def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
self.operation_services = OperationService()
self.simulator_controller = SimulatorController()
analyze_category, groups = self.algorithm_service.get_analyze_groups()
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.flow_service.get_analyze_groups()
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an analyzer",
displayControl=False)
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
template_specification[common.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu",
section_name='connectivity',
controlPage=None,
title="Select an algorithm",
displayControl=False,
subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
## This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.flow_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.flow_service.get_algorithm_by_identifier(
algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
algorithm.input_tree = self.flow_service.prepare_adapter(
project.id, algorithm)
algorithms.append(algorithm)
template_specification = dict(
mainContent="flow/algorithms_list",
algorithms=algorithms,
title="Select an algorithm",
section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification,
algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
OperationService().group_operation_launch(
common.get_logged_user().id,
common.get_current_project().id, int(algorithm_id), int(step_key),
**data)
redirect_url = self._compute_back_link('operations',
common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.flow_service.get_algorithm_by_identifier(adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
step_key, algorithm,
**data)
self._populate_section(algorithm, template_specification, is_burst)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algorithm.algorithm_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(
project.id,
step_key,
algorithm,
submit_link,
not not_reset,
is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification,
algorithm.displayname)
return template_specification
@expose_fragment("flow/reduce_dimension_select")
def gettemplatefordimensionselect(self,
entity_gid=None,
select_name="",
reset_session='False',
parameters_prefix="dimensions",
required_dimension=1,
expected_shape="",
operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid
the GID of the entity for which is displayed the component
select_name
the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix
a string which will be used for computing the names of the component
required_dimension
the expected dimension for the resulted array
expected_shape and operations
used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
``expected_shape=x,512,x`` and ``operations='x,<,x``
"""
template_params = {
"select_name": "",
"data": [],
"parameters_prefix": parameters_prefix,
"array_shape": "",
"required_dimension": required_dimension,
"currentDim": "",
"required_dim_msg": "",
"expected_shape": expected_shape,
"operations": operations
}
#if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not string2bool(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items()
if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray(
).parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(
list(array_shape), dimensions, selected_agg_functions)
if required_dimension is not None and current_dim != int(
required_dimension):
template_params[
"required_dim_msg"] = "Please select a " + str(
required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(
current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels'
) and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
#make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions')
and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions)
== len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = {}
for function_key in function:
func_dict[
function_key] = default_agg_functions[
function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in xrange(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items,
selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in xrange(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@expose_fragment("flow/type2component/datatype2select_simple")
def getfiltereddatatypes(self, name, parent_div, tree_session_key,
filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
common.set_error_message(
"Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(
FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
#Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][
FILTER_TYPE] == 'date':
try:
temp_date = string2date(filters[FILTER_VALUES][i], False)
filters[FILTER_VALUES][i] = temp_date
except ValueError:
raise
#In order for the filter object not to "stack up" on multiple calls to
#this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
#Get dataTypes that match the filters from DB then populate with values
values, total_count = InputTreeManager(
).populate_option_values_for_dtype(common.get_current_project().id,
datatype, new_filter,
self.context.get_current_step())
#Create a dictionary that matches what the template expects
parameters = {
ABCAdapter.KEY_NAME: name,
ABCAdapter.KEY_FILTERABLE: availablefilter,
ABCAdapter.KEY_TYPE: ABCAdapter.TYPE_SELECT,
ABCAdapter.KEY_OPTIONS: values,
ABCAdapter.KEY_DATATYPE: datatype
}
if total_count > MAXIMUM_DATA_TYPES_DISPLAYED:
parameters[KEY_WARNING] = WARNING_OVERFLOW
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[
ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and string2bool(
str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(
values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected in [str(vv['value']) for vv in values]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
template_specification = {
"inputRow": parameters,
"disabled": False,
"parentDivId": parent_div,
common.KEY_SESSION_TREE: tree_session_key
}
return self.fill_default_attributes(template_specification)
def _get_node(self, input_tree, name):
"""
Given a input tree and a variable name, check to see if any default filters exist.
"""
for entry in input_tree:
if (ABCAdapter.KEY_DATATYPE in entry
and ABCAdapter.KEY_NAME in entry
and str(entry[ABCAdapter.KEY_NAME]) == str(name)):
return entry
if entry.get(ABCAdapter.KEY_ATTRIBUTES) is not None:
in_attr = self._get_node(entry[ABCAdapter.KEY_ATTRIBUTES],
name)
if in_attr is not None:
return in_attr
if entry.get(ABCAdapter.KEY_OPTIONS) is not None:
in_options = self._get_node(entry[ABCAdapter.KEY_OPTIONS],
name)
if in_options is not None:
return in_options
return None
def execute_post(self, project_id, submit_url, step_key, algorithm,
**data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
result = self.flow_service.fire_operation(adapter_instance,
common.get_logged_user(),
project_id, **data)
# Store input data in session, for informing user of it.
step = self.flow_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None,
copy.deepcopy(data))
if isinstance(adapter_instance, ABCDisplayer):
if isinstance(result, dict):
result[common.
KEY_OPERATION_ID] = adapter_instance.operation_id
return result
else:
common.set_error_message(
"Invalid result returned from Displayer! Dictionary is expected!"
)
else:
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid, excep:
errors = excep.unpack_errors()
except OperationException, excep1:
self.logger.exception("Error while executing a Launch procedure:" +
excep1.message)
common.set_error_message(excep1.message)
class FlowController(base.BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
base.BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@cherrypy.expose
@using_template('base_template')
@logged()
@base.settings()
@context_selected()
def step(self, step_key=None):
"""
Choose exact action/adapter for current step.
"""
category = self.flow_service.get_category_by_id(step_key)
if category is None:
message = 'Inconsistent Step Name! Please excuse the wrong link!'
base.set_warning_message(message)
self.logger.warning(message + '- Wrong step:' + str(step_key))
raise cherrypy.HTTPRedirect('/tvb')
step_name = category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an algorithm",
displayControl=False)
adapters_list = []
for algo_group in self.flow_service.get_groups_for_categories(
[category]):
if algo_group.ui_display < 0:
continue
adapter_link = self.get_url_adapter(step_key, algo_group.id)
adapters_list.append({
base.KEY_TITLE: algo_group.displayname,
'link': adapter_link,
'description': algo_group.description,
'subsection': algo_group.subsection_name
})
self.analyze_adapters = adapters_list
template_specification[base.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@context_selected()
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu",
section_name='connectivity',
controlPage=None,
title="Select an algorithm",
displayControl=False,
subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
## This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@cherrypy.expose
@base.settings()
@logged()
@context_selected()
@using_template('base_template')
def prepare_group_launch(self, group_gid, step_key, adapter_key, **data):
"""
Recieves as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of gid's for all the datatypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data['range_param_name']
del data['range_param_name']
data[PARAM_RANGE_1] = range_param_name
data[range_param_name] = ','.join([dt.gid for dt in datatypes])
OperationService().group_operation_launch(
base.get_logged_user().id,
base.get_current_project().id, int(adapter_key), int(step_key),
**data)
redirect_url = self._compute_back_link('operations',
base.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@context_selected()
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = base.get_current_project()
algo_group = self.flow_service.get_algo_group_by_identifier(
adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algo_group is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
if cherrypy.request.method == 'POST':
back_indicator = back_page if back_page == 'burst' else 'operations'
success_url = self._compute_back_link(back_indicator, project)
data[base.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
success_url, step_key,
algo_group, **data)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algo_group.group_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(
project.id, step_key, algo_group, submit_link, not not_reset)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if base.KEY_SUBMIT_LINK not in template_specification:
template_specification[base.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[base.KEY_DISPLAY_MENU] = False
else:
template_specification[base.KEY_DISPLAY_MENU] = True
template_specification[base.KEY_BACK_PAGE] = back_page_link
template_specification[base.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algo_group)
if (back_page is not None and back_page in ['operations', 'data']
and not (base.KEY_SECTION in template_specification
and template_specification[base.KEY_SECTION]
== 'connectivity')):
template_specification[base.KEY_SECTION] = 'project'
return template_specification
@cherrypy.expose
@using_template("flow/reduce_dimension_select")
@logged()
def gettemplatefordimensionselect(self,
entity_gid=None,
select_name="",
reset_session='False',
parameters_prefix="dimensions",
required_dimension=1,
expected_shape="",
operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid - the GID of the entity for which is displayed the component
select_name - the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix - a string which will be used for computing the names of the component
required_dimension - the expected dimension for the resulted array
expected_shape and operations - used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
expected_shape='x,512,x' and operations='x,<,x'
"""
template_params = dict()
template_params["select_name"] = ""
template_params["data"] = []
template_params["parameters_prefix"] = parameters_prefix
template_params["array_shape"] = ""
template_params["required_dimension"] = required_dimension
template_params["currentDim"] = ""
template_params["required_dim_msg"] = ""
template_params["expected_shape"] = expected_shape
template_params["operations"] = operations
#if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not eval(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items()
if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray(
).parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(
list(array_shape), dimensions, selected_agg_functions)
if required_dimension is not None and current_dim != int(
required_dimension):
template_params[
"required_dim_msg"] = "Please select a " + str(
required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(
current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels'
) and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
#make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions')
and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions)
== len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = dict()
for function_key in function:
func_dict[
function_key] = default_agg_functions[
function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in xrange(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items,
selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in xrange(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@cherrypy.expose
@using_template("flow/type2component/datatype2select_simple")
@logged()
def getfiltereddatatypes(self, name, parent_div, tree_session_key,
filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
base.set_error_message(
"Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(
FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
#Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][
FILTER_TYPE] == 'date':
try:
filter_ = string2date(filter_, False)
filters[FILTER_VALUES][i] = filter_
except ValueError, excep:
raise excep
#In order for the filter object not to "stack up" on multiple calls to
#this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
#Get dataTypes that match the filters from DB then populate with values
datatypes = self.flow_service.get_available_datatypes(
base.get_current_project().id, datatype, new_filter)
values = self.flow_service.populate_values(
datatypes, datatype, self.context.get_current_step())
#Create a dictionary that matches what the template expects
parameters = dict()
parameters[ABCAdapter.KEY_NAME] = name
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[
ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and eval(
str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(
values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected is not None and previous_selected in [
str(vv['value']) for vv in values
]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
parameters[ABCAdapter.KEY_FILTERABLE] = availablefilter
parameters[ABCAdapter.KEY_TYPE] = ABCAdapter.TYPE_SELECT
parameters[ABCAdapter.KEY_OPTIONS] = values
parameters[ABCAdapter.KEY_DATATYPE] = datatype
template_specification = {
"inputRow": parameters,
"disabled": False,
"parentDivId": parent_div,
base.KEY_SESSION_TREE: tree_session_key
}
return self.fill_default_attributes(template_specification)
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.flow_service.get_analyze_groups()
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an analyzer",
displayControl=False)
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
template_specification[common.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu",
section_name='connectivity',
controlPage=None,
title="Select an algorithm",
displayControl=False,
subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
# This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.flow_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.flow_service.get_algorithm_by_identifier(
algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
algorithm.input_tree = self.flow_service.prepare_adapter(algorithm)
algorithms.append(algorithm)
template_specification = dict(
mainContent="flow/algorithms_list",
algorithms=algorithms,
title="Select an algorithm",
section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification,
algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
OperationService().group_operation_launch(
common.get_logged_user().id,
common.get_current_project().id, int(algorithm_id), int(step_key),
**data)
redirect_url = self._compute_back_link('operations',
common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.flow_service.get_algorithm_by_identifier(adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
step_key, algorithm,
**data)
self._populate_section(algorithm, template_specification, is_burst)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algorithm.algorithm_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
not_reset = True
template_specification = self.get_template_for_adapter(
project.id,
step_key,
algorithm,
submit_link,
not not_reset,
is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification,
algorithm.displayname)
return template_specification
@expose_fragment("flow/reduce_dimension_select")
def gettemplatefordimensionselect(self,
entity_gid=None,
select_name="",
reset_session='False',
parameters_prefix="dimensions",
required_dimension=1,
expected_shape="",
operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid
the GID of the entity for which is displayed the component
select_name
the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix
a string which will be used for computing the names of the component
required_dimension
the expected dimension for the resulted array
expected_shape and operations
used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
``expected_shape=x,512,x`` and ``operations='x,<,x``
"""
template_params = {
"select_name": "",
"data": [],
"parameters_prefix": parameters_prefix,
"array_shape": "",
"required_dimension": required_dimension,
"currentDim": "",
"required_dim_msg": "",
"expected_shape": expected_shape,
"operations": operations
}
# if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not string2bool(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items()
if k.startswith(starts_with_str))
from tvb.datatypes.arrays import MappedArray
dimensions, selected_agg_functions, required_dimension, _ = MappedArray(
).parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(
list(array_shape), dimensions, selected_agg_functions)
if required_dimension is not None and current_dim != int(
required_dimension):
template_params[
"required_dim_msg"] = "Please select a " + str(
required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(
current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels'
) and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
# make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions')
and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions)
== len(array_shape)):
# will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = {}
for function_key in function:
func_dict[
function_key] = default_agg_functions[
function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in range(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items,
selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in range(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@expose_fragment("flow/type2component/datatype2select_simple")
def getfiltereddatatypes(self, name, parent_div, tree_session_key,
filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
common.set_error_message(
"Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(
FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
# Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][
FILTER_TYPE] == 'date':
try:
temp_date = string2date(filters[FILTER_VALUES][i], False)
filters[FILTER_VALUES][i] = temp_date
except ValueError:
raise
# In order for the filter object not to "stack up" on multiple calls to
# this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
# Get dataTypes that match the filters from DB then populate with values
values, total_count = InputTreeManager(
).populate_option_values_for_dtype(common.get_current_project().id,
datatype, new_filter,
self.context.get_current_step())
# Create a dictionary that matches what the template expects
parameters = {
ABCAdapter.KEY_NAME: name,
ABCAdapter.KEY_FILTERABLE: availablefilter,
ABCAdapter.KEY_TYPE: ABCAdapter.TYPE_SELECT,
ABCAdapter.KEY_OPTIONS: values,
ABCAdapter.KEY_DATATYPE: datatype
}
if total_count > MAXIMUM_DATA_TYPES_DISPLAYED:
parameters[KEY_WARNING] = WARNING_OVERFLOW
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[
ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and string2bool(
str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(
values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected in [str(vv['value']) for vv in values]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
template_specification = {
"inputRow": parameters,
"disabled": False,
"parentDivId": parent_div,
common.KEY_SESSION_TREE: tree_session_key
}
return self.fill_default_attributes(template_specification)
def _get_node(self, input_tree, name):
"""
Given a input tree and a variable name, check to see if any default filters exist.
"""
for entry in input_tree:
if (ABCAdapter.KEY_DATATYPE in entry
and ABCAdapter.KEY_NAME in entry
and str(entry[ABCAdapter.KEY_NAME]) == str(name)):
return entry
if entry.get(ABCAdapter.KEY_ATTRIBUTES) is not None:
in_attr = self._get_node(entry[ABCAdapter.KEY_ATTRIBUTES],
name)
if in_attr is not None:
return in_attr
if entry.get(ABCAdapter.KEY_OPTIONS) is not None:
in_options = self._get_node(entry[ABCAdapter.KEY_OPTIONS],
name)
if in_options is not None:
return in_options
return None
def execute_post(self, project_id, submit_url, step_key, algorithm,
**data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
form = adapter_instance.get_form()(project_id=project_id)
form.fill_from_post(data)
dt_dict = None
if form.validate():
dt_dict = form.get_dict()
if dt_dict is None:
raise formencode.Invalid(
"Could not build a dict out of this form!", {},
None,
error_dict=form.get_errors_dict())
adapter_instance.submit_form(form)
result = self.flow_service.fire_operation(adapter_instance,
common.get_logged_user(),
project_id, **dt_dict)
# Store input data in session, for informing user of it.
step = self.flow_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None,
copy.deepcopy(data))
if isinstance(adapter_instance, ABCDisplayer):
if isinstance(result, dict):
result[common.
KEY_OPERATION_ID] = adapter_instance.operation_id
return result
else:
common.set_error_message(
"Invalid result returned from Displayer! Dictionary is expected!"
)
else:
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid as excep:
errors = excep.unpack_errors()
common.set_error_message("Invalid form inputs")
self.logger.warning("Invalid form inputs %s" % errors)
except OperationException as excep1:
self.logger.exception("Error while executing a Launch procedure:" +
excep1.message)
common.set_error_message(excep1.message)
previous_step = self.context.get_current_substep()
should_reset = previous_step is None or data.get(
common.KEY_ADAPTER) != previous_step
template_specification = self.get_template_for_adapter(
project_id, step_key, algorithm, submit_url, should_reset)
if (errors is not None) and (template_specification is not None):
template_specification[common.KEY_ERRORS] = errors
template_specification[
common.KEY_OPERATION_ID] = adapter_instance.operation_id
return template_specification
def get_template_for_adapter(self,
project_id,
step_key,
stored_adapter,
submit_url,
session_reset=True,
is_burst=True):
""" Get Input HTML Interface template or a given adapter """
try:
if session_reset:
self.context.clean_from_session()
group = None
# Cache some values in session, for performance
previous_tree = self.context.get_current_input_tree()
previous_sub_step = self.context.get_current_substep()
category = self.flow_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
adapter_instance = self.flow_service.prepare_adapter(
stored_adapter)
if adapter_instance.get_input_tree() is None:
adapter_form = self.flow_service.prepare_adapter_form(
adapter_instance, project_id)
template_specification = dict(submitLink=submit_url,
form=adapter_form,
title=title)
# TODO: to be removed when all forms are migrated
else:
if not session_reset and previous_tree is not None and previous_sub_step == stored_adapter.id:
adapter_interface = previous_tree
else:
adapter_interface = self.flow_service.prepare_adapter_tree_interface(
adapter_instance, project_id,
stored_adapter.fk_category)
self.context.add_adapter_to_session(
stored_adapter, adapter_interface)
current_defaults = self.context.get_current_default()
if current_defaults is not None:
# Change default values in tree, according to selected input
adapter_interface = InputTreeManager.fill_defaults(
adapter_interface, current_defaults)
template_specification = dict(submitLink=submit_url,
inputList=adapter_interface,
title=title)
self._populate_section(stored_adapter, template_specification,
is_burst)
return template_specification
except OperationException as oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
common.set_warning_message(
'Inconsistent Adapter! Please review the link (development problem)!'
)
return None
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def readserverstaticfile(self, coded_path):
"""
Retrieve file from Local storage, having a File System Path.
"""
try:
with open(url2path(coded_path), "rb") as f:
return f.read()
except Exception as excep:
self.logger.error("Could not retrieve file from path:" +
str(coded_path))
self.logger.exception(excep)
def _read_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
dataset_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
entity_dt = h5.load_from_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity_dt, dataset_name)
if callable(result):
if kwargs:
result = result(**kwargs)
else:
result = result()
return result
@expose_json
def invoke_adapter(self, algo_id, method_name, entity_gid, **kwargs):
algorithm = self.flow_service.get_algorithm_by_identifier(algo_id)
adapter_instance = ABCAdapter.build_adapter(algorithm)
entity = ABCAdapter.load_entity_by_gid(entity_gid)
storage_path = self.files_helper.get_project_folder(
entity.parent_operation.project, str(entity.fk_from_operation))
adapter_instance.storage_path = storage_path
method = getattr(adapter_instance, method_name)
if kwargs:
return method(entity_gid, **kwargs)
return method(entity_gid)
@expose_json
def read_from_h5_file(self,
entity_gid,
method_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
method_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
entity_h5 = h5.h5_file_for_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity_h5, method_name)
if kwargs:
result = result(**kwargs)
else:
result = result()
entity_h5.close()
return self._prepare_result(result, flatten)
@expose_json
def read_datatype_attribute(self,
entity_gid,
dataset_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
"""
Retrieve from a given DataType a property or a method result.
:returns: JSON representation of the attribute.
:param entity_gid: GID for DataType entity
:param dataset_name: name of the dataType property /method
:param flatten: result should be flatten before return (use with WebGL data mainly e.g vertices/triangles)
Ignored if the attribute is not an ndarray
:param datatype_kwargs: if passed, will contain a dictionary of type {'name' : 'gid'}, and for each such
pair, a load_entity will be performed and kwargs will be updated to contain the result
:param kwargs: extra parameters to be passed when dataset_name is method.
"""
result = self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
return self._prepare_result(result, flatten)
def _prepare_result(self, result, flatten):
if isinstance(result, numpy.ndarray):
# for ndarrays honor the flatten kwarg and convert to lists as ndarrs are not json-able
if flatten is True or flatten == "True":
result = result.flatten()
return result.tolist()
else:
return result
@expose_numpy_array
def read_binary_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
return self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
@expose_fragment("flow/genericAdapterFormFields")
def get_simple_adapter_interface(self,
algorithm_id,
parent_div='',
is_uploader=False):
"""
AJAX exposed method. Will return only the interface for a adapter, to
be used when tabs are needed.
"""
curent_project = common.get_current_project()
is_uploader = string2bool(is_uploader)
template_specification = self.get_adapter_template(
curent_project.id, algorithm_id, is_uploader)
template_specification[common.KEY_PARENT_DIV] = parent_div
return self.fill_default_attributes(template_specification)
@expose_fragment("flow/full_adapter_interface")
def getadapterinterface(self, project_id, algorithm_id, back_page=None):
"""
AJAX exposed method. Will return only a piece of a page,
to be integrated as part in another page.
