def get_surface_model_parameters_data(self, default_selected_model_param=None):
"""
Returns a dictionary which contains all the data needed for drawing the
model parameters.
"""
context_model_parameters = base.get_from_session(KEY_CONTEXT_MPS)
if default_selected_model_param is None:
default_selected_model_param = context_model_parameters.prepared_model_parameter_names.values()[0]
equation_displayer = EquationDisplayer()
equation_displayer.trait.bound = interface.INTERFACE_ATTRIBUTES_ONLY
input_list = equation_displayer.interface[interface.INTERFACE_ATTRIBUTES]
input_list[0] = self._lock_midpoints(input_list[0])
options = []
for original_param, modified_param in context_model_parameters.prepared_model_parameter_names.items():
attributes = deepcopy(input_list)
self._fill_default_values(attributes, modified_param)
option = {'name': original_param, 'value': modified_param, 'attributes': attributes}
options.append(option)
input_list = [{'name': 'model_param', 'type': 'select', 'default': default_selected_model_param,
'label': 'Model param', 'required': True, 'options': options}]
input_list = ABCAdapter.prepare_param_names(input_list)
return {base.KEY_PARAMETERS_CONFIG: False, 'inputList': input_list,
'applied_equations': context_model_parameters.get_configure_info()}
def prepare_adapter(self, project_id, algo_group):
"""
Having a given Adapter, specified by Module and ClassName,
create a instance of it and return the instance.
Actually return a Tuple: Adapter Instance, Dictionary for Adapter
Interface specification.
"""
adapter_module = algo_group.module.replace('-', '.')
adapter_name = algo_group.classname
try:
# Prepare Adapter Interface, by populating with existent data,
# in case of a parameter of type DataType.
group = dao.find_group(adapter_module, adapter_name,
algo_group.init_parameter)
adapter_instance = self.build_adapter_instance(group)
interface = adapter_instance.get_input_tree()
interface = self.prepare_parameters(interface, project_id,
group.fk_category)
interface = ABCAdapter.prepare_param_names(interface)
return group, interface
except Exception, excep:
self.logger.exception(excep)
self.logger.error('Not found:' + adapter_name + ' in:' +
adapter_module)
raise OperationException("Could not prepare " + adapter_name)
def get_creator_and_interface(self,
creator_module,
creator_class,
datatype_instance,
lock_midpoint_for_eq=None):
"""
Returns a Tuple: a creator instance and a dictionary for the creator interface.
The interface is prepared for rendering, it is populated with existent data, in case of a
parameter of type DataType. The name of the attributes are also prefixed to identify groups.
"""
algo_group = self.flow_service.get_algorithm_by_module_and_class(
creator_module, creator_class)[1]
group, _ = self.flow_service.prepare_adapter(
base.get_current_project().id, algo_group)
#I didn't use the interface(from the above line) returned by the method 'prepare_adapter' from flow service
# because the selects that display dataTypes will also have the 'All' entry.
datatype_instance.trait.bound = traited_interface.INTERFACE_ATTRIBUTES_ONLY
input_list = datatype_instance.interface[
traited_interface.INTERFACE_ATTRIBUTES]
if lock_midpoint_for_eq is not None:
for idx in lock_midpoint_for_eq:
input_list[idx] = self._lock_midpoints(input_list[idx])
category = self.flow_service.get_visualisers_category()
input_list = self.flow_service.prepare_parameters(
input_list,
base.get_current_project().id, category.id)
input_list = ABCAdapter.prepare_param_names(input_list)
return self.flow_service.build_adapter_instance(group), input_list
def test_multidimensional_array(self):
"""
Test the generation of a multi-dimensional array.
"""
input_tree = TraitAdapter().get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
resulted_html = _template2string(self.template_specification)
soup = BeautifulSoup(resulted_html)
#Find dictionary div which should be dict_+${dict_var_name}
dict_div = soup.findAll('div', attrs=dict(id="dict_test_dict"))
self.assertEqual(len(dict_div), 1, 'Dictionary div not found')
dict_entries = soup.findAll(
'input', attrs=dict(name=re.compile('^test_dict_parameters*')))
self.assertEqual(len(dict_entries), 2, 'Not all entries found')
for i in range(2):
if dict_entries[i]['name'] == "test_dict_parameters_W":
self.assertEqual(dict_entries[0]['value'], "-6.0",
"Incorrect values")
if dict_entries[i]['name'] == "test_dict_parameters_V":
self.assertEqual(dict_entries[1]['value'], "-3.0",
"Incorrect values")
array_entry = soup.findAll('input', attrs=dict(name='test_array'))
self.assertEqual(len(array_entry), 1, 'Array entry not found')
self.assertEqual(array_entry[0]['value'], "[[-3.0, -6.0], [3.0, 6.0]]",
"Wrong value stored")
def get_surface_model_parameters_data(self, default_selected_model_param=None):
"""
Returns a dictionary which contains all the data needed for drawing the
model parameters.
