def testRule(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
response_get_compartment = c.post('/json/get_rule/', {
'rule_ind': '0',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'rule_id'], listOfRules.index(rule))
self.assertEqual(json_response[u'rule_type'], 1)
self.assertEqual(
json_response[u'variable'],
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('total_ras_gtp')))
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/rules/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_rule = c.post(
'/edit/rules/', {
'action':
'save',
'rule_id':
listOfRules.index(rule),
'rule_type':
1,
'variable_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId(
'total_mapk_activated')),
'rule_expression':
"75*ras_gtp",
})
self.assertEqual(response_save_rule.status_code, 200)
self.assertEqual(response_save_rule.context['form'].getErrors(), [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
self.assertEqual(rule.getType(), 1)
self.assertEqual(
rule.getVariable(),
sbml_model.listOfVariables.getBySbmlId('total_mapk_activated'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("75*ras_gtp", rawFormula=True)
self.assertEqual(
simplify(rule.getDefinition().getDeveloppedInternalMathFormula() -
formula.getDeveloppedInternalMathFormula()), 0)
response_delete_rule = c.post('/edit/rules/', {
'action': 'delete',
'rule_id': 0
})
self.assertEqual(response_delete_rule.status_code, 200)
self.assertEqual(response_delete_rule.context['form'].getErrors(), [])
def testRule(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
response_get_compartment = c.post('/json/get_rule/', {
'rule_ind': '0',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'rule_id'], listOfRules.index(rule))
self.assertEqual(json_response[u'rule_type'], 1)
self.assertEqual(json_response[u'variable'], listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('total_ras_gtp')))
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/rules/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_rule = c.post('/edit/rules/', {
'action': 'save',
'rule_id': listOfRules.index(rule),
'rule_type': 1,
'variable_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('total_mapk_activated')),
'rule_expression': "75*ras_gtp",
})
self.assertEqual(response_save_rule.status_code, 200)
self.assertEqual(response_save_rule.context['form'].getErrors(), [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfRules = sbml_model.listOfRules + sbml_model.listOfInitialAssignments
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
rule = listOfRules[0]
self.assertEqual(rule.getType(), 1)
self.assertEqual(rule.getVariable(), sbml_model.listOfVariables.getBySbmlId('total_mapk_activated'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("75*ras_gtp", rawFormula=True)
self.assertEqual(simplify(rule.getDefinition().getDeveloppedInternalMathFormula()-formula.getDeveloppedInternalMathFormula()), 0)
response_delete_rule = c.post('/edit/rules/', {
'action': 'delete',
'rule_id': 0
})
self.assertEqual(response_delete_rule.status_code, 200)
self.assertEqual(response_delete_rule.context['form'].getErrors(), [])
def testCompartment(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('cell')
response_get_compartment = c.post('/json/get_compartment/', {
'sbml_id': 'cell',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfCompartments.index(compartment))
self.assertEqual(json_response[u'sbml_id'], compartment.getSbmlId())
self.assertEqual(json_response[u'name'], compartment.getName())
self.assertEqual(json_response[u'value'], compartment.getValue())
self.assertEqual(json_response[u'constant'], 1 if compartment.constant else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/compartments/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_compartment = c.post('/edit/compartments/', {
'action': 'save',
'compartment_id': sbml_model.listOfCompartments.index(compartment),
'compartment_name': "New name",
'compartment_sbml_id': "new_name",
'compartment_size': 75,
'compartment_unit': 2,
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_compartment.status_code, 200)
self.assertEqual(response_save_compartment.context['getErrors'], [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_name')
self.assertTrue(compartment is not None)
self.assertEqual(compartment.getName(), "New name")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.constant, True)
self.assertEqual(compartment.getUnits(), sbml_model.listOfUnitDefinitions[2])
response_delete_compartment = c.post('/edit/compartments/', {
'action': 'delete',
'compartment_id': sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], ['Compartment contains 25 species'])
response_save_new_compartment = c.post('/edit/compartments/', {
