def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelx8Ow70.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
response_create_experiment = c.post('/data/', {
'action': 'save',
'experiment_id': "",
'experiment_name': "Enzymatic reaction",
'experiment_notes': "Something"
})
self.assertEqual(response_create_experiment.status_code, 200)
self.assertEqual(
[experiment.name for experiment in response_create_experiment.context['experimental_data']],
[u'Enzymatic reaction']
)
experiment_id = response_create_experiment.context['experimental_data'][0].id
# Testing conditions
response_choose_experiment = c.get('/data/%d/' % experiment_id)
self.assertEqual(response_choose_experiment.status_code, 200)
self.assertEqual(response_choose_experiment.context['experiment_name'], u'Enzymatic reaction')
self.assertEqual(
[condition.name for condition in response_choose_experiment.context['conditions']],
[]
)
response_new_condition = c.post('/data/%d/' % experiment_id, {
'action': 'save',
'condition_id': "",
'condition_name': "Test condition",
'condition_notes': "Some notes"
})
self.assertEqual(response_new_condition.status_code, 200)
self.assertEqual(
[condition.name for condition in response_new_condition.context['conditions']],
[u'Test condition']
)
condition_id = response_new_condition.context['conditions'][0].id
response_choose_experiment = c.get('/data/%d/%d/' % (experiment_id, condition_id))
self.assertEqual(response_choose_experiment.status_code, 200)
self.assertEqual(len(response_choose_experiment.context['experiment_initial_data']), 0)
response_add_treatment = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'treatment',
'action': 'save',
'id': "",
'name': 'Substrate',
'time': 0,
'value': 15
})
self.assertEqual(response_add_treatment.status_code, 200)
self.assertEqual(len(response_add_treatment.context['experiment_initial_data']), 1)
self.assertEqual(len(response_add_treatment.context['experiment_data']), 0)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 0,
'value': 0,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 1)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 10,
'value': 10,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 2)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 20,
'value': 15,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 3)
response_add_observation = c.post('/data/%d/%d/' % (experiment_id, condition_id), {
'data_type': 'observation',
'action': 'save',
'id': "",
'name': 'Product',
'time': 50,
'value': 15,
'stddev': 0,
'steady_state': 'off',
'min_steady_state': "0",
'max_steady_state': "0"
})
self.assertEqual(response_add_observation.status_code, 200)
self.assertEqual(len(response_add_observation.context['experiment_data']), 4)
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual(
[dataset for dataset in response_get_fit_data.context['experimental_data_sets']],
[u'Enzymatic reaction']
)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {
'dataset_ind': 0
})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(SbmlModel.objects.filter(project=project)[0].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())), ['Product', 'Substrate'])
self.assertEqual(doc.model.listOfSpecies.index(doc.getByXPath(mapping['Substrate'])), 0)
self.assertEqual(doc.model.listOfSpecies.index(doc.getByXPath(mapping['Product'])), 3)
response_create_optimization = c.post('/fit/data/', {
'action': 'create',
'dataset_0': experiment_id,
'list_dataset_0_data_species_0_value': "Product",
'list_dataset_0_species_0_value': 3,
'list_dataset_0_data_species_1_value': "Substrate",
'list_dataset_0_species_1_value': 0,
'parameter_0_active': "on",
'parameter_0_id': 0,
'parameter_0_name': "Binding rate",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 0,
'parameter_1_name': "Unbinding rate",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-4,
'parameter_1_max': 1e+4,
'parameter_1_precision': 7,
'parameter_2_active': "on",
'parameter_2_id': 0,
'parameter_2_name': "Catalytic rate",
'parameter_2_value': 1.0,
'parameter_2_min': 1e-4,
'parameter_2_max': 1e+4,
'parameter_2_precision': 7,
'nb_cores': 2,
'lambda': 0.001,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 2000,
'freeze_count': 100,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(response_create_optimization.context['form'].getErrors(), [])
sleep(5)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Running")
sleep(10)
response_get_optimization = c.get('/fit/%s/' % response_list_optimizations.context['optimizations'][0][0].optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