"""
template_specification = self.get_adapter_template(
project_id, algorithm_id, False, back_page)
template_specification["isCallout"] = True
return self.fill_default_attributes(template_specification)
def get_adapter_template(self,
project_id,
algorithm_id,
is_upload=False,
back_page=None):
"""
Get the template for an adapter based on the algo group id.
"""
if not (project_id and int(project_id) and
(algorithm_id is not None) and int(algorithm_id)):
return ""
algorithm = self.flow_service.get_algorithm_by_identifier(algorithm_id)
if is_upload:
submit_link = "/project/launchloader/" + str(
project_id) + "/" + str(algorithm_id)
else:
submit_link = self.get_url_adapter(algorithm.fk_category,
algorithm.id, back_page)
current_step = self.context.get_current_substep()
if current_step is None or str(current_step) != str(algorithm_id):
self.context.clean_from_session()
template_specification = self.get_template_for_adapter(
project_id, algorithm.fk_category, algorithm, submit_link,
is_upload)
if template_specification is None:
return ""
template_specification[common.KEY_DISPLAY_MENU] = not is_upload
return template_specification
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reloadoperation(self, operation_id, **_):
"""Redirect to Operation Input selection page,
with input data already selected."""
operation = self.flow_service.load_operation(operation_id)
data = parse_json_parameters(operation.parameters)
self.context.add_adapter_to_session(operation.algorithm, None, data)
category_id = operation.algorithm.fk_category
algo_id = operation.fk_from_algo
raise cherrypy.HTTPRedirect("/flow/" + str(category_id) + "/" +
str(algo_id) + "?not_reset=True")
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reload_burst_operation(self, operation_id, is_group, **_):
"""
Find out from which burst was this operation launched. Set that burst as the selected one and
redirect to the burst page.
"""
is_group = int(is_group)
if not is_group:
operation = self.flow_service.load_operation(int(operation_id))
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = self.flow_service.load_operation(int(first_op.id))
operation.burst.prepare_after_load()
common.add2session(common.KEY_BURST_CONFIG, operation.burst)
raise cherrypy.HTTPRedirect("/burst/")
@expose_json
def stop_operation(self, operation_id, is_group, remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
operation_service = OperationService()
result = False
if int(is_group) == 0:
result = operation_service.stop_operation(operation_id)
if remove_after_stop:
ProjectService().remove_operation(operation_id)
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
operations_in_group = ProjectService.get_operations_in_group(
op_group)
for operation in operations_in_group:
tmp_res = operation_service.stop_operation(operation.id)
if remove_after_stop:
ProjectService().remove_operation(operation.id)
result = result or tmp_res
return result
@expose_json
def stop_burst_operation(self,
operation_id,
is_group,
remove_after_stop=False):
"""
For a given operation id that is part of a burst just stop the given burst.
:returns True when stopped operation was successfully.
"""
operation_id = int(operation_id)
if int(is_group) == 0:
operation = self.flow_service.load_operation(operation_id)
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = self.flow_service.load_operation(int(first_op.id))
try:
burst_service = BurstService()
result = burst_service.stop_burst(operation.burst)
if remove_after_stop:
current_burst = common.get_from_session(
common.KEY_BURST_CONFIG)
if current_burst and current_burst.id == operation.burst.id:
common.remove_from_session(common.KEY_BURST_CONFIG)
result = burst_service.cancel_or_remove_burst(
operation.burst.id) or result
return result
except Exception as ex:
self.logger.exception(ex)
return False
def fill_default_attributes(self, template_dictionary, title='-'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
if common.KEY_TITLE not in template_dictionary:
template_dictionary[common.KEY_TITLE] = title
if common.KEY_PARENT_DIV not in template_dictionary:
template_dictionary[common.KEY_PARENT_DIV] = ''
if common.KEY_PARAMETERS_CONFIG not in template_dictionary:
template_dictionary[common.KEY_PARAMETERS_CONFIG] = False
template_dictionary[
common.KEY_INCLUDE_RESOURCES] = 'flow/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
##### Below this point are operations that might be moved to different #####
##### controller #####
NEW_SELECTION_NAME = 'New selection'
def _get_available_selections(self, datatype_gid):
"""
selection retrieval common to selection component and connectivity selection
"""
curent_project = common.get_current_project()
selections = self.flow_service.get_selections_for_project(
curent_project.id, datatype_gid)
names, sel_values = [], []
for selection in selections:
names.append(selection.ui_name)
sel_values.append(selection.selected_nodes)
return names, sel_values
@expose_fragment('visualizers/commons/channel_selector_opts')
def get_available_selections(self, **data):
sel_names, sel_values = self._get_available_selections(
data['datatype_gid'])
return dict(namedSelections=list(zip(sel_names, sel_values)))
@expose_json
def store_measure_points_selection(self, ui_name, **data):
"""
Save a MeasurePoints selection (new or update existing entity).
"""
if ui_name and ui_name != self.NEW_SELECTION_NAME:
sel_project_id = common.get_current_project().id
# client sends integers as strings:
selection = json.dumps(
[int(s) for s in json.loads(data['selection'])])
datatype_gid = data['datatype_gid']
self.flow_service.save_measure_points_selection(
ui_name, selection, datatype_gid, sel_project_id)
return [True, 'Selection saved successfully.']
else:
error_msg = self.NEW_SELECTION_NAME + " or empty name are not valid as selection names."
return [False, error_msg]
@expose_fragment(
"visualizers/pse_discrete/inserting_new_threshold_spec_bar")
def create_row_of_specs(self, count):
return dict(id_increment_count=count)
@expose_json
def store_pse_filter(self, config_name, **data):
# this will need to be updated in such a way that the expose_json actually gets used
## also this is going to be changed to be storing through the flow service and dao. Stay updated
try:
##this is to check whether there is already an entry in the
for i, (name, Val) in enumerate(self.PSE_names_list):
if name == config_name:
self.PSE_names_list[i] = (
config_name,
(data['threshold_value'] + "," +
data['threshold_type'] + "," + data['not_presence'])
) # replace the previous occurence of the config name, and carry on.
self.get_pse_filters()
return [
True, 'Selected Text stored, and selection updated'
]
self.PSE_names_list.append(
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence'])))
except AttributeError:
self.PSE_names_list = [
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence']))
]
self.get_pse_filters()
return [True, 'Selected Text stored, and selection updated']
@expose_fragment("visualizers/commons/channel_selector_opts")
def get_pse_filters(self):
try:
return dict(namedSelections=self.PSE_names_list)
except AttributeError:
return dict(
namedSelections=[]
) # this will give us back atleast the New Selection option in the select
except:
raise
@expose_json
def store_exploration_section(self, val_range, step, dt_group_guid):
"""
Launching method for further simulations.
"""
range_list = [float(num) for num in val_range.split(",")]
step_list = [float(num) for num in step.split(",")]
datatype_group_ob = ProjectService().get_datatypegroup_by_gid(
dt_group_guid)
operation_grp = datatype_group_ob.parent_operation_group
operation_obj = self.flow_service.load_operation(
datatype_group_ob.fk_from_operation)
parameters = json.loads(operation_obj.parameters)
range1name, range1_dict = json.loads(operation_grp.range1)
range2name, range2_dict = json.loads(operation_grp.range2)
parameters[RANGE_PARAMETER_1] = range1name
parameters[RANGE_PARAMETER_2] = range2name
##change the existing simulator parameters to be min max step types
range1_dict = {
constants.ATT_MINVALUE: range_list[0],
constants.ATT_MAXVALUE: range_list[1],
constants.ATT_STEP: step_list[0]
}
range2_dict = {
constants.ATT_MINVALUE: range_list[2],
constants.ATT_MAXVALUE: range_list[3],
constants.ATT_STEP: step_list[1]
}
parameters[range1name] = json.dumps(
range1_dict) # this is for the x axis parameter
parameters[range2name] = json.dumps(
range2_dict) # this is for the y axis parameter
OperationService().group_operation_launch(
common.get_logged_user().id,
common.get_current_project().id, operation_obj.algorithm.id,
operation_obj.algorithm.fk_category, datatype_group_ob,
**parameters)
return [True, 'Stored the exploration material successfully']
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.flow_service.get_analyze_groups()
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu", section_name=step_name, controlPage=None,
title="Select an analyzer", displayControl=False)
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(analyze_category.id, adapter_group.children[0].id)
adapters_list.append({common.KEY_TITLE: adapter_group.name,
'link': adapter_link,
'description': adapter_group.description,
'subsection': adapter_group.children[0].subsection_name})
self.analyze_adapters = adapters_list
template_specification[common.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu", section_name='connectivity', controlPage=None,
title="Select an algorithm", displayControl=False, subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
## This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.flow_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.flow_service.get_algorithm_by_identifier(algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
algorithm.input_tree = self.flow_service.prepare_adapter(project.id, algorithm)
algorithms.append(algorithm)
template_specification = dict(mainContent="flow/algorithms_list", algorithms=algorithms,
title="Select an algorithm", section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification, algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
OperationService().group_operation_launch(common.get_logged_user().id, common.get_current_project().id,
int(algorithm_id), int(step_key), **data)
redirect_url = self._compute_back_link('operations', common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self, step_key, adapter_key, cancel=False, back_page=None, not_reset=False, **data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.flow_service.get_algorithm_by_identifier(adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link, step_key, algorithm, **data)
self._populate_section(algorithm, template_specification, is_burst)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algorithm.algorithm_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(project.id, step_key, algorithm,
submit_link, not not_reset, is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algorithm.displayname)
return template_specification
@expose_fragment("flow/reduce_dimension_select")
def gettemplatefordimensionselect(self, entity_gid=None, select_name="", reset_session='False',
parameters_prefix="dimensions", required_dimension=1,
expected_shape="", operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid
the GID of the entity for which is displayed the component
select_name
the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix
a string which will be used for computing the names of the component
required_dimension
the expected dimension for the resulted array
expected_shape and operations
used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
``expected_shape=x,512,x`` and ``operations='x,<,x``
"""
template_params = {"select_name": "",
"data": [],
"parameters_prefix": parameters_prefix,
"array_shape": "",
"required_dimension": required_dimension,
"currentDim": "",
"required_dim_msg": "",
"expected_shape": expected_shape,
"operations": operations}
#if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not string2bool(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items() if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray().parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(list(array_shape), dimensions,
selected_agg_functions)
if required_dimension is not None and current_dim != int(required_dimension):
template_params["required_dim_msg"] = "Please select a " + str(required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels') and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
#make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions') and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions) == len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = {}
for function_key in function:
func_dict[function_key] = default_agg_functions[function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in xrange(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items, selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in xrange(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@expose_fragment("flow/type2component/datatype2select_simple")
def getfiltereddatatypes(self, name, parent_div, tree_session_key, filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
common.set_error_message("Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
#Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][FILTER_TYPE] == 'date':
try:
temp_date = string2date(filters[FILTER_VALUES][i], False)
filters[FILTER_VALUES][i] = temp_date
except ValueError:
raise
#In order for the filter object not to "stack up" on multiple calls to
#this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
#Get dataTypes that match the filters from DB then populate with values
values, total_count = InputTreeManager().populate_option_values_for_dtype(
common.get_current_project().id,
datatype, new_filter,
self.context.get_current_step() )
#Create a dictionary that matches what the template expects
parameters = {ABCAdapter.KEY_NAME: name,
ABCAdapter.KEY_FILTERABLE: availablefilter,
ABCAdapter.KEY_TYPE: ABCAdapter.TYPE_SELECT,
ABCAdapter.KEY_OPTIONS: values,
ABCAdapter.KEY_DATATYPE: datatype}
if total_count > MAXIMUM_DATA_TYPES_DISPLAYED:
parameters[KEY_WARNING] = WARNING_OVERFLOW
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and string2bool(str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected in [str(vv['value']) for vv in values]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
template_specification = {"inputRow": parameters, "disabled": False,
"parentDivId": parent_div, common.KEY_SESSION_TREE: tree_session_key}
return self.fill_default_attributes(template_specification)
def _get_node(self, input_tree, name):
"""
Given a input tree and a variable name, check to see if any default filters exist.