'action': 'save',
'compartment_id': "",
'compartment_name': "New compartment",
'compartment_sbml_id': "new_compartment",
'compartment_size': 75,
'compartment_unit': "",
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_new_compartment.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_compartment')
self.assertTrue(compartment != None)
self.assertEqual(compartment.getName(), "New compartment")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.getUnits(), None)
self.assertEqual(compartment.constant, True)
response_delete_compartment = c.post('/edit/compartments/', {
'action': 'delete',
'compartment_id': sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], [])
def testEvents(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/events/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_event = c.post('/edit/events/', {
'action': 'save',
'event_id': '',
'event_sbmlid': 'test_event',
'event_name': "Test event",
'event_trigger': "time==0",
'event_priority': "",
'event_delay': "",
'event_assignment_0_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression': 'ras_gtp*2'
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_get_event = c.post('/json/get_event/', {
'event_ind': '0',
})
self.assertEqual(response_get_event.status_code, 200)
json_response = loads(response_get_event.content.decode('utf-8'))
self.assertEqual(json_response[u'event_ind'], 0)
self.assertEqual(json_response[u'event_name'], "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==0", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(json_response[u'event_trigger'], rawFormula=True)
self.assertEqual(simplify(formula.getDeveloppedInternalMathFormula()-formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(json_response[u'event_delay'], "")
self.assertEqual(json_response[u'list_of_assignments'][0][0], listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(json_response[u'list_of_assignments'][0][2], rawFormula=True)
self.assertEqual(simplify(formula.getDeveloppedInternalMathFormula()-formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertTrue(u'event_assignment_variable_1' not in json_response)
# Modifying an event
response_save_event = c.post('/edit/events/', {
'action': 'save',
'event_id': '0',
'event_sbmlid': 'test_event',
'event_name': "Test event",
'event_trigger': "time==100",
'event_priority': "",
'event_delay': "",
'event_assignment_0_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression': 'ras_gtp*2',
'event_assignment_1_id': listOfVariables.index(sbml_model.listOfVariables.getBySbmlId('ras_gdp')),
'event_assignment_1_expression': 'ras_gdp/2',
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
event = sbml_model.listOfEvents[0]
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies()
or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
self.assertEqual(event.getNameOrSbmlId(), "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==100", rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.trigger.getDeveloppedInternalMathFormula()),
0)
self.assertEqual(event.priority, None)
self.assertEqual(event.delay, None)
self.assertEqual(event.listOfEventAssignments[0].getVariable(), sbml_model.listOfVariables.getBySbmlId('ras_gtp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.listOfEventAssignments[0].getDefinition().getDeveloppedInternalMathFormula()),
0)
self.assertEqual(event.listOfEventAssignments[1].getVariable(), sbml_model.listOfVariables.getBySbmlId('ras_gdp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gdp/2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() - event.listOfEventAssignments[1].getDefinition().getDeveloppedInternalMathFormula()),
0)
response_delete_event = c.post('/edit/events/', {
'action': 'delete',
'event_id': 0
})
self.assertEqual(response_delete_event.status_code, 200)
self.assertEqual(response_delete_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfEvents), 0)
def testReactions(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/reactions/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
self.assertEqual(
[t_reaction.getReactionDescription() for t_reaction in response_choose_model.context['list_of_reactions']],
[t_reaction.getReactionDescription() for t_reaction in sbml_model.listOfReactions]
)
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_4'
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfReactions.index(reaction))
self.assertEqual(json_response[u'sbml_id'], reaction.getSbmlId())
self.assertEqual(json_response[u'name'], reaction.getName())
self.assertEqual(json_response[u'kinetic_law'], reaction.kineticLaw.getPrettyPrintMathFormula())
self.assertEqual(json_response[u'reaction_type'], reaction.getReactionType())