sleep(240)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Finished")
response_get_optimization = c.get(
'/fit/%s/' % response_list_optimizations.context['optimizations'][0][0].optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores)-1] < 0.24)
def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project,
'/models/',
status_code=302,
target_status_code=200)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
files_folder = join(dirname(__file__), "files")
comp_files_folder = join(files_folder, "comp_model")
model_filename = join(comp_files_folder, "modelcEvRcX.xml")
response_load_submodel_1 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_1.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model_filename = join(comp_files_folder, "modelEHfev9.xml")
response_load_submodel_2 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_2.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 2)
model_filename = join(comp_files_folder, "modelI1vrys.xml")
response_load_submodel_3 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_3.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 3)
model_filename = join(comp_files_folder, "modelz9xdww.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 4)
response_choose_model = c.post('/fit/data/', {
'action': 'choose_model',
'model_id': 3
})
self.assertEqual(response_choose_model.status_code, 200)
experiment_filename = join(files_folder, "ras_data.xml")
response_import_data = c.post(
'/data/', {
'action': 'import',
'docfile': open(experiment_filename, 'rb')
})
self.assertEqual(response_import_data.status_code, 200)
self.assertEqual([
experiment.name
for experiment in response_import_data.context['experimental_data']
], [u'Ras-GTP quantifications'])
experiment_id = response_import_data.context['experimental_data'][0].id
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual([
dataset for dataset in
response_get_fit_data.context['experimental_data_sets']
], [u'Ras-GTP quantifications'])
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {'dataset_ind': 0})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(
response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(
SbmlModel.objects.filter(project=project)[3].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())),
['FGF2', 'Total Ras-GTP'])
self.assertEqual(
doc.getModelInstance().listOfSpecies.index(
doc.getByXPath(mapping['FGF2'], instance=True)), 4)
self.assertEqual(
doc.getModelInstance().listOfSpecies.index(
doc.getByXPath(mapping['Total Ras-GTP'], instance=True)), 13)
response_create_optimization = c.post(
'/fit/data/',
{
'action': 'create',
'dataset_0':
experiment_id, #response_get_fit_data.context['experimental_data_sets'][0].id,
'list_dataset_0_data_species_0_value': "FGF2",
'list_dataset_0_species_0_value': 4,
'list_dataset_0_data_species_1_value': "Total Ras-GTP",
'list_dataset_0_species_1_value': 13,
'parameter_0_id': 1,
'parameter_0_name': "SOS activation by FGF2",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 1,
'parameter_1_name':
"SOS inactivation by Mapk catalytic constant",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-6,
'parameter_1_max': 1e+6,
'parameter_1_precision': 7,
'nb_cores': 2,
'lambda': 0.02,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 200,
'freeze_count': 1,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(
response_create_optimization.context['form'].getErrors(), [])
sleep(10)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(
response_list_optimizations.context['optimizations'][0][0].status,
"Running")
sleep(10)
optimization_id = response_list_optimizations.context['optimizations'][
0][0].optimization_id
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
max_time = 360
sleep(360)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(
response_list_optimizations.context['optimizations'][0][0].status,
"Finished")
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores) - 1] < 1.01)
def testOptimization(self):
user = User.objects.filter(username='******')[0]
self.assertEqual(len(Project.objects.filter(user=user)), 1)
project = Project.objects.filter(user=user)[0]
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 0)
if isdir(join(settings.MEDIA_ROOT, project.folder)):
rmtree(join(settings.MEDIA_ROOT, project.folder))
mkdir(join(settings.MEDIA_ROOT, project.folder))
c = Client()
self.assertTrue(c.login(username='******', password='******'))
response_choose_project = c.get('/project/%s/' % project.folder)