"""
for entry in input_tree:
if (ABCAdapter.KEY_DATATYPE in entry and ABCAdapter.KEY_NAME in entry
and str(entry[ABCAdapter.KEY_NAME]) == str(name)):
return entry
if entry.get(ABCAdapter.KEY_ATTRIBUTES) is not None:
in_attr = self._get_node(entry[ABCAdapter.KEY_ATTRIBUTES], name)
if in_attr is not None:
return in_attr
if entry.get(ABCAdapter.KEY_OPTIONS) is not None:
in_options = self._get_node(entry[ABCAdapter.KEY_OPTIONS], name)
if in_options is not None:
return in_options
return None
def execute_post(self, project_id, submit_url, step_key, algorithm, **data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
result = self.flow_service.fire_operation(adapter_instance, common.get_logged_user(), project_id, **data)
# Store input data in session, for informing user of it.
step = self.flow_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None, copy.deepcopy(data))
if isinstance(adapter_instance, ABCDisplayer):
if isinstance(result, dict):
result[common.KEY_OPERATION_ID] = adapter_instance.operation_id
return result
else:
common.set_error_message("Invalid result returned from Displayer! Dictionary is expected!")
else:
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid, excep:
errors = excep.unpack_errors()
except OperationException, excep1:
self.logger.exception("Error while executing a Launch procedure:" + excep1.message)
common.set_error_message(excep1.message)
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
self.operation_services = OperationService()
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
self.operation_services = OperationService()
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.algorithm_service.get_analyze_groups(
)
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu",
section_name=step_name,
controlPage=None,
title="Select an analyzer",
displayControl=False)
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(
analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(
analyze_category.id, adapter_group.children[0].id)
adapters_list.append({
common.KEY_TITLE:
adapter_group.name,
'link':
adapter_link,
'description':
adapter_group.description,
'subsection':
adapter_group.children[0].subsection_name
})
self.analyze_adapters = adapters_list
template_specification[common.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu",
section_name='connectivity',
controlPage=None,
title="Select an algorithm",
displayControl=False,
subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
# This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.algorithm_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.algorithm_service.get_algorithm_by_identifier(
algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
adapter_instance = self.algorithm_service.prepare_adapter(
algorithm)
adapter_form = self.algorithm_service.prepare_adapter_form(
adapter_instance, project.id)
algorithm.form = self.render_adapter_form(adapter_form)
algorithms.append(algorithm)
template_specification = dict(
mainContent="flow/algorithms_list",
algorithms=algorithms,
title="Select an algorithm",
section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification,
algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
self.operation_services.group_operation_launch(
common.get_logged_user().id, common.get_current_project(),
int(algorithm_id), int(step_key), **data)
redirect_url = self._compute_back_link('operations',
common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self,
step_key,
adapter_key,
cancel=False,
back_page=None,
not_reset=False,
**data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.algorithm_service.get_algorithm_by_identifier(
adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link,
step_key, algorithm,
**data)
self._populate_section(algorithm, template_specification, is_burst)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers
and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algorithm.algorithm_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
not_reset = True
template_specification = self.get_template_for_adapter(
project.id,
step_key,
algorithm,
submit_link,
not not_reset,
is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification,
algorithm.displayname)
return template_specification
@expose_fragment('form_fields/options_field')
@settings
@context_selected
def get_filtered_datatypes(self, dt_module, dt_class, filters,
has_all_option, has_none_option):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
index_class = getattr(sys.modules[dt_module], dt_class)()
filters_dict = json.loads(filters)
fields = []
operations = []
values = []
for idx in range(len(filters_dict['fields'])):
fields.append(filters_dict['fields'][idx])
operations.append(filters_dict['operations'][idx])
values.append(filters_dict['values'][idx])
filter = FilterChain(fields=fields,
operations=operations,
values=values)
project = common.get_current_project()
form = Form(project_id=project.id, draw_ranges=True)
data_type_gid_attr = DataTypeGidAttr(
linked_datatype=REGISTRY.get_datatype_for_index(index_class))
data_type_gid_attr.required = not string2bool(has_none_option)
select_field = TraitDataTypeSelectField(
data_type_gid_attr,
form,
conditions=filter,
has_all_option=string2bool(has_all_option))
return {'options': select_field.options()}
def execute_post(self, project_id, submit_url, step_key, algorithm,
**data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
form = adapter_instance.get_form()(project_id=project_id)
if 'fill_defaults' in data:
form.fill_from_post_plus_defaults(data)
else:
form.fill_from_post(data)
view_model = None
if form.validate():
try:
view_model = form.get_view_model()()
form.fill_trait(view_model)
except NotImplementedError:
self.logger.exception(
"Form and/or ViewModel not fully implemented for " +
str(form))
raise InvalidFormValues(
"Invalid form inputs! Could not find a model for this form!",
error_dict=form.get_errors_dict())
else:
raise InvalidFormValues(
"Invalid form inputs! Could not fill algorithm from the given inputs!",
error_dict=form.get_errors_dict())
adapter_instance.submit_form(form)
if issubclass(type(adapter_instance), ABCDisplayer):
adapter_instance.current_project_id = project_id
adapter_instance.user_id = common.get_logged_user().id
result = adapter_instance.launch(view_model)
if isinstance(result, dict):
return result
else:
common.set_error_message(
"Invalid result returned from Displayer! Dictionary is expected!"
)
return {}
result = self.operation_services.fire_operation(
adapter_instance,
common.get_logged_user(),
project_id,
view_model=view_model)
# Store input data in session, for informing user of it.
step = self.algorithm_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None,
copy.deepcopy(data))
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid as excep:
errors = excep.unpack_errors()
common.set_error_message("Invalid form inputs")
self.logger.warning("Invalid form inputs %s" % errors)
except (OperationException, LaunchException,
TraitValueError) as excep1:
self.logger.exception("Error while executing a Launch procedure:" +
excep1.message)
common.set_error_message(excep1.message)
except InvalidFormValues as excep2:
message, errors = excep2.display_full_errors()
common.set_error_message(message)
self.logger.warning("%s \n %s" % (message, errors))
previous_step = self.context.get_current_substep()
should_reset = previous_step is None or data.get(
common.KEY_ADAPTER) != previous_step
template_specification = self.get_template_for_adapter(
project_id, step_key, algorithm, submit_url, should_reset)
if (errors is not None) and (template_specification is not None):
template_specification[common.KEY_ERRORS] = errors
template_specification[
common.KEY_OPERATION_ID] = adapter_instance.operation_id
return template_specification
def get_template_for_adapter(self,
project_id,
step_key,
stored_adapter,
submit_url,
session_reset=True,
is_burst=True):
""" Get Input HTML Interface template or a given adapter """
try:
if session_reset:
self.context.clean_from_session()
group = None
category = self.algorithm_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
adapter_instance = self.algorithm_service.prepare_adapter(
stored_adapter)
adapter_form = self.algorithm_service.prepare_adapter_form(
adapter_instance, project_id)
template_specification = dict(
submitLink=submit_url,
adapter_form=self.render_adapter_form(adapter_form),
title=title)
self._populate_section(stored_adapter, template_specification,
is_burst)
return template_specification
except OperationException as oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
common.set_warning_message(
'Inconsistent Adapter! Please review the link (development problem)!'
)
return None
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def readserverstaticfile(self, coded_path):
"""
Retrieve file from Local storage, having a File System Path.
"""
try:
with open(url2path(coded_path), "rb") as f:
return f.read()
except Exception as excep:
self.logger.error("Could not retrieve file from path:" +
str(coded_path))
self.logger.exception(excep)
def _read_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
dataset_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
entity_dt = h5.load_from_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity_dt, dataset_name)
if callable(result):
if kwargs:
result = result(**kwargs)
else:
result = result()
return result
@expose_json
def invoke_adapter(self, algo_id, method_name, entity_gid, **kwargs):
algorithm = self.algorithm_service.get_algorithm_by_identifier(algo_id)
adapter_instance = ABCAdapter.build_adapter(algorithm)
entity = ABCAdapter.load_entity_by_gid(entity_gid)
storage_path = self.files_helper.get_project_folder(
entity.parent_operation.project, str(entity.fk_from_operation))
adapter_instance.storage_path = storage_path
method = getattr(adapter_instance, method_name)
if kwargs:
return method(entity_gid, **kwargs)
return method(entity_gid)
@expose_json
def read_from_h5_file(self,
entity_gid,
method_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" +
method_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
entity_h5 = h5.h5_file_for_index(entity)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity_h5, method_name)
if kwargs:
result = result(**kwargs)
else:
result = result()
entity_h5.close()
return self._prepare_result(result, flatten)
@expose_json
def read_datatype_attribute(self,
entity_gid,
dataset_name,
flatten=False,
datatype_kwargs='null',
**kwargs):
"""
Retrieve from a given DataType a property or a method result.
:returns: JSON representation of the attribute.
:param entity_gid: GID for DataType entity
:param dataset_name: name of the dataType property /method
:param flatten: result should be flatten before return (use with WebGL data mainly e.g vertices/triangles)
Ignored if the attribute is not an ndarray
:param datatype_kwargs: if passed, will contain a dictionary of type {'name' : 'gid'}, and for each such
pair, a load_entity will be performed and kwargs will be updated to contain the result
:param kwargs: extra parameters to be passed when dataset_name is method.