self.assertEqual(json_response[u'reaction_type_name'], KineticLaw.reactionTypes[reaction.getReactionType()])
self.assertEqual(json_response[u'reversible'], reaction.reversible)
self.assertEqual(json_response[u'list_of_reactants'], [
[
sbml_model.listOfSpecies.index(reactant.getSpecies()),
reactant.stoichiometry.getPrettyPrintMathFormula()
]
for reactant in reaction.listOfReactants
])
self.assertEqual(json_response[u'list_of_modifiers'], [
[
sbml_model.listOfSpecies.index(modifier.getSpecies()),
modifier.stoichiometry.getPrettyPrintMathFormula()
]
for modifier in reaction.listOfModifiers
])
self.assertEqual(json_response[u'list_of_products'], [
[
sbml_model.listOfSpecies.index(product.getSpecies()),
product.stoichiometry.getPrettyPrintMathFormula()
]
for product in reaction.listOfProducts
])
response_delete_reaction = c.post('/edit/reactions/', {
'action': 'delete',
'reaction_id': 2
})
self.assertEqual(response_delete_reaction.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfReactions), 21)
self.assertEqual(sbml_model.listOfReactions.getBySbmlId('reaction_4'), None)
response_create_creation = c.post('/edit/reactions/', {
'action': 'save',
'reaction_id': "",
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_create_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP")
response_modify_creation = c.post('/edit/reactions/', {
'action': 'save',
'reaction_id': sbml_model.listOfReactions.index(reaction),
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP, modified",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_modify_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP, modified")
def testSpecies(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('ras_gtp')
response_get_species = c.post('/json/get_species/', {
'sbml_id': 'ras_gtp'
})
self.assertEqual(response_get_species.status_code, 200)
json_response = loads(response_get_species.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfSpecies.index(species))
self.assertEqual(json_response[u'sbml_id'], species.getSbmlId())
self.assertEqual(json_response[u'name'], species.getName())
self.assertEqual(json_response[u'compartment_name'], species.getCompartment().getName())
self.assertEqual(json_response[u'compartment_id'], sbml_model.listOfCompartments.index(species.getCompartment()))
self.assertEqual(json_response[u'value'], species.getValue())
self.assertEqual(json_response[u'isConcentration'], 1 if not species.hasOnlySubstanceUnits else 0)
self.assertEqual(json_response[u'constant'], 1 if species.constant else 0)
self.assertEqual(json_response[u'boundaryCondition'], 1 if species.boundaryCondition else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'], "Project")
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'], "SOS-Ras-MAPK with n17")
response_save_species = c.post('/edit/species/', {
'action': 'save',
'species_id': 2,
'species_name': "New name",
'species_sbml_id': "new_name",
'species_value': 75,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "on",
'species_boundary': "on",
'species_sboterm': "",
})
self.assertEqual(response_save_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_name')
self.assertTrue(species is not None)
self.assertEqual(species.getName(), "New name")
self.assertEqual(species.getValue(), 75)
self.assertEqual(species.hasOnlySubstanceUnits, True)
self.assertEqual(species.constant, True)
self.assertEqual(species.boundaryCondition, True)
response_delete_species = c.post('/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
self.assertEqual(response_delete_species.context['getErrors'], ['Species is used in reactions'])
response_save_new_species = c.post('/edit/species/', {
'action': 'save',
'species_id': "",
'species_name': "New species",
'species_sbml_id': "new_species",
'species_value': 2500,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "off",
'species_boundary': "off",
'species_sboterm': "",
})
self.assertEqual(response_save_new_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertTrue(species != None)
self.assertEqual(species.getName(), "New species")
self.assertEqual(species.getValue(), 2500)
self.assertEqual(species.isConcentration(), False)
self.assertEqual(species.getCompartment().getName(), "cell")
self.assertEqual(species.constant, False)
self.assertEqual(species.boundaryCondition, False)
response_delete_species = c.post('/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertEqual(species, None)
def testSpecies(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('ras_gtp')
response_get_species = c.post('/json/get_species/',
{'sbml_id': 'ras_gtp'})
self.assertEqual(response_get_species.status_code, 200)
