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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,79 +1,79 @@ | ||
| # from biosimulators_utils.model_lang.rba.utils import get_parameters_variables_outputs_for_simulation | ||
| # from biosimulators_utils.sedml.data_model import SteadyStateSimulation | ||
| # import math | ||
| # import os | ||
| # import unittest | ||
| # | ||
| # | ||
| # class RbaUtilsTestCase(unittest.TestCase): | ||
| # FIXTURES_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba') | ||
| # | ||
| # def test_get_parameters_variables_for_simulation(self): | ||
| # filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| # params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation) | ||
| # | ||
| # self.assertEqual(len(params), 1620) | ||
| # | ||
| # param = next(param for param in params if param.id == 'parameter_amino_acid_concentration_Y_MIN') | ||
| # self.assertEqual(param.name, 'Value of parameter "Y_MIN" of function "amino_acid_concentration"') | ||
| # self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN') | ||
| # self.assertEqual(param.new_value, '-inf') | ||
| # | ||
| # self.assertEqual(len(sims), 1) | ||
| # sim = sims[0] | ||
| # self.assertIsInstance(sim, SteadyStateSimulation) | ||
| # self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669') | ||
| # self.assertEqual(sim.algorithm.changes, []) | ||
| # | ||
| # self.assertEqual(len(vars), 15766) | ||
| # | ||
| # self.assertEqual(vars[0].id, 'objective') | ||
| # self.assertEqual(vars[0].name, 'Value of objective') | ||
| # self.assertEqual(vars[0].target, 'objective') | ||
| # | ||
| # var = next(var for var in vars if var.id == 'M_pqq_p') | ||
| # self.assertEqual(var.name, 'Dual of constraint "M_pqq_p"') | ||
| # self.assertEqual(var.target, 'constraints.M_pqq_p') | ||
| # | ||
| # var = next(var for var in vars if var.id == 'test_process_2_machinery') | ||
| # self.assertEqual(var.name, 'Primal of variable "test_process_2_machinery"') | ||
| # self.assertEqual(var.target, 'variables.test_process_2_machinery') | ||
| # | ||
| # def test_get_parameters_variables_for_simulation_native_ids_data_types(self): | ||
| # filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| # params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation, native_ids=True, native_data_types=True) | ||
| # | ||
| # self.assertEqual(len(params), 1620) | ||
| # | ||
| # param = next(param for param in params if param.id == 'amino_acid_concentration.Y_MIN') | ||
| # self.assertEqual(param.name, None) | ||
| # self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN') | ||
| # self.assertEqual(param.new_value, -math.inf) | ||
| # | ||
| # self.assertEqual(len(sims), 1) | ||
| # sim = sims[0] | ||
| # self.assertIsInstance(sim, SteadyStateSimulation) | ||
| # self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669') | ||
| # self.assertEqual(sim.algorithm.changes, []) | ||
| # | ||
| # self.assertEqual(len(vars), 15766) | ||
| # | ||
| # self.assertEqual(vars[0].id, None) | ||
| # self.assertEqual(vars[0].name, None) | ||
| # self.assertEqual(vars[0].target, 'objective') | ||
| # | ||
| # var = next(var for var in vars if var.id == 'M_pqq_p') | ||
| # self.assertEqual(var.name, None) | ||
| # self.assertEqual(var.target, 'constraints.M_pqq_p') | ||
| # | ||
| # var = next(var for var in vars if var.id == 'test_process_2_machinery') | ||
| # self.assertEqual(var.name, None) | ||
| # self.assertEqual(var.target, 'variables.test_process_2_machinery') | ||
| # | ||
| # def test_get_parameters_variables_for_simulation_error_handling(self): | ||
| # with self.assertRaises(ValueError): | ||
| # get_parameters_variables_outputs_for_simulation(None, None, None) | ||
| # | ||
| # filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| # with self.assertRaises(NotImplementedError): | ||
| # get_parameters_variables_outputs_for_simulation(filename, None, None) | ||
| from biosimulators_utils.model_lang.rba.utils import get_parameters_variables_outputs_for_simulation | ||
| from biosimulators_utils.sedml.data_model import SteadyStateSimulation | ||
| import math | ||
| import os | ||
| import unittest | ||
|
|
||
|
|
||
| class RbaUtilsTestCase(unittest.TestCase): | ||
| FIXTURES_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba') | ||
|
|
||
| def test_get_parameters_variables_for_simulation(self): | ||
| filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation) | ||
|
|
||
| self.assertEqual(len(params), 1620) | ||
|
|
||
| param = next(param for param in params if param.id == 'parameter_amino_acid_concentration_Y_MIN') | ||
| self.assertEqual(param.name, 'Value of parameter "Y_MIN" of function "amino_acid_concentration"') | ||
| self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN') | ||
| self.assertEqual(param.new_value, '-inf') | ||
|
|
||
| self.assertEqual(len(sims), 1) | ||
| sim = sims[0] | ||
| self.assertIsInstance(sim, SteadyStateSimulation) | ||
| self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669') | ||
| self.assertEqual(sim.algorithm.changes, []) | ||
|
|
||
| self.assertEqual(len(vars), 15766) | ||
|
|
||
| self.assertEqual(vars[0].id, 'objective') | ||
| self.assertEqual(vars[0].name, 'Value of objective') | ||
| self.assertEqual(vars[0].target, 'objective') | ||
|
|
||
| var = next(var for var in vars if var.id == 'M_pqq_p') | ||
| self.assertEqual(var.name, 'Dual of constraint "M_pqq_p"') | ||
| self.assertEqual(var.target, 'constraints.M_pqq_p') | ||
|
|
||
| var = next(var for var in vars if var.id == 'test_process_2_machinery') | ||