"""
result = self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
return self._prepare_result(result, flatten)
def _prepare_result(self, result, flatten):
if isinstance(result, numpy.ndarray):
# for ndarrays honor the flatten kwarg and convert to lists as ndarrs are not json-able
if flatten is True or flatten == "True":
result = result.flatten()
return result.tolist()
else:
return result
@expose_numpy_array
def read_binary_datatype_attribute(self,
entity_gid,
dataset_name,
datatype_kwargs='null',
**kwargs):
return self._read_datatype_attribute(entity_gid, dataset_name,
datatype_kwargs, **kwargs)
@expose_fragment("flow/genericAdapterFormFields")
def get_simple_adapter_interface(self,
algorithm_id,
parent_div='',
is_uploader=False):
"""
AJAX exposed method. Will return only the interface for a adapter, to
be used when tabs are needed.
"""
curent_project = common.get_current_project()
is_uploader = string2bool(is_uploader)
template_specification = self.get_adapter_template(
curent_project.id, algorithm_id, is_uploader)
template_specification[common.KEY_PARENT_DIV] = parent_div
return self.fill_default_attributes(template_specification)
@expose_fragment("flow/full_adapter_interface")
def getadapterinterface(self, project_id, algorithm_id, back_page=None):
"""
AJAX exposed method. Will return only a piece of a page,
to be integrated as part in another page.
"""
template_specification = self.get_adapter_template(
project_id, algorithm_id, False, back_page)
template_specification["isCallout"] = True
return self.fill_default_attributes(template_specification)
def get_adapter_template(self,
project_id,
algorithm_id,
is_upload=False,
back_page=None):
"""
Get the template for an adapter based on the algo group id.
"""
if not (project_id and int(project_id) and
(algorithm_id is not None) and int(algorithm_id)):
return ""
algorithm = self.algorithm_service.get_algorithm_by_identifier(
algorithm_id)
if is_upload:
submit_link = "/project/launchloader/" + str(
project_id) + "/" + str(algorithm_id)
else:
submit_link = self.get_url_adapter(algorithm.fk_category,
algorithm.id, back_page)
current_step = self.context.get_current_substep()
if current_step is None or str(current_step) != str(algorithm_id):
self.context.clean_from_session()
template_specification = self.get_template_for_adapter(
project_id, algorithm.fk_category, algorithm, submit_link,
is_upload)
if template_specification is None:
return ""
template_specification[common.KEY_DISPLAY_MENU] = not is_upload
return template_specification
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reloadoperation(self, operation_id, **_):
"""Redirect to Operation Input selection page,
with input data already selected."""
operation = OperationService.load_operation(operation_id)
data = parse_json_parameters(operation.parameters)
self.context.add_adapter_to_session(operation.algorithm, None, data)
category_id = operation.algorithm.fk_category
algo_id = operation.fk_from_algo
raise cherrypy.HTTPRedirect("/flow/" + str(category_id) + "/" +
str(algo_id) + "?not_reset=True")
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reload_burst_operation(self, operation_id, is_group, **_):
"""
Find out from which burst was this operation launched. Set that burst as the selected one and
redirect to the burst page.
"""
is_group = int(is_group)
if not is_group:
operation = OperationService.load_operation(int(operation_id))
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = OperationService.load_operation(int(first_op.id))
SimulatorController().copy_simulator_configuration(operation.burst.id)
raise cherrypy.HTTPRedirect("/burst/")
@expose_json
def cancel_or_remove_operation(self,
operation_id,
is_group,
remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
operation_id = int(operation_id)
is_group = int(is_group) != 0
if isinstance(remove_after_stop, str):
remove_after_stop = bool(remove_after_stop)
return SimulatorController.cancel_or_remove_operation(
operation_id, is_group, remove_after_stop)
def fill_default_attributes(self, template_dictionary, title='-'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
if common.KEY_TITLE not in template_dictionary:
template_dictionary[common.KEY_TITLE] = title
if common.KEY_PARENT_DIV not in template_dictionary:
template_dictionary[common.KEY_PARENT_DIV] = ''
if common.KEY_PARAMETERS_CONFIG not in template_dictionary:
template_dictionary[common.KEY_PARAMETERS_CONFIG] = False
template_dictionary[
common.KEY_INCLUDE_RESOURCES] = 'flow/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
NEW_SELECTION_NAME = 'New selection'
def _get_available_selections(self, datatype_gid):
"""
selection retrieval common to selection component and connectivity selection
"""
curent_project = common.get_current_project()
selections = self.algorithm_service.get_selections_for_project(
curent_project.id, datatype_gid)
names, sel_values = [], []
for selection in selections:
names.append(selection.ui_name)
sel_values.append(selection.selected_nodes)
return names, sel_values
@expose_fragment('visualizers/commons/channel_selector_opts')
def get_available_selections(self, **data):
sel_names, sel_values = self._get_available_selections(
data['datatype_gid'])
return dict(namedSelections=list(zip(sel_names, sel_values)))
@expose_json
def store_measure_points_selection(self, ui_name, **data):
"""
Save a MeasurePoints selection (new or update existing entity).
"""
if ui_name and ui_name != self.NEW_SELECTION_NAME:
sel_project_id = common.get_current_project().id
# client sends integers as strings:
selection = json.dumps(
[int(s) for s in json.loads(data['selection'])])
datatype_gid = data['datatype_gid']
self.algorithm_service.save_measure_points_selection(
ui_name, selection, datatype_gid, sel_project_id)
return [True, 'Selection saved successfully.']
else:
error_msg = self.NEW_SELECTION_NAME + " or empty name are not valid as selection names."
return [False, error_msg]
@expose_fragment(
"visualizers/pse_discrete/inserting_new_threshold_spec_bar")
def create_row_of_specs(self, count):
return dict(id_increment_count=count)
@expose_json
def store_pse_filter(self, config_name, **data):
# this will need to be updated in such a way that the expose_json actually gets used
## also this is going to be changed to be storing through the flow service and dao. Stay updated
try:
##this is to check whether there is already an entry in the
for i, (name, Val) in enumerate(self.PSE_names_list):
if name == config_name:
self.PSE_names_list[i] = (
config_name,
(data['threshold_value'] + "," +
data['threshold_type'] + "," + data['not_presence'])
) # replace the previous occurence of the config name, and carry on.
self.get_pse_filters()
return [
True, 'Selected Text stored, and selection updated'
]
self.PSE_names_list.append(
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence'])))
except AttributeError:
self.PSE_names_list = [
(config_name,
(data['threshold_value'] + "," + data['threshold_type'] +
"," + data['not_presence']))
]
self.get_pse_filters()
return [True, 'Selected Text stored, and selection updated']
@expose_fragment("visualizers/commons/channel_selector_opts")
def get_pse_filters(self):
try:
return dict(namedSelections=self.PSE_names_list)
except AttributeError:
return dict(
namedSelections=[]
) # this will give us back atleast the New Selection option in the select
except:
raise
@expose_json
def store_exploration_section(self, val_range, step, dt_group_guid):
"""
Launching method for further simulations.
"""
range_list = [float(num) for num in val_range.split(",")]
step_list = [float(num) for num in step.split(",")]
datatype_group_ob = ProjectService().get_datatypegroup_by_gid(
dt_group_guid)
operation_grp = datatype_group_ob.parent_operation_group
operation_obj = OperationService.load_operation(
datatype_group_ob.fk_from_operation)
parameters = json.loads(operation_obj.parameters)
range1name, range1_dict = json.loads(operation_grp.range1)
range2name, range2_dict = json.loads(operation_grp.range2)
parameters[RANGE_PARAMETER_1] = range1name
parameters[RANGE_PARAMETER_2] = range2name
# change the existing simulator parameters to be min max step types
range1_dict = {
constants.ATT_MINVALUE: range_list[0],
constants.ATT_MAXVALUE: range_list[1],
constants.ATT_STEP: step_list[0]
}
range2_dict = {
constants.ATT_MINVALUE: range_list[2],
constants.ATT_MAXVALUE: range_list[3],
constants.ATT_STEP: step_list[1]
}
parameters[range1name] = json.dumps(
range1_dict) # this is for the x axis parameter
parameters[range2name] = json.dumps(
range2_dict) # this is for the y axis parameter
OperationService().group_operation_launch(
common.get_logged_user().id, common.get_current_project(),
operation_obj.algorithm.id, operation_obj.algorithm.fk_category,
datatype_group_ob, **parameters)
return [True, 'Stored the exploration material successfully']
class FlowController(BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@expose_page
@settings
@context_selected
def step_analyzers(self):
"""
Choose exact action/adapter for current step.
"""
try:
analyze_category, groups = self.flow_service.get_analyze_groups()
step_name = analyze_category.displayname.lower()
template_specification = dict(mainContent="header_menu", section_name=step_name, controlPage=None,
title="Select an analyzer", displayControl=False)
adapters_list = []
for adapter_group in groups:
if len(adapter_group.children) > 1:
ids = [str(child.id) for child in adapter_group.children]
ids = ','.join(ids)
adapter_link = '/flow/show_group_of_algorithms/' + str(analyze_category.id) + "/" + ids
else:
adapter_link = self.get_url_adapter(analyze_category.id, adapter_group.children[0].id)
adapters_list.append({common.KEY_TITLE: adapter_group.name,
'link': adapter_link,
'description': adapter_group.description,
'subsection': adapter_group.children[0].subsection_name})
self.analyze_adapters = adapters_list
template_specification[common.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
except ValueError:
message = 'Could not load analyzers!'