self.assertRedirects(response_choose_project, '/models/', status_code=302, target_status_code=200)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
files_folder = join(dirname(__file__), "files")
comp_files_folder = join(files_folder, "comp_model")
model_filename = join(comp_files_folder, "modelcEvRcX.xml")
response_load_submodel_1 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_1.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 1)
model_filename = join(comp_files_folder, "modelEHfev9.xml")
response_load_submodel_2 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_2.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 2)
model_filename = join(comp_files_folder, "modelI1vrys.xml")
response_load_submodel_3 = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_submodel_3.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 3)
model_filename = join(comp_files_folder, "modelz9xdww.xml")
response_load_model = c.post('/models/', {
'action': 'load_model',
'docfile': open(model_filename, 'rb')
})
self.assertEqual(response_load_model.status_code, 200)
self.assertEqual(len(SbmlModel.objects.filter(project=project)), 4)
response_choose_model = c.post('/fit/data/', {
'action': 'choose_model',
'model_id': 3
})
self.assertEqual(response_choose_model.status_code, 200)
experiment_filename = join(files_folder, "ras_data.xml")
response_import_data = c.post('/data/', {
'action': 'import',
'docfile': open(experiment_filename, 'rb')
})
self.assertEqual(response_import_data.status_code, 200)
self.assertEqual(
[experiment.name for experiment in response_import_data.context['experimental_data']],
[u'Ras-GTP quantifications']
)
experiment_id = response_import_data.context['experimental_data'][0].id
response_get_fit_data = c.get('/fit/data/')
self.assertEqual(response_get_fit_data.status_code, 200)
self.assertEqual(
[dataset for dataset in response_get_fit_data.context['experimental_data_sets']],
[u'Ras-GTP quantifications']
)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 0)
response_add_dataset = c.post('/json/add_dataset/', {
'dataset_ind': 0
})
self.assertEqual(response_add_dataset.status_code, 200)
mapping = loads(response_add_dataset.content.decode('utf-8'))['model_xpaths']
sbml_filename = str(SbmlModel.objects.filter(project=project)[3].sbml_file)
doc = SbmlDocument()
doc.readSbmlFromFile(join(settings.MEDIA_ROOT, sbml_filename))
self.assertEqual(sorted(list(mapping.keys())), ['FGF2', 'Total Ras-GTP'])
self.assertEqual(doc.getModelInstance().listOfSpecies.index(doc.getByXPath(mapping['FGF2'], instance=True)), 4)
self.assertEqual(doc.getModelInstance().listOfSpecies.index(doc.getByXPath(mapping['Total Ras-GTP'], instance=True)), 13)
response_create_optimization = c.post('/fit/data/', {
'action': 'create',
'dataset_0': experiment_id, #response_get_fit_data.context['experimental_data_sets'][0].id,
'list_dataset_0_data_species_0_value': "FGF2",
'list_dataset_0_species_0_value': 4,
'list_dataset_0_data_species_1_value': "Total Ras-GTP",
'list_dataset_0_species_1_value': 13,
'parameter_0_id': 1,
'parameter_0_name': "SOS activation by FGF2",
'parameter_0_value': 1.0,
'parameter_0_min': 1e-4,
'parameter_0_max': 1e+4,
'parameter_0_precision': 7,
'parameter_1_active': "on",
'parameter_1_id': 1,
'parameter_1_name': "SOS inactivation by Mapk catalytic constant",
'parameter_1_value': 1.0,
'parameter_1_min': 1e-6,
'parameter_1_max': 1e+6,
'parameter_1_precision': 7,
'nb_cores': 2,
'lambda': 0.02,
'score_precision': 0.001,
'param_precision': 7,
'initial_temperature': 1,
'initial_moves': 200,
'freeze_count': 1,
'negative_penalty': 0
})
self.assertEqual(response_create_optimization.status_code, 200)
self.assertEqual(response_create_optimization.context['form'].getErrors(), [])
sleep(10)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(len(response_list_optimizations.context['optimizations']), 1)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Running")
sleep(10)
optimization_id = response_list_optimizations.context['optimizations'][0][0].optimization_id
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
max_time = 360
sleep(360)
response_list_optimizations = c.get('/fit/list/')
self.assertEqual(response_list_optimizations.status_code, 200)
self.assertEqual(response_list_optimizations.context['optimizations'][0][0].status, "Finished")
response_get_optimization = c.get('/fit/%s/' % optimization_id)
self.assertEqual(response_get_optimization.status_code, 200)
scores = response_get_optimization.context['score_values']
self.assertTrue(scores[len(scores)-1] < 1.01)