| self.assertEqual(var.name, 'Primal of variable "test_process_2_machinery"') | ||
| self.assertEqual(var.target, 'variables.test_process_2_machinery') | ||
|
|
||
| def test_get_parameters_variables_for_simulation_native_ids_data_types(self): | ||
| filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation, native_ids=True, native_data_types=True) | ||
|
|
||
| self.assertEqual(len(params), 1620) | ||
|
|
||
| param = next(param for param in params if param.id == 'amino_acid_concentration.Y_MIN') | ||
| self.assertEqual(param.name, None) | ||
| self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN') | ||
| self.assertEqual(param.new_value, -math.inf) | ||
|
|
||
| self.assertEqual(len(sims), 1) | ||
| sim = sims[0] | ||
| self.assertIsInstance(sim, SteadyStateSimulation) | ||
| self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669') | ||
| self.assertEqual(sim.algorithm.changes, []) | ||
|
|
||
| self.assertEqual(len(vars), 15766) | ||
|
|
||
| self.assertEqual(vars[0].id, None) | ||
| self.assertEqual(vars[0].name, None) | ||
| self.assertEqual(vars[0].target, 'objective') | ||
|
|
||
| var = next(var for var in vars if var.id == 'M_pqq_p') | ||
| self.assertEqual(var.name, None) | ||
| self.assertEqual(var.target, 'constraints.M_pqq_p') | ||
|
|
||
| var = next(var for var in vars if var.id == 'test_process_2_machinery') | ||
| self.assertEqual(var.name, None) | ||
| self.assertEqual(var.target, 'variables.test_process_2_machinery') | ||
|
|
||
| def test_get_parameters_variables_for_simulation_error_handling(self): | ||
| with self.assertRaises(ValueError): | ||
| get_parameters_variables_outputs_for_simulation(None, None, None) | ||
|
|
||
| filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| with self.assertRaises(NotImplementedError): | ||
| get_parameters_variables_outputs_for_simulation(filename, None, None) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,40 +1,40 @@ | ||
| # from biosimulators_utils.model_lang.rba import validation | ||
| # from biosimulators_utils.utils.core import flatten_nested_list_of_strings | ||
| # import os | ||
| # import rba | ||
| # import unittest | ||
| # | ||
| # | ||
| # class RbaValidationTestCase(unittest.TestCase): | ||
| # FIXTURE_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba') | ||
| # | ||
| # def test(self): | ||
| # filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| # errors, warnings, model = validation.validate_model(filename) | ||
| # self.assertEqual(errors, []) | ||
| # self.assertEqual(warnings, []) | ||
| # self.assertIsInstance(model, rba.model.RbaModel) | ||
| # | ||
| # filename = None | ||
| # errors, warnings, model = validation.validate_model(filename) | ||
| # self.assertIn('is not a path', flatten_nested_list_of_strings(errors)) | ||
| # self.assertEqual(warnings, []) | ||
| # self.assertEqual(model, None) | ||
| # | ||
| # filename = os.path.join(self.FIXTURE_DIRNAME, 'not exist.zip') | ||
| # errors, warnings, model = validation.validate_model(filename) | ||
| # self.assertIn('does not exist', flatten_nested_list_of_strings(errors)) | ||
| # self.assertEqual(warnings, []) | ||
| # self.assertEqual(model, None) | ||
| # | ||
| # filename = __file__ | ||
| # errors, warnings, model = validation.validate_model(filename) | ||
| # self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors)) | ||
| # self.assertEqual(warnings, []) | ||
| # self.assertEqual(model, None) | ||
| # | ||
| # filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT-invalid.zip') | ||
| # errors, warnings, model = validation.validate_model(filename) | ||
| # self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors)) | ||
| # self.assertEqual(warnings, []) | ||
| # self.assertEqual(model, None) | ||
| from biosimulators_utils.model_lang.rba import validation | ||
| from biosimulators_utils.utils.core import flatten_nested_list_of_strings | ||
| import os | ||
| import rba | ||
| import unittest | ||
|
|
||
|
|
||
| class RbaValidationTestCase(unittest.TestCase): | ||
| FIXTURE_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba') | ||
|
|
||
| def test(self): | ||
| filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT.zip') | ||
| errors, warnings, model = validation.validate_model(filename) | ||
| self.assertEqual(errors, []) | ||
| self.assertEqual(warnings, []) | ||
| self.assertIsInstance(model, rba.model.RbaModel) | ||
|
|
||
| filename = None | ||
| errors, warnings, model = validation.validate_model(filename) | ||
| self.assertIn('is not a path', flatten_nested_list_of_strings(errors)) | ||
| self.assertEqual(warnings, []) | ||
| self.assertEqual(model, None) | ||
|
|
||
| filename = os.path.join(self.FIXTURE_DIRNAME, 'not exist.zip') | ||
| errors, warnings, model = validation.validate_model(filename) | ||
| self.assertIn('does not exist', flatten_nested_list_of_strings(errors)) | ||
| self.assertEqual(warnings, []) | ||
| self.assertEqual(model, None) | ||
|
|
||
| filename = __file__ | ||
| errors, warnings, model = validation.validate_model(filename) | ||
| self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors)) | ||
| self.assertEqual(warnings, []) | ||
| self.assertEqual(model, None) | ||
|
|
||
| filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT-invalid.zip') | ||
| errors, warnings, model = validation.validate_model(filename) | ||
| self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors)) | ||
| self.assertEqual(warnings, []) | ||
| self.assertEqual(model, None) |
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