common.set_warning_message(message)
self.logger.warning(message)
raise cherrypy.HTTPRedirect('/tvb')
@expose_page
@settings
@context_selected
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu", section_name='connectivity', controlPage=None,
title="Select an algorithm", displayControl=False, subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
## This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@expose_page
@settings
@context_selected
def show_group_of_algorithms(self, step_key, algorithm_ids):
project = common.get_current_project()
category = self.flow_service.get_category_by_id(step_key)
algorithms = []
for i in algorithm_ids.split(','):
algorithm_id = int(i)
algorithm = self.flow_service.get_algorithm_by_identifier(algorithm_id)
algorithm.link = self.get_url_adapter(step_key, algorithm_id)
algorithm.input_tree = self.flow_service.prepare_adapter(project.id, algorithm)
algorithms.append(algorithm)
template_specification = dict(mainContent="flow/algorithms_list", algorithms=algorithms,
title="Select an algorithm", section_name=category.displayname.lower())
self._populate_section(algorithms[0], template_specification)
self.fill_default_attributes(template_specification, algorithms[0].group_name)
return template_specification
@expose_page
@settings
@context_selected
def prepare_group_launch(self, group_gid, step_key, algorithm_id, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data.pop('range_param_name')
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join(dt.gid for dt in datatypes)
OperationService().group_operation_launch(common.get_logged_user().id, common.get_current_project().id,
int(algorithm_id), int(step_key), **data)
redirect_url = self._compute_back_link('operations', common.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@expose_page
@settings
@context_selected
def default(self, step_key, adapter_key, cancel=False, back_page=None, not_reset=False, **data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = common.get_current_project()
algorithm = self.flow_service.get_algorithm_by_identifier(adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algorithm is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
is_burst = back_page not in ['operations', 'data']
if cherrypy.request.method == 'POST':
data[common.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link, step_key, algorithm, **data)
self._populate_section(algorithm, template_specification, is_burst)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algorithm.algorithm_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
not_reset = True
template_specification = self.get_template_for_adapter(project.id, step_key, algorithm,
submit_link, not not_reset, is_burst=is_burst)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if common.KEY_SUBMIT_LINK not in template_specification:
template_specification[common.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[common.KEY_DISPLAY_MENU] = False
else:
template_specification[common.KEY_DISPLAY_MENU] = True
template_specification[common.KEY_BACK_PAGE] = back_page_link
template_specification[common.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algorithm.displayname)
return template_specification
@expose_fragment("flow/reduce_dimension_select")
def gettemplatefordimensionselect(self, entity_gid=None, select_name="", reset_session='False',
parameters_prefix="dimensions", required_dimension=1,
expected_shape="", operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid
the GID of the entity for which is displayed the component
select_name
the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix
a string which will be used for computing the names of the component
required_dimension
the expected dimension for the resulted array
expected_shape and operations
used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
``expected_shape=x,512,x`` and ``operations='x,<,x``
"""
template_params = {"select_name": "",
"data": [],
"parameters_prefix": parameters_prefix,
"array_shape": "",
"required_dimension": required_dimension,
"currentDim": "",
"required_dim_msg": "",
"expected_shape": expected_shape,
"operations": operations}
# if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not string2bool(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items() if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray().parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(list(array_shape), dimensions,
selected_agg_functions)
if required_dimension is not None and current_dim != int(required_dimension):
template_params["required_dim_msg"] = "Please select a " + str(required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels') and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
# make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions') and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions) == len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = {}
for function_key in function:
func_dict[function_key] = default_agg_functions[function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in range(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items, selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in range(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@expose_fragment("flow/type2component/datatype2select_simple")
def getfiltereddatatypes(self, name, parent_div, tree_session_key, filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
common.set_error_message("Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
# Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][FILTER_TYPE] == 'date':
try:
temp_date = string2date(filters[FILTER_VALUES][i], False)
filters[FILTER_VALUES][i] = temp_date
except ValueError:
raise
# In order for the filter object not to "stack up" on multiple calls to
# this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
# Get dataTypes that match the filters from DB then populate with values
values, total_count = InputTreeManager().populate_option_values_for_dtype(
common.get_current_project().id,
datatype, new_filter,
self.context.get_current_step())
# Create a dictionary that matches what the template expects
parameters = {ABCAdapter.KEY_NAME: name,
ABCAdapter.KEY_FILTERABLE: availablefilter,
ABCAdapter.KEY_TYPE: ABCAdapter.TYPE_SELECT,
ABCAdapter.KEY_OPTIONS: values,
ABCAdapter.KEY_DATATYPE: datatype}
if total_count > MAXIMUM_DATA_TYPES_DISPLAYED:
parameters[KEY_WARNING] = WARNING_OVERFLOW
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and string2bool(str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected in [str(vv['value']) for vv in values]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
template_specification = {"inputRow": parameters, "disabled": False,
"parentDivId": parent_div, common.KEY_SESSION_TREE: tree_session_key}
return self.fill_default_attributes(template_specification)
def _get_node(self, input_tree, name):
"""
Given a input tree and a variable name, check to see if any default filters exist.
"""
for entry in input_tree:
if (ABCAdapter.KEY_DATATYPE in entry and ABCAdapter.KEY_NAME in entry
and str(entry[ABCAdapter.KEY_NAME]) == str(name)):
return entry
if entry.get(ABCAdapter.KEY_ATTRIBUTES) is not None:
in_attr = self._get_node(entry[ABCAdapter.KEY_ATTRIBUTES], name)
if in_attr is not None:
return in_attr
if entry.get(ABCAdapter.KEY_OPTIONS) is not None:
in_options = self._get_node(entry[ABCAdapter.KEY_OPTIONS], name)
if in_options is not None:
return in_options
return None
def execute_post(self, project_id, submit_url, step_key, algorithm, **data):
""" Execute HTTP POST on a generic step."""
errors = None
adapter_instance = ABCAdapter.build_adapter(algorithm)
try:
result = self.flow_service.fire_operation(adapter_instance, common.get_logged_user(), project_id, **data)
# Store input data in session, for informing user of it.
step = self.flow_service.get_category_by_id(step_key)
if not step.rawinput:
self.context.add_adapter_to_session(None, None, copy.deepcopy(data))
if isinstance(adapter_instance, ABCDisplayer):
if isinstance(result, dict):
result[common.KEY_OPERATION_ID] = adapter_instance.operation_id
return result
else:
common.set_error_message("Invalid result returned from Displayer! Dictionary is expected!")
else:
if isinstance(result, list):
result = "Launched %s operations." % len(result)
common.set_important_message(str(result))
except formencode.Invalid as excep:
errors = excep.unpack_errors()
except OperationException as excep1:
self.logger.exception("Error while executing a Launch procedure:" + excep1.message)
common.set_error_message(excep1.message)
previous_step = self.context.get_current_substep()
should_reset = previous_step is None or data.get(common.KEY_ADAPTER) != previous_step
template_specification = self.get_template_for_adapter(project_id, step_key, algorithm,
submit_url, should_reset)
if (errors is not None) and (template_specification is not None):
template_specification[common.KEY_ERRORS] = errors
template_specification[common.KEY_OPERATION_ID] = adapter_instance.operation_id
return template_specification
def get_template_for_adapter(self, project_id, step_key, stored_adapter, submit_url, session_reset=True,
is_burst=True):
""" Get Input HTML Interface template or a given adapter """
try:
if session_reset:
self.context.clean_from_session()
group = None
# Cache some values in session, for performance
previous_tree = self.context.get_current_input_tree()
previous_sub_step = self.context.get_current_substep()
if not session_reset and previous_tree is not None and previous_sub_step == stored_adapter.id:
adapter_interface = previous_tree
else:
adapter_interface = self.flow_service.prepare_adapter(project_id, stored_adapter)
self.context.add_adapter_to_session(stored_adapter, adapter_interface)
category = self.flow_service.get_category_by_id(step_key)
title = "Fill parameters for step " + category.displayname.lower()
if group:
title = title + " - " + group.displayname
current_defaults = self.context.get_current_default()
if current_defaults is not None:
# Change default values in tree, according to selected input
adapter_interface = InputTreeManager.fill_defaults(adapter_interface, current_defaults)
template_specification = dict(submitLink=submit_url, inputList=adapter_interface, title=title)
self._populate_section(stored_adapter, template_specification, is_burst)
return template_specification
except OperationException as oexc:
self.logger.error("Inconsistent Adapter")
self.logger.exception(oexc)
common.set_warning_message('Inconsistent Adapter! Please review the link (development problem)!')
return None
@cherrypy.expose
@handle_error(redirect=False)
@check_user
def readserverstaticfile(self, coded_path):
"""
Retrieve file from Local storage, having a File System Path.
"""
try:
with open(url2path(coded_path), "rb") as f:
return f.read()
except Exception as excep:
self.logger.error("Could not retrieve file from path:" + str(coded_path))
self.logger.exception(excep)
def _read_datatype_attribute(self, entity_gid, dataset_name, datatype_kwargs='null', **kwargs):
self.logger.debug("Starting to read HDF5: " + entity_gid + "/" + dataset_name + "/" + str(kwargs))
entity = ABCAdapter.load_entity_by_gid(entity_gid)
datatype_kwargs = json.loads(datatype_kwargs)
if datatype_kwargs:
for key, value in six.iteritems(datatype_kwargs):
kwargs[key] = ABCAdapter.load_entity_by_gid(value)
result = getattr(entity, dataset_name)
if callable(result):
if kwargs:
result = result(**kwargs)
else:
result = result()
return result
@expose_json
def read_datatype_attribute(self, entity_gid, dataset_name, flatten=False, datatype_kwargs='null', **kwargs):
"""
Retrieve from a given DataType a property or a method result.
:returns: JSON representation of the attribute.
:param entity_gid: GID for DataType entity
:param dataset_name: name of the dataType property /method
:param flatten: result should be flatten before return (use with WebGL data mainly e.g vertices/triangles)
Ignored if the attribute is not an ndarray
:param datatype_kwargs: if passed, will contain a dictionary of type {'name' : 'gid'}, and for each such
pair, a load_entity will be performed and kwargs will be updated to contain the result
:param kwargs: extra parameters to be passed when dataset_name is method.
"""
result = self._read_datatype_attribute(entity_gid, dataset_name, datatype_kwargs, **kwargs)
if isinstance(result, numpy.ndarray):
# for ndarrays honor the flatten kwarg and convert to lists as ndarrs are not json-able
if flatten is True or flatten == "True":
result = result.flatten()
return result.tolist()
else:
return result
@expose_numpy_array
def read_binary_datatype_attribute(self, entity_gid, dataset_name, datatype_kwargs='null', **kwargs):
return self._read_datatype_attribute(entity_gid, dataset_name, datatype_kwargs, **kwargs)
@expose_fragment("flow/genericAdapterFormFields")
def get_simple_adapter_interface(self, algorithm_id, parent_div='', is_uploader=False):
"""
AJAX exposed method. Will return only the interface for a adapter, to
be used when tabs are needed.
"""
curent_project = common.get_current_project()
is_uploader = string2bool(is_uploader)
template_specification = self.get_adapter_template(curent_project.id, algorithm_id, is_uploader)
template_specification[common.KEY_PARENT_DIV] = parent_div
return self.fill_default_attributes(template_specification)
@expose_fragment("flow/full_adapter_interface")
def getadapterinterface(self, project_id, algorithm_id, back_page=None):
"""
AJAX exposed method. Will return only a piece of a page,
to be integrated as part in another page.
"""
template_specification = self.get_adapter_template(project_id, algorithm_id, False, back_page)
template_specification["isCallout"] = True
return self.fill_default_attributes(template_specification)
def get_adapter_template(self, project_id, algorithm_id, is_upload=False, back_page=None):
"""
Get the template for an adapter based on the algo group id.