json_response = loads(response_get_species.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfSpecies.index(species))
self.assertEqual(json_response[u'sbml_id'], species.getSbmlId())
self.assertEqual(json_response[u'name'], species.getName())
self.assertEqual(json_response[u'compartment_name'],
species.getCompartment().getName())
self.assertEqual(
json_response[u'compartment_id'],
sbml_model.listOfCompartments.index(species.getCompartment()))
self.assertEqual(json_response[u'value'], species.getValue())
self.assertEqual(json_response[u'isConcentration'],
1 if not species.hasOnlySubstanceUnits else 0)
self.assertEqual(json_response[u'constant'],
1 if species.constant else 0)
self.assertEqual(json_response[u'boundaryCondition'],
1 if species.boundaryCondition else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/species/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_species = c.post(
'/edit/species/', {
'action': 'save',
'species_id': 2,
'species_name': "New name",
'species_sbml_id': "new_name",
'species_value': 75,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "on",
'species_boundary': "on",
'species_sboterm': "",
})
self.assertEqual(response_save_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_name')
self.assertTrue(species is not None)
self.assertEqual(species.getName(), "New name")
self.assertEqual(species.getValue(), 75)
self.assertEqual(species.hasOnlySubstanceUnits, True)
self.assertEqual(species.constant, True)
self.assertEqual(species.boundaryCondition, True)
response_delete_species = c.post(
'/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
self.assertEqual(response_delete_species.context['getErrors'],
['Species is used in reactions'])
response_save_new_species = c.post(
'/edit/species/', {
'action': 'save',
'species_id': "",
'species_name': "New species",
'species_sbml_id': "new_species",
'species_value': 2500,
'species_value_type': 0,
'species_compartment': 0,
'species_unit': 2,
'species_constant': "off",
'species_boundary': "off",
'species_sboterm': "",
})
self.assertEqual(response_save_new_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertTrue(species != None)
self.assertEqual(species.getName(), "New species")
self.assertEqual(species.getValue(), 2500)
self.assertEqual(species.isConcentration(), False)
self.assertEqual(species.getCompartment().getName(), "cell")
self.assertEqual(species.constant, False)
self.assertEqual(species.boundaryCondition, False)
response_delete_species = c.post(
'/edit/species/', {
'action': 'delete',
'species_id': sbml_model.listOfSpecies.index(species)
})
self.assertEqual(response_delete_species.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
species = sbml_model.listOfSpecies.getBySbmlId('new_species')
self.assertEqual(species, None)
def testLocalParameter(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)
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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
parameter = sbml_model.listOfParameters.getBySbmlId('sos_ras_gdp_comp')
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'kinetic_law'], '-1 * sos_ras_gdp * sos_ras_gdp_decomp + ras_gdp * sos * sos_ras_gdp_comp')
response_get_parameter = c.post('/json/get_parameter/', {
'sbml_id': 'sos_ras_gdp_comp',
'reaction': ''
})
self.assertEqual(response_get_parameter.status_code, 200)
json_response = loads(response_get_parameter.content.decode('utf-8'))
self.assertEqual(json_response[u'id'], sbml_model.listOfParameters.index(parameter))
self.assertEqual(json_response[u'reaction_id'], "")
response_to_local_parameter = c.post('/edit/parameters/', {
'action': 'save',
'parameter_id': json_response[u'id'],
'parameter_name': json_response[u'name'],
'parameter_sbml_id': json_response[u'sbml_id'],
'parameter_value': json_response[u'value'],
'parameter_unit': json_response[u'unit_id'],
'parameter_constant': "on" if json_response[u'constant'] == 1 else "",
'parameter_scope': 1,
'parameter_sboterm': "",
})
self.assertEqual(response_to_local_parameter.status_code, 200)
self.assertEqual(response_to_local_parameter.context['getErrors'], [])
self.assertEqual(response_to_local_parameter.context['form'].getErrors(), [])
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(
json_response[u'kinetic_law'],
'-1 * sos_ras_gdp * sos_ras_gdp_decomp + sos_ras_gdp_comp * ras_gdp * sos'
)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_2')
self.assertEqual(
str(reaction.kineticLaw.getDefinition().getInternalMathFormula()),
"_local_0_sos_ras_gdp_comp*ras_gdp*sos - sos_ras_gdp*sos_ras_gdp_decomp"
)
self.assertEqual(sbml_model.listOfParameters.getBySbmlId("sos_ras_gdp_comp"), None)
response_get_parameter = c.post('/json/get_parameter/', {
'sbml_id': 'sos_ras_gdp_comp',