"""
context_model_parameters = common.get_from_session(KEY_CONTEXT_MPS)
if default_selected_model_param is None:
default_selected_model_param = context_model_parameters.prepared_model_parameter_names.values()[0]
equation_displayer = EquationDisplayer()
equation_displayer.trait.bound = interface.INTERFACE_ATTRIBUTES_ONLY
input_list = equation_displayer.interface[interface.INTERFACE_ATTRIBUTES]
input_list[0] = self._lock_midpoints(input_list[0])
options = []
for original_param, modified_param in context_model_parameters.prepared_model_parameter_names.items():
attributes = deepcopy(input_list)
self._fill_default_values(attributes, modified_param)
option = {'name': original_param, 'value': modified_param, 'attributes': attributes}
options.append(option)
input_list = [{'name': 'model_param', 'type': 'select', 'default': default_selected_model_param,
'label': 'Model param', 'required': True, 'options': options}]
input_list = ABCAdapter.prepare_param_names(input_list)
return {common.KEY_PARAMETERS_CONFIG: False, 'inputList': input_list,
'applied_equations': context_model_parameters.get_configure_info()}
def get_select_existent_entities(self, label, entity_type, entity_gid=None):
"""
Returns the dictionary needed for drawing the select which display all
the created entities of the specified type.
"""
project_id = common.get_current_project().id
category = self.flow_service.get_visualisers_category()
interface = [{'name': 'existentEntitiesSelect', 'label': label, 'type': entity_type}]
if entity_gid is not None:
interface[0]['default'] = entity_gid
interface = self.flow_service.prepare_parameters(interface, project_id, category.id)
interface = ABCAdapter.prepare_param_names(interface)
return interface
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
xml_group_path = os.path.join('tests', 'framework', 'interfaces', 'web', "test_group.xml")
algo_group = dao.find_group('tvb.tests.framework.adapters.testgroupadapter', 'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[common.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
def get_select_existent_entities(self, label, entity_type, entity_gid=None):
"""
Returns the dictionary needed for drawing the select which display all
the created entities of the specified type.
"""
project_id = base.get_current_project().id
category = self.flow_service.get_visualisers_category()
interface = [{'name': 'existentEntitiesSelect', 'label': label, 'type': entity_type}]
if entity_gid is not None:
interface[0]['default'] = entity_gid
interface = self.flow_service.prepare_parameters(interface, project_id, category.id)
interface = ABCAdapter.prepare_param_names(interface)
return interface
def build_portlet_interface(self, portlet_configuration, project_id):
"""
From a portlet_id and a project_id, first build the portlet
entity then get it's configurable interface.
:param portlet_configuration: a portlet configuration entity. It holds at the
least the portlet_id, and in case any default parameters were saved
they can be rebuilt from the analyzers // visualizer parameters
:param project_id: the id of the current project
:returns: the portlet interface will be of the following form::
[{'interface': adapter_interface,
'prefix': prefix_for_parameter_names,
'subalg': {algorithm_field_name: default_algorithm_value},
'algo_group': algorithm_group,
'alg_ui_name': displayname},
......]
A list of dictionaries for each adapter that makes up the portlet.
"""
portlet_entity = dao.get_portlet_by_id(
portlet_configuration.portlet_id)
if portlet_entity is None:
raise InvalidPortletConfiguration(
"No portlet entity located in database with id=%s. "
"Portlet configuration %s is not valid." %
(portlet_configuration.portlet_id, portlet_configuration))
portlet_configurer = PortletConfigurer(portlet_entity)
portlet_interface = portlet_configurer.get_configurable_interface()
self.logger.debug("Created interface for portlet " +
str([portlet_entity]))
for adapter_conf in portlet_interface:
interface = adapter_conf.interface
interface = FlowService().prepare_parameters(
interface, project_id, adapter_conf.group.fk_category)
interface = ABCAdapter.prepare_param_names(interface,
adapter_conf.prefix)
adapter_conf.interface = interface
portlet_configurer.update_default_values(portlet_interface,
portlet_configuration)
portlet_configurer.prefix_adapters_parameters(portlet_interface)
return portlet_interface
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
xml_group_path = os.path.join('tests', 'framework', 'interfaces',
'web', "test_group.xml")
algo_group = dao.find_group(
'tvb.tests.framework.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[common.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
def get_creator_and_interface(self, creator_module, creator_class, datatype_instance, lock_midpoint_for_eq=None):
"""
Returns a Tuple: a creator instance and a dictionary for the creator interface.
The interface is prepared for rendering, it is populated with existent data, in case of a
parameter of type DataType. The name of the attributes are also prefixed to identify groups.