"""
if not (project_id and int(project_id) and (algorithm_id is not None) and int(algorithm_id)):
return ""
algorithm = self.flow_service.get_algorithm_by_identifier(algorithm_id)
if is_upload:
submit_link = "/project/launchloader/" + str(project_id) + "/" + str(algorithm_id)
else:
submit_link = self.get_url_adapter(algorithm.fk_category, algorithm.id, back_page)
current_step = self.context.get_current_substep()
if current_step is None or str(current_step) != str(algorithm_id):
self.context.clean_from_session()
template_specification = self.get_template_for_adapter(project_id, algorithm.fk_category, algorithm,
submit_link, is_upload)
if template_specification is None:
return ""
template_specification[common.KEY_DISPLAY_MENU] = not is_upload
return template_specification
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reloadoperation(self, operation_id, **_):
"""Redirect to Operation Input selection page,
with input data already selected."""
operation = self.flow_service.load_operation(operation_id)
data = parse_json_parameters(operation.parameters)
self.context.add_adapter_to_session(operation.algorithm, None, data)
category_id = operation.algorithm.fk_category
algo_id = operation.fk_from_algo
raise cherrypy.HTTPRedirect("/flow/" + str(category_id) + "/" + str(algo_id) + "?not_reset=True")
@cherrypy.expose
@handle_error(redirect=True)
@context_selected
def reload_burst_operation(self, operation_id, is_group, **_):
"""
Find out from which burst was this operation launched. Set that burst as the selected one and
redirect to the burst page.
"""
is_group = int(is_group)
if not is_group:
operation = self.flow_service.load_operation(int(operation_id))
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = self.flow_service.load_operation(int(first_op.id))
operation.burst.prepare_after_load()
common.add2session(common.KEY_BURST_CONFIG, operation.burst)
raise cherrypy.HTTPRedirect("/burst/")
@expose_json
def stop_operation(self, operation_id, is_group, remove_after_stop=False):
"""
Stop the operation given by operation_id. If is_group is true stop all the
operations from that group.
"""
operation_service = OperationService()
result = False
if int(is_group) == 0:
result = operation_service.stop_operation(operation_id)
if remove_after_stop:
ProjectService().remove_operation(operation_id)
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
operations_in_group = ProjectService.get_operations_in_group(op_group)
for operation in operations_in_group:
tmp_res = operation_service.stop_operation(operation.id)
if remove_after_stop:
ProjectService().remove_operation(operation.id)
result = result or tmp_res
return result
@expose_json
def stop_burst_operation(self, operation_id, is_group, remove_after_stop=False):
"""
For a given operation id that is part of a burst just stop the given burst.
:returns True when stopped operation was successfully.
"""
operation_id = int(operation_id)
if int(is_group) == 0:
operation = self.flow_service.load_operation(operation_id)
else:
op_group = ProjectService.get_operation_group_by_id(operation_id)
first_op = ProjectService.get_operations_in_group(op_group)[0]
operation = self.flow_service.load_operation(int(first_op.id))
try:
burst_service = BurstService()
result = burst_service.stop_burst(operation.burst)
if remove_after_stop:
current_burst = common.get_from_session(common.KEY_BURST_CONFIG)
if current_burst and current_burst.id == operation.burst.id:
common.remove_from_session(common.KEY_BURST_CONFIG)
result = burst_service.cancel_or_remove_burst(operation.burst.id) or result
return result
except Exception as ex:
self.logger.exception(ex)
return False
def fill_default_attributes(self, template_dictionary, title='-'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
if common.KEY_TITLE not in template_dictionary:
template_dictionary[common.KEY_TITLE] = title
if common.KEY_PARENT_DIV not in template_dictionary:
template_dictionary[common.KEY_PARENT_DIV] = ''
if common.KEY_PARAMETERS_CONFIG not in template_dictionary:
template_dictionary[common.KEY_PARAMETERS_CONFIG] = False
template_dictionary[common.KEY_INCLUDE_RESOURCES] = 'flow/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
##### Below this point are operations that might be moved to different #####
##### controller #####
NEW_SELECTION_NAME = 'New selection'
def _get_available_selections(self, datatype_gid):
"""
selection retrieval common to selection component and connectivity selection
"""
curent_project = common.get_current_project()
selections = self.flow_service.get_selections_for_project(curent_project.id, datatype_gid)
names, sel_values = [], []
for selection in selections:
names.append(selection.ui_name)
sel_values.append(selection.selected_nodes)
return names, sel_values
@expose_fragment('visualizers/commons/channel_selector_opts')
def get_available_selections(self, **data):
sel_names, sel_values = self._get_available_selections(data['datatype_gid'])
return dict(namedSelections=zip(sel_names, sel_values))
@expose_json
def store_measure_points_selection(self, ui_name, **data):
"""
Save a MeasurePoints selection (new or update existing entity).
"""
if ui_name and ui_name != self.NEW_SELECTION_NAME:
sel_project_id = common.get_current_project().id
# client sends integers as strings:
selection = json.dumps([int(s) for s in json.loads(data['selection'])])
datatype_gid = data['datatype_gid']
self.flow_service.save_measure_points_selection(ui_name, selection, datatype_gid, sel_project_id)
return [True, 'Selection saved successfully.']
else:
error_msg = self.NEW_SELECTION_NAME + " or empty name are not valid as selection names."
return [False, error_msg]
@expose_fragment("visualizers/pse_discrete/inserting_new_threshold_spec_bar")
def create_row_of_specs(self, count):
return dict(id_increment_count=count)
@expose_json
def store_pse_filter(self, config_name, **data):
# this will need to be updated in such a way that the expose_json actually gets used
## also this is going to be changed to be storing through the flow service and dao. Stay updated
try:
##this is to check whether there is already an entry in the
for i, (name, Val) in enumerate(self.PSE_names_list):
if name == config_name:
self.PSE_names_list[i] = (config_name, (
data['threshold_value'] + "," + data['threshold_type'] + "," + data[
'not_presence'])) # replace the previous occurence of the config name, and carry on.
self.get_pse_filters()
return [True, 'Selected Text stored, and selection updated']
self.PSE_names_list.append(
(config_name, (data['threshold_value'] + "," + data['threshold_type'] + "," + data['not_presence'])))
except AttributeError:
self.PSE_names_list = [
(config_name, (data['threshold_value'] + "," + data['threshold_type'] + "," + data['not_presence']))]
self.get_pse_filters()
return [True, 'Selected Text stored, and selection updated']
@expose_fragment("visualizers/commons/channel_selector_opts")
def get_pse_filters(self):
try:
return dict(namedSelections=self.PSE_names_list)
except AttributeError:
return dict(namedSelections=[]) # this will give us back atleast the New Selection option in the select
except:
raise
@expose_json
def store_exploration_section(self, val_range, step, dt_group_guid):
"""
Launching method for further simulations.
"""
range_list = [float(num) for num in val_range.split(",")]
step_list = [float(num) for num in step.split(",")]
datatype_group_ob = ProjectService().get_datatypegroup_by_gid(dt_group_guid)
operation_grp = datatype_group_ob.parent_operation_group
operation_obj = self.flow_service.load_operation(datatype_group_ob.fk_from_operation)
parameters = json.loads(operation_obj.parameters)
range1name, range1_dict = json.loads(operation_grp.range1)
range2name, range2_dict = json.loads(operation_grp.range2)
parameters[RANGE_PARAMETER_1] = range1name
parameters[RANGE_PARAMETER_2] = range2name
##change the existing simulator parameters to be min max step types
range1_dict = {constants.ATT_MINVALUE: range_list[0],
constants.ATT_MAXVALUE: range_list[1],
constants.ATT_STEP: step_list[0]}
range2_dict = {constants.ATT_MINVALUE: range_list[2],
constants.ATT_MAXVALUE: range_list[3],
constants.ATT_STEP: step_list[1]}
parameters[range1name] = json.dumps(range1_dict) # this is for the x axis parameter
parameters[range2name] = json.dumps(range2_dict) # this is for the y axis parameter
OperationService().group_operation_launch(common.get_logged_user().id, common.get_current_project().id,
operation_obj.algorithm.id, operation_obj.algorithm.fk_category,
datatype_group_ob, **parameters)
return [True, 'Stored the exploration material successfully']
class FlowController(base.BaseController):
"""
This class takes care of executing steps in projects.
"""
def __init__(self):
base.BaseController.__init__(self)
self.context = SelectedAdapterContext()
self.files_helper = FilesHelper()
@cherrypy.expose
@using_template('base_template')
@logged()
@base.settings()
@context_selected()
def step(self, step_key=None):
"""
Choose exact action/adapter for current step.
"""
category = self.flow_service.get_category_by_id(step_key)
if category is None:
message = 'Inconsistent Step Name! Please excuse the wrong link!'
base.set_warning_message(message)
self.logger.warning(message + '- Wrong step:' + str(step_key))
raise cherrypy.HTTPRedirect('/tvb')
step_name = category.displayname.lower()
template_specification = dict(mainContent="header_menu", section_name=step_name, controlPage=None,
title="Select an algorithm", displayControl=False)
adapters_list = []
for algo_group in self.flow_service.get_groups_for_categories([category]):
if algo_group.ui_display < 0:
continue
adapter_link = self.get_url_adapter(step_key, algo_group.id)
adapters_list.append({base.KEY_TITLE: algo_group.displayname,
'link': adapter_link,
'description': algo_group.description,
'subsection': algo_group.subsection_name})
self.analyze_adapters = adapters_list
template_specification[base.KEY_SUBMENU_LIST] = adapters_list
return self.fill_default_attributes(template_specification)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@context_selected()
def step_connectivity(self):
"""
Display menu for Connectivity Footer tab.
"""
template_specification = dict(mainContent="header_menu", section_name='connectivity', controlPage=None,
title="Select an algorithm", displayControl=False, subsection_name='step',
submenu_list=self.connectivity_submenu)
return self.fill_default_attributes(template_specification)
@staticmethod
def _compute_back_link(back_indicator, project):
"""
Based on a simple indicator, compute URL for anchor BACK.
"""
if back_indicator is None:
## This applies to Connectivity and other visualizers when RELAUNCH button is used from Operation page.
back_page_link = None
elif back_indicator == 'burst':
back_page_link = "/burst"
elif back_indicator == 'operations':
back_page_link = '/project/viewoperations/' + str(project.id)
else:
back_page_link = '/project/editstructure/' + str(project.id)
return back_page_link
@cherrypy.expose
@base.settings()
@logged()
@context_selected()
@using_template('base_template')
def prepare_group_launch(self, group_gid, step_key, adapter_key, **data):
"""
Receives as input a group gid and an algorithm given by category and id, along
with data that gives the name of the required input parameter for the algorithm.
Having these generate a range of GID's for all the DataTypes in the group and
launch a new operation group.