'reaction': '1'
})
self.assertEqual(response_get_parameter.status_code, 200)
json_response = loads(response_get_parameter.content.decode('utf-8'))
response_list_parameters = c.get('/edit/parameters/')
self.assertEqual(response_list_parameters.status_code, 200)
list_of_parameters = [param.getSbmlId() for param in response_list_parameters.context['list_of_parameters']]
response_to_global_parameter = c.post('/edit/parameters/', {
'action': 'save',
'parameter_id': list_of_parameters.index("sos_ras_gdp_comp"),
'parameter_name': json_response[u'name'],
'parameter_sbml_id': json_response[u'sbml_id'],
'parameter_value': json_response[u'value'],
'parameter_unit': json_response[u'unit_id'],
'parameter_constant': "on" if json_response[u'constant'] == 1 else "",
'parameter_scope': 0,
'parameter_sboterm': "",
})
self.assertEqual(response_to_global_parameter.status_code, 200)
self.assertEqual(response_to_global_parameter.context['getErrors'], [])
self.assertEqual(response_to_global_parameter.context['form'].getErrors(), [])
response_get_reaction = c.post('/json/get_reaction/', {
'sbml_id': 'reaction_2',
})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
# print json_response
self.assertEqual(
json_response[u'kinetic_law'],
'-1 * sos_ras_gdp * sos_ras_gdp_decomp + ras_gdp * sos * sos_ras_gdp_comp'
)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_2')
self.assertEqual(
str(reaction.kineticLaw.getDefinition().getInternalMathFormula()),
"ras_gdp*sos*sos_ras_gdp_comp - sos_ras_gdp*sos_ras_gdp_decomp"
)
self.assertEqual(sbml_model.listOfParameters.getBySbmlId("sos_ras_gdp_comp").getSbmlId(), "sos_ras_gdp_comp")
def testEvents(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/events/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_event = c.post(
'/edit/events/', {
'action':
'save',
'event_id':
'',
'event_sbmlid':
'test_event',
'event_name':
"Test event",
'event_trigger':
"time==0",
'event_priority':
"",
'event_delay':
"",
'event_assignment_0_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression':
'ras_gtp*2'
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
response_get_event = c.post('/json/get_event/', {
'event_ind': '0',
})
self.assertEqual(response_get_event.status_code, 200)
json_response = loads(response_get_event.content.decode('utf-8'))
self.assertEqual(json_response[u'event_ind'], 0)
self.assertEqual(json_response[u'event_name'], "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==0", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(
json_response[u'event_trigger'], rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(json_response[u'event_delay'], "")
self.assertEqual(
json_response[u'list_of_assignments'][0][0],
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2", rawFormula=True)
formula_response = MathFormula(sbml_model)
formula_response.setPrettyPrintMathFormula(
json_response[u'list_of_assignments'][0][2], rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
formula_response.getDeveloppedInternalMathFormula()), 0)
self.assertTrue(u'event_assignment_variable_1' not in json_response)
# Modifying an event
response_save_event = c.post(
'/edit/events/', {
'action':
'save',
'event_id':
'0',
'event_sbmlid':
'test_event',
'event_name':
"Test event",
'event_trigger':
"time==100",
'event_priority':
"",
'event_delay':
"",
'event_assignment_0_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gtp')),
'event_assignment_0_expression':
'ras_gtp*2',
'event_assignment_1_id':
listOfVariables.index(
sbml_model.listOfVariables.getBySbmlId('ras_gdp')),
'event_assignment_1_expression':
'ras_gdp/2',
})
self.assertEqual(response_save_event.status_code, 200)
self.assertEqual(response_save_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
event = sbml_model.listOfEvents[0]
listOfVariables = []
for variable in sbml_model.listOfVariables:
if ((variable.isParameter() and variable.isGlobal())
or variable.isSpecies() or variable.isCompartment()
or variable.isStoichiometry()):
listOfVariables.append(variable)
self.assertEqual(event.getNameOrSbmlId(), "Test event")
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("time==100", rawFormula=True)
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.trigger.getDeveloppedInternalMathFormula()), 0)
self.assertEqual(event.priority, None)
self.assertEqual(event.delay, None)
self.assertEqual(event.listOfEventAssignments[0].getVariable(),
sbml_model.listOfVariables.getBySbmlId('ras_gtp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gtp*2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.listOfEventAssignments[0].getDefinition(
).getDeveloppedInternalMathFormula()), 0)
self.assertEqual(event.listOfEventAssignments[1].getVariable(),