"""
algo_group = self.flow_service.get_algorithm_by_module_and_class(creator_module, creator_class)[1]
group, _ = self.flow_service.prepare_adapter(common.get_current_project().id, algo_group)
#I didn't use the interface(from the above line) returned by the method 'prepare_adapter' from flow service
# because the selects that display dataTypes will also have the 'All' entry.
datatype_instance.trait.bound = traited_interface.INTERFACE_ATTRIBUTES_ONLY
input_list = datatype_instance.interface[traited_interface.INTERFACE_ATTRIBUTES]
if lock_midpoint_for_eq is not None:
for idx in lock_midpoint_for_eq:
input_list[idx] = self._lock_midpoints(input_list[idx])
category = self.flow_service.get_visualisers_category()
input_list = self.flow_service.prepare_parameters(input_list, common.get_current_project().id, category.id)
input_list = ABCAdapter.prepare_param_names(input_list)
return self.flow_service.build_adapter_instance(group), input_list
def build_portlet_interface(self, portlet_configuration, project_id):
"""
From a portlet_id and a project_id, first build the portlet
entity then get it's configurable interface.
:param portlet_configuration: a portlet configuration entity. It holds at the
least the portlet_id, and in case any default parameters were saved
they can be rebuilt from the analyzers // visualizer parameters
:param project_id: the id of the current project
:returns: the portlet interface will be of the following form::
[{'interface': adapter_interface,
'prefix': prefix_for_parameter_names,
'subalg': {algorithm_field_name: default_algorithm_value},
'algo_group': algorithm_group,
'alg_ui_name': displayname},
......]
A list of dictionaries for each adapter that makes up the portlet.
"""
portlet_entity = dao.get_portlet_by_id(portlet_configuration.portlet_id)
if portlet_entity is None:
raise InvalidPortletConfiguration(
"No portlet entity located in database with id=%s. "
"Portlet configuration %s is not valid." % (portlet_configuration.portlet_id, portlet_configuration)
)
portlet_configurer = PortletConfigurer(portlet_entity)
portlet_interface = portlet_configurer.get_configurable_interface()
self.logger.debug("Created interface for portlet " + str([portlet_entity]))
for adapter_conf in portlet_interface:
interface = adapter_conf.interface
interface = FlowService().prepare_parameters(interface, project_id, adapter_conf.group.fk_category)
interface = ABCAdapter.prepare_param_names(interface, adapter_conf.prefix)
adapter_conf.interface = interface
portlet_configurer.update_default_values(portlet_interface, portlet_configuration)
portlet_configurer.prefix_adapters_parameters(portlet_interface)
return portlet_interface
def prepare_adapter(self, project_id, algo_group):
"""
Having a given Adapter, specified by Module and ClassName,
create a instance of it and return the instance.
Actually return a Tuple: Adapter Instance, Dictionary for Adapter
Interface specification.
"""
adapter_module = algo_group.module.replace('-', '.')
adapter_name = algo_group.classname
try:
# Prepare Adapter Interface, by populating with existent data,
# in case of a parameter of type DataType.
group = dao.find_group(adapter_module, adapter_name, algo_group.init_parameter)
adapter_instance = self.build_adapter_instance(group)
interface = adapter_instance.get_input_tree()
interface = self.prepare_parameters(interface, project_id, group.fk_category)
interface = ABCAdapter.prepare_param_names(interface)
return group, interface
except Exception, excep:
self.logger.exception(excep)
self.logger.error('Not found:' + adapter_name + ' in:' + adapter_module)
raise OperationException("Could not prepare " + adapter_name)
def test_multidimensional_array(self):
"""
Test the generation of a multi-dimensional array.
"""
input_tree = TraitAdapter().get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
resulted_html = _template2string(self.template_specification)
soup = BeautifulSoup(resulted_html)
#Find dictionary div which should be dict_+${dict_var_name}
dict_div = soup.findAll('div', attrs=dict(id="dict_test_dict"))
self.assertEqual(len(dict_div), 1, 'Dictionary div not found')
dict_entries = soup.findAll('input', attrs=dict(name=re.compile('^test_dict_parameters*')))
self.assertEqual(len(dict_entries), 2, 'Not all entries found')
for i in range(2):
if dict_entries[i]['name'] == "test_dict_parameters_W":
self.assertEqual(dict_entries[0]['value'], "-6.0", "Incorrect values")
if dict_entries[i]['name'] == "test_dict_parameters_V":
self.assertEqual(dict_entries[1]['value'], "-3.0", "Incorrect values")
array_entry = soup.findAll('input', attrs=dict(name='test_array'))
self.assertEqual(len(array_entry), 1, 'Array entry not found')
self.assertEqual(array_entry[0]['value'], "[[-3.0, -6.0], [3.0, 6.0]]", "Wrong value stored")
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('interfaces', 'web')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('interfaces', 'web', "test_group.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[base.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)