"""
prj_service = ProjectService()
dt_group = prj_service.get_datatypegroup_by_gid(group_gid)
datatypes = prj_service.get_datatypes_from_datatype_group(dt_group.id)
range_param_name = data['range_param_name']
del data['range_param_name']
data[RANGE_PARAMETER_1] = range_param_name
data[range_param_name] = ','.join([dt.gid for dt in datatypes])
OperationService().group_operation_launch(base.get_logged_user().id, base.get_current_project().id,
int(adapter_key), int(step_key), **data)
redirect_url = self._compute_back_link('operations', base.get_current_project())
raise cherrypy.HTTPRedirect(redirect_url)
@cherrypy.expose
@using_template('base_template')
@base.settings()
@logged()
@context_selected()
def default(self, step_key, adapter_key, cancel=False, back_page=None, not_reset=False, **data):
"""
Render a specific adapter.
'data' are arguments for POST
"""
project = base.get_current_project()
algo_group = self.flow_service.get_algo_group_by_identifier(adapter_key)
back_page_link = self._compute_back_link(back_page, project)
if algo_group is None:
raise cherrypy.HTTPRedirect("/tvb?error=True")
if cherrypy.request.method == 'POST' and cancel:
raise cherrypy.HTTPRedirect(back_page_link)
submit_link = self.get_url_adapter(step_key, adapter_key, back_page)
if cherrypy.request.method == 'POST':
back_indicator = back_page if back_page == 'burst' else 'operations'
success_url = self._compute_back_link(back_indicator, project)
data[base.KEY_ADAPTER] = adapter_key
template_specification = self.execute_post(project.id, submit_link, success_url,
step_key, algo_group, **data)
else:
if (('Referer' not in cherrypy.request.headers or
('Referer' in cherrypy.request.headers and 'step' not in cherrypy.request.headers['Referer']))
and 'View' in algo_group.group_category.displayname):
# Avoid reset in case of Visualizers, as a supplementary GET
# might be enforced by MPLH5 on FF.
not_reset = True
template_specification = self.get_template_for_adapter(project.id, step_key, algo_group,
submit_link, not not_reset)
if template_specification is None:
raise cherrypy.HTTPRedirect('/tvb')
if KEY_CONTROLLS not in template_specification:
template_specification[KEY_CONTROLLS] = None
if base.KEY_SUBMIT_LINK not in template_specification:
template_specification[base.KEY_SUBMIT_LINK] = submit_link
if KEY_CONTENT not in template_specification:
template_specification[KEY_CONTENT] = "flow/full_adapter_interface"
template_specification[base.KEY_DISPLAY_MENU] = False
else:
template_specification[base.KEY_DISPLAY_MENU] = True
template_specification[base.KEY_BACK_PAGE] = back_page_link
template_specification[base.KEY_ADAPTER] = adapter_key
template_specification[ABCDisplayer.KEY_IS_ADAPTER] = True
self.fill_default_attributes(template_specification, algo_group)
if (back_page is not None and back_page in ['operations', 'data'] and
not (base.KEY_SECTION in template_specification
and template_specification[base.KEY_SECTION] == 'connectivity')):
template_specification[base.KEY_SECTION] = 'project'
return template_specification
@cherrypy.expose
@using_template("flow/reduce_dimension_select")
@logged()
def gettemplatefordimensionselect(self, entity_gid=None, select_name="", reset_session='False',
parameters_prefix="dimensions", required_dimension=1,
expected_shape="", operations=""):
"""
Returns the HTML which contains the selects components which allows the user
to reduce the dimension of a multi-dimensional array.
We try to obtain the aggregation_functions from the entity, which is a list of lists.
For each dimension should be a list with the supported aggregation functions. We
create a DICT for each of those lists. The key will be the name of the function and
the value will be its label.
entity_gid
the GID of the entity for which is displayed the component
select_name
the name of the parent select. The select in which
is displayed the entity with the given GID
parameters_prefix
a string which will be used for computing the names of the component
required_dimension
the expected dimension for the resulted array
expected_shape and operations
used for applying conditions on the resulted array
e.g.: If the resulted array is a 3D array and we want that the length of the second
dimension to be smaller then 512 then the expected_shape and operations should be:
``expected_shape=x,512,x`` and ``operations='x,<,x``
"""
template_params = dict()
template_params["select_name"] = ""
template_params["data"] = []
template_params["parameters_prefix"] = parameters_prefix
template_params["array_shape"] = ""
template_params["required_dimension"] = required_dimension
template_params["currentDim"] = ""
template_params["required_dim_msg"] = ""
template_params["expected_shape"] = expected_shape
template_params["operations"] = operations
#if reload => populate the selected values
session_dict = self.context.get_current_default()
dimensions = {1: [0], 3: [0]}
selected_agg_functions = {}
if not eval(str(reset_session)) and session_dict is not None:
starts_with_str = select_name + "_" + parameters_prefix + "_"
ui_sel_items = dict((k, v) for k, v in session_dict.items() if k.startswith(starts_with_str))
dimensions, selected_agg_functions, required_dimension, _ = MappedArray().parse_selected_items(ui_sel_items)
template_params["selected_items"] = dimensions
template_params["selected_functions"] = selected_agg_functions
aggregation_functions = []
default_agg_functions = self.accepted__aggregation_functions()
labels_set = ["Time", "Channel", "Line"]
if entity_gid is not None:
actual_entity = ABCAdapter.load_entity_by_gid(entity_gid)
if hasattr(actual_entity, 'shape'):
array_shape = actual_entity.shape
new_shape, current_dim = self._compute_current_dimension(list(array_shape), dimensions,
selected_agg_functions)
if required_dimension is not None and current_dim != int(required_dimension):
template_params["required_dim_msg"] = "Please select a " + str(required_dimension) + "D array"
if not current_dim:
template_params["currentDim"] = "1 element"
else:
template_params["currentDim"] = str(current_dim) + "D array"
template_params["array_shape"] = json.dumps(new_shape)
if hasattr(actual_entity, 'dimensions_labels') and actual_entity.dimensions_labels is not None:
labels_set = actual_entity.dimensions_labels
#make sure there exists labels for each dimension
while len(labels_set) < len(array_shape):
labels_set.append("Undefined")
if (hasattr(actual_entity, 'aggregation_functions') and actual_entity.aggregation_functions is not None
and len(actual_entity.aggregation_functions) == len(array_shape)):
#will be a list of lists of aggregation functions
defined_functions = actual_entity.aggregation_functions
for function in defined_functions:
if not len(function):
aggregation_functions.append({})
else:
func_dict = dict()
for function_key in function:
func_dict[function_key] = default_agg_functions[function_key]
aggregation_functions.append(func_dict)
else:
for _ in array_shape:
aggregation_functions.append(default_agg_functions)
result = []
for i, shape in enumerate(array_shape):
labels = []
values = []
for j in xrange(shape):
labels.append(labels_set[i] + " " + str(j))
values.append(entity_gid + "_" + str(i) + "_" + str(j))
result.append([labels, values, aggregation_functions[i]])
template_params["select_name"] = select_name
template_params["data"] = result
return template_params
return template_params
@staticmethod
def _compute_current_dimension(array_shape, selected_items, selected_functions):
"""
If the user reloads an operation we have to compute the current dimension of the array
and also the shape of the array based on his selections
"""
current_dim = len(array_shape)
for i in xrange(len(array_shape)):
if i in selected_items and len(selected_items[i]) > 0:
array_shape[i] = len(selected_items[i])
if len(selected_items[i]) == 1:
current_dim -= 1
if i in selected_functions and selected_functions[i] != 'none':
array_shape[i] = 1
if i not in selected_items or len(selected_items[i]) > 1:
current_dim -= 1
return array_shape, current_dim
@staticmethod
def accepted__aggregation_functions():
"""
Returns the list of aggregation functions that may be
applied on arrays.
"""
return {"sum": "Sum", "average": "Average"}
@cherrypy.expose
@using_template("flow/type2component/datatype2select_simple")
@logged()
def getfiltereddatatypes(self, name, parent_div, tree_session_key, filters):
"""
Given the name from the input tree, the dataType required and a number of
filters, return the available dataType that satisfy the conditions imposed.
"""
previous_tree = self.context.get_session_tree_for_key(tree_session_key)
if previous_tree is None:
base.set_error_message("Adapter Interface not in session for filtering!")
raise cherrypy.HTTPRedirect("/tvb?error=True")
current_node = self._get_node(previous_tree, name)
if current_node is None:
raise Exception("Could not find node :" + name)
datatype = current_node[ABCAdapter.KEY_DATATYPE]
filters = json.loads(filters)
availablefilter = json.loads(FilterChain.get_filters_for_type(datatype))
for i, filter_ in enumerate(filters[FILTER_FIELDS]):
#Check for filter input of type 'date' as these need to be converted
if filter_ in availablefilter and availablefilter[filter_][FILTER_TYPE] == 'date':
try:
filter_ = string2date(filter_, False)
filters[FILTER_VALUES][i] = filter_
except ValueError, excep:
raise excep
#In order for the filter object not to "stack up" on multiple calls to
#this method, create a deepCopy to work with
if ABCAdapter.KEY_CONDITION in current_node:
new_filter = copy.deepcopy(current_node[ABCAdapter.KEY_CONDITION])
else:
new_filter = FilterChain()
new_filter.fields.extend(filters[FILTER_FIELDS])
new_filter.operations.extend(filters[FILTER_OPERATIONS])
new_filter.values.extend(filters[FILTER_VALUES])
#Get dataTypes that match the filters from DB then populate with values
datatypes = self.flow_service.get_available_datatypes(base.get_current_project().id, datatype, new_filter)
values = self.flow_service.populate_values(datatypes, datatype, self.context.get_current_step())
#Create a dictionary that matches what the template expects
parameters = dict()
parameters[ABCAdapter.KEY_NAME] = name
if ABCAdapter.KEY_REQUIRED in current_node:
parameters[ABCAdapter.KEY_REQUIRED] = current_node[ABCAdapter.KEY_REQUIRED]
if len(values) > 0 and eval(str(parameters[ABCAdapter.KEY_REQUIRED])):
parameters[ABCAdapter.KEY_DEFAULT] = str(values[-1][ABCAdapter.KEY_VALUE])
previous_selected = self.context.get_current_default(name)
if previous_selected is not None and previous_selected in [str(vv['value']) for vv in values]:
parameters[ABCAdapter.KEY_DEFAULT] = previous_selected
parameters[ABCAdapter.KEY_FILTERABLE] = availablefilter
parameters[ABCAdapter.KEY_TYPE] = ABCAdapter.TYPE_SELECT
parameters[ABCAdapter.KEY_OPTIONS] = values
parameters[ABCAdapter.KEY_DATATYPE] = datatype
template_specification = {"inputRow": parameters, "disabled": False,
"parentDivId": parent_div, base.KEY_SESSION_TREE: tree_session_key}
return self.fill_default_attributes(template_specification)