sbml_model.listOfVariables.getBySbmlId('ras_gdp'))
formula = MathFormula(sbml_model)
formula.setPrettyPrintMathFormula("ras_gdp/2")
self.assertEqual(
simplify(formula.getDeveloppedInternalMathFormula() -
event.listOfEventAssignments[1].getDefinition(
).getDeveloppedInternalMathFormula()), 0)
response_delete_event = c.post('/edit/events/', {
'action': 'delete',
'event_id': 0
})
self.assertEqual(response_delete_event.status_code, 200)
self.assertEqual(response_delete_event.context['form'].getErrors(), [])
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfEvents), 0)
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 testCompartment(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('cell')
response_get_compartment = c.post('/json/get_compartment/', {
'sbml_id': 'cell',
})
self.assertEqual(response_get_compartment.status_code, 200)
json_response = loads(response_get_compartment.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfCompartments.index(compartment))
self.assertEqual(json_response[u'sbml_id'], compartment.getSbmlId())
self.assertEqual(json_response[u'name'], compartment.getName())
self.assertEqual(json_response[u'value'], compartment.getValue())
self.assertEqual(json_response[u'constant'],
1 if compartment.constant else 0)
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/compartments/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
response_save_compartment = c.post(
'/edit/compartments/', {
'action': 'save',
'compartment_id':
sbml_model.listOfCompartments.index(compartment),
'compartment_name': "New name",
'compartment_sbml_id': "new_name",
'compartment_size': 75,
'compartment_unit': 2,
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_compartment.status_code, 200)
self.assertEqual(response_save_compartment.context['getErrors'], [])
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId('new_name')
self.assertTrue(compartment is not None)
self.assertEqual(compartment.getName(), "New name")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.constant, True)
self.assertEqual(compartment.getUnits(),
sbml_model.listOfUnitDefinitions[2])
response_delete_compartment = c.post(
'/edit/compartments/', {
'action': 'delete',
'compartment_id':
sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'],
['Compartment contains 25 species'])
response_save_new_compartment = c.post(
'/edit/compartments/', {
'action': 'save',
'compartment_id': "",
'compartment_name': "New compartment",
'compartment_sbml_id': "new_compartment",
'compartment_size': 75,
'compartment_unit': "",
'compartment_constant': "on",
'compartment_sboterm': "",
})
self.assertEqual(response_save_new_compartment.status_code, 200)
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
compartment = sbml_model.listOfCompartments.getBySbmlId(
'new_compartment')
self.assertTrue(compartment != None)
self.assertEqual(compartment.getName(), "New compartment")
self.assertEqual(compartment.getValue(), 75)
self.assertEqual(compartment.getUnits(), None)
self.assertEqual(compartment.constant, True)
response_delete_compartment = c.post(
'/edit/compartments/', {
'action': 'delete',
'compartment_id':
sbml_model.listOfCompartments.index(compartment)
})
self.assertEqual(response_delete_compartment.status_code, 200)
self.assertEqual(response_delete_compartment.context['getErrors'], [])
def testReactions(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/reactions/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
self.assertEqual([
t_reaction.getReactionDescription() for t_reaction in
response_choose_model.context['list_of_reactions']
], [
t_reaction.getReactionDescription()
for t_reaction in sbml_model.listOfReactions
])
response_get_reaction = c.post('/json/get_reaction/',
{'sbml_id': 'reaction_4'})
self.assertEqual(response_get_reaction.status_code, 200)
json_response = loads(response_get_reaction.content.decode('utf-8'))
self.assertEqual(json_response[u'id'],
sbml_model.listOfReactions.index(reaction))
self.assertEqual(json_response[u'sbml_id'], reaction.getSbmlId())
self.assertEqual(json_response[u'name'], reaction.getName())
self.assertEqual(json_response[u'kinetic_law'],
reaction.kineticLaw.getPrettyPrintMathFormula())
self.assertEqual(json_response[u'reaction_type'],
reaction.getReactionType())
self.assertEqual(json_response[u'reaction_type_name'],
KineticLaw.reactionTypes[reaction.getReactionType()])
self.assertEqual(json_response[u'reversible'], reaction.reversible)
self.assertEqual(json_response[u'list_of_reactants'], [[
sbml_model.listOfSpecies.index(reactant.getSpecies()),
reactant.stoichiometry.getPrettyPrintMathFormula()
] for reactant in reaction.listOfReactants])
self.assertEqual(json_response[u'list_of_modifiers'], [[
