stuff exported.extend(exporter.export_compartments(self.archive.mnm_compartments)) exported.extend(exporter.export_entities(self.archive.mnm_entities)) exported.extend(exporter.export_activities(self.archive.mnm_activities + self.archive.import_activities)) exported.extend(exporter.export_models_exp_design(self.archive.working_models)) # export models info exported.extend(exporter.models_nr_and_probabilities(self.archive.working_models)) # + probabilities and numbers exported.append(exporter.modeh_replacement(self.cost_model)) # export design elements (modeh eqiv) exported.extend(exporter.design_constraints_basic()) # export rules forcing and restricting exp design for exp in self.archive.known_results: exp_descriptions = [res.exp_description for res in exp.results] for des in exp_descriptions: exported.extend(exporter.ban_experiment(des)) # export ban experiment(s) (from old exps) exported.append(exporter.constant_for_calculating_score(self.calculate_constant_for_scores())) # calculate constant for scores and export it exported.extend(exporter.advanced_exp_design_rules()) # export scoring rules/optimisation if self.use_costs: # * export cost, and optimisation rule for that exported.extend(exporter.cost_rules(self.cost_model)) exported.extend(exporter.cost_minimisation_rules()) else: pass exported.extend(exporter.experiment_design_rules()) # export design rules exported.extend(exporter.interventions_rules()) exported.extend(exporter.predictions_rules()) exported.extend(exporter.models_rules(len(self.archive.mnm_activities + self.archive.import_activities))) return exported
def prepare_input_elements(self): exped_entities = exporter.export_entities(self.archive.mnm_entities) exped_compartments = exporter.export_compartments(self.archive.mnm_compartments) exped_activities = exporter.export_activities(self.archive.mnm_activities + self.archive.import_activities) # not flattened output = [exped_entities, exped_compartments, exped_activities] # flattened return [val for sublist in output for val in sublist]
def test_export_entities_properties(self):
# entity with properties to test the second part of the method
ent3 = mnm_repr.Protein('e3', 'none', 'none', [mnm_repr.Catalyses(mnm_repr.Activity('a1', None, [], []))])
ent4 = mnm_repr.Complex('e4', 'none', 'none', [mnm_repr.Transports(mnm_repr.Activity('a2', None, [], []))])
exported = exporter.export_entities([ent3, ent4])
self.assertEqual("\nprotein(e3,none).", exported[0])
self.assertEqual("\ncatalyses(e3,none,a1).", exported[1])
self.assertEqual("\ncomplex(e4,none).", exported[2])
self.assertEqual("\ntransports(e4,none,a2).", exported[3])
def prepare_input_elements(self):
exped_entities = exporter.export_entities(self.archive.mnm_entities)
exped_compartments = exporter.export_compartments(
self.archive.mnm_compartments)
exped_activities = exporter.export_activities(
self.archive.mnm_activities + self.archive.import_activities)
# not flattened
output = [exped_entities, exped_compartments, exped_activities]
# flattened
return [val for sublist in output for val in sublist]
def test_export_entities_alone(self):
# get one of entity types; no need to test all (they do the same thing)
ent1 = mnm_repr.Gene('e1')
ent2 = mnm_repr.Metabolite('e2')
ent3 = mnm_repr.Protein('e3')
ent4 = mnm_repr.Complex('e4')
exported = exporter.export_entities([ent1, ent2, ent3, ent4])
self.assertEqual("\ngene(e1,none).", exported[0])
self.assertEqual("\nmetabolite(e2,none).", exported[1])
self.assertEqual("\nprotein(e3,none).", exported[2])
self.assertEqual("\ncomplex(e4,none).", exported[3])
def test_export_entities_alone(self):
# get one of entity types; no need to test all (they do the same thing)
ent1 = mnm_repr.Gene('e1')
ent2 = mnm_repr.Metabolite('e2')
ent3 = mnm_repr.Protein('e3')
ent4 = mnm_repr.Complex('e4')
exported = exporter.export_entities([ent1, ent2, ent3, ent4])
self.assertEqual("\ngene(e1,none).", exported[0])
self.assertEqual("\nmetabolite(e2,none).", exported[1])
self.assertEqual("\nprotein(e3,none).", exported[2])
self.assertEqual("\ncomplex(e4,none).", exported[3])
def test_export_entities_properties(self):
# entity with properties to test the second part of the method
ent3 = mnm_repr.Protein(
'e3', 'none', 'none',
[mnm_repr.Catalyses(mnm_repr.Activity('a1', None, [], []))])
ent4 = mnm_repr.Complex(
'e4', 'none', 'none',
[mnm_repr.Transports(mnm_repr.Activity('a2', None, [], []))])
exported = exporter.export_entities([ent3, ent4])
self.assertEqual("\nprotein(e3,none).", exported[0])
self.assertEqual("\ncatalyses(e3,none,a1).", exported[1])
self.assertEqual("\ncomplex(e4,none).", exported[2])
self.assertEqual("\ntransports(e4,none,a2).", exported[3])
def prepare_input_in_vivo(self, expD): copied_model = copy(self.model) copied_model.ID = 'copied_%s' % self.model.ID copied_model.apply_interventions(expD.interventions) exported_ent = exporter.export_entities(self.all_ent) exported_comp = exporter.export_compartments(self.all_comp) exported_act = exporter.export_activities(self.all_act + self.archive.import_activities) exported_model = exporter.export_models_exp_design([copied_model]) exported_model_rules = exporter.models_rules(len(copied_model.intermediate_activities)) exported_display = exporter.export_display_for_oracle(expD) exported_prediction_rules = exporter.predictions_rules() inp = [exported_display, exported_ent, exported_comp, exported_act, exported_model, exported_prediction_rules, exported_model_rules] inp = [val for sublist in inp for val in sublist] return inp
def prepare_input_for_exp_design(self):
exported = []
# export hide/show stuff
exported.extend(exporter.hide_show_statements())
exported.extend(
exporter.export_compartments(self.archive.mnm_compartments))
exported.extend(exporter.export_entities(self.archive.mnm_entities))
exported.extend(
exporter.export_activities(self.archive.mnm_activities +
self.archive.import_activities))
# export models info
exported.extend(
exporter.export_models_exp_design(self.archive.working_models))
# + probabilities and numbers
exported.extend(
exporter.models_nr_and_probabilities(self.archive.working_models))
# export design elements (modeh eqiv)
exported.append(exporter.modeh_replacement(self.cost_model))
# export rules forcing and restricting exp design
exported.extend(exporter.design_constraints_basic())
for exp in self.archive.known_results:
exp_descriptions = [res.exp_description for res in exp.results]
for des in exp_descriptions:
# export ban experiment(s) (from old exps)
exported.extend(exporter.ban_experiment(des))
# calculate constant for scores and export it
exported.append(
exporter.constant_for_calculating_score(
self.calculate_constant_for_scores()))
# export scoring rules/optimisation
exported.extend(exporter.advanced_exp_design_rules())
# * export cost, and optimisation rule for that
if self.use_costs:
exported.extend(exporter.cost_rules(self.cost_model))
exported.extend(exporter.cost_minimisation_rules())
else:
pass
# export design rules
exported.extend(exporter.experiment_design_rules())
exported.extend(exporter.interventions_rules())
exported.extend(exporter.predictions_rules())
exported.extend(
exporter.models_rules(
len(self.archive.mnm_activities +
self.archive.import_activities)))
return exported