sbml_model.listOfSpecies.index(modifier.getSpecies()),
modifier.stoichiometry.getPrettyPrintMathFormula()
] for modifier in reaction.listOfModifiers])
self.assertEqual(json_response[u'list_of_products'], [[
sbml_model.listOfSpecies.index(product.getSpecies()),
product.stoichiometry.getPrettyPrintMathFormula()
] for product in reaction.listOfProducts])
response_delete_reaction = c.post('/edit/reactions/', {
'action': 'delete',
'reaction_id': 2
})
self.assertEqual(response_delete_reaction.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
self.assertEqual(len(sbml_model.listOfReactions), 21)
self.assertEqual(sbml_model.listOfReactions.getBySbmlId('reaction_4'),
None)
response_create_creation = c.post(
'/edit/reactions/', {
'action': 'save',
'reaction_id': "",
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_create_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(), "Ras activation by SOS-Ras-GDP")
response_modify_creation = c.post(
'/edit/reactions/', {
'action': 'save',
'reaction_id': sbml_model.listOfReactions.index(reaction),
'reaction_sbml_id': "reaction_4",
'reaction_name': "Ras activation by SOS-Ras-GDP, modified",
'reaction_reactant_0': 1,
'reaction_reactant_0_stoichiometry': "1",
'reaction_modifier_0': 3,
'reaction_modifier_0_stoichiometry': "1",
'reaction_product_0': 2,
'reaction_product_0_stoichiometry': "1",
'reaction_type': 1,
'reaction_parameter_0': 2,
'reaction_parameter_1': 3,
'reaction_sboterm': ""
})
self.assertEqual(response_modify_creation.status_code, 200)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
reaction = sbml_model.listOfReactions.getBySbmlId('reaction_4')
self.assertEqual(len(sbml_model.listOfReactions), 22)
self.assertEqual(reaction.getName(),
"Ras activation by SOS-Ras-GDP, modified")
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 testUnits(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)
files_folder = join(dirname(__file__), "files")
model_filename = join(files_folder, "modelqlzB7i.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)
model = SbmlModel.objects.filter(project=project)[0]
sbml_doc = SbmlDocument()
sbml_doc.readSbmlFromFile(
join(settings.MEDIA_ROOT, str(model.sbml_file)))
sbml_model = sbml_doc.getModelInstance()
response_choose_project = c.post('/models/', {
'action': 'choose_project',
'project_id': 0
})
self.assertEqual(response_choose_project.status_code, 200)
self.assertEqual(response_choose_project.context['project_name'],
"Project")
response_choose_model = c.post('/edit/units/', {
'action': 'choose_model',
'model_id': 0
})
self.assertEqual(response_choose_model.status_code, 200)
self.assertEqual(response_choose_model.context['model_name'],
"SOS-Ras-MAPK with n17")
self.assertEqual(response_choose_model.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds'
])
response_save_unit = c.post(
'/edit/units/', {
'action': 'save',
'unit_definition_id': '',
'unit_definition_name': "Nanomolars",
'unit_definition_identifier': "nanomolars",
'subunit_id_0': list(Unit.unit_id.values()).index("mole"),
'subunit_exponent_0': 1,
'subunit_scale_0': -9,
'subunit_multiplier_0': 1,
'subunit_id_1': list(Unit.unit_id.values()).index("litre"),
'subunit_exponent_1': -1,
'subunit_scale_1': 1,
'subunit_multiplier_1': 1,
})
self.assertEqual(response_save_unit.status_code, 200)
self.assertEqual(response_save_unit.context['form'].getErrors(), [])
self.assertEqual(response_save_unit.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds', 'Nanomolars'
])
response_get_unit_definition = c.post(
'/json/get_unit_definition/', {
'id':
response_save_unit.context['unit_definitions'].index(
'Nanomolars'),
})
self.assertEqual(response_get_unit_definition.status_code, 200)
json_response = loads(
response_get_unit_definition.content.decode('utf-8'))
self.assertEqual(json_response[u'unit_id'], "nanomolars")
self.assertEqual(json_response[u'name'], "Nanomolars")
self.assertEqual(json_response[u'desc'], "nmole.litre^-1")
self.assertEqual(json_response[u'list_of_units'][0],
[u'nmole', 20, u'mole', 1, -9, 1.0])
self.assertEqual(json_response[u'list_of_units'][1],
[u'litre^-1', 16, u'litre', -1, 1, 1.0])
response_delete_unit_definition = c.post(
'/edit/units/', {
'action':
'delete',
'id':
response_save_unit.context['unit_definitions'].index(
'Nanomolars')
})
self.assertEqual(response_delete_unit_definition.status_code, 200)
self.assertEqual(
response_delete_unit_definition.context['unit_definitions'], [
'Litre', 'Nanomoles', 'Nanomoles per litre', 'Seconds',
'per Seconds', 'per Nanomoles ', 'Dimensionless',
'per Nanomoles per Seconds', 'Nanomoles per seconds',
'Nanomoles per litre per seconds',
'per Nanomoles per liter per Seconds'
])