WIP TVB-3122. Fix Sonar warnings

tvb_contrib/tvb/contrib/cosimulation/cosim_monitors.py

@@ -42,7 +42,7 @@ def _sample_with_tvb_monitor(self, step, state):
         This method provides output from TVB Monitor classes, and should be set to a TVB Monitor parent class.
         Use the original signature.
         """
-        raise NotImplemented
+        raise NotImplementedError
 
     def _get_sample(self, current_step, start_step, n_steps, history, cosim):
         end_step = start_step + n_steps
@@ -79,7 +79,7 @@ def sample(self, current_step, start_step, n_steps, cosim_history, history):
         This method provides monitor output, and should be overridden by subclasses.
         Use the original signature.
         """
-        raise NotImplemented
+        raise NotImplementedError
 
 
 class CosimMonitorFromCoupling(CosimMonitor):

tvb_framework/tvb/adapters/forms/monitor_forms.py

@@ -36,6 +36,9 @@
 from tvb.datatypes.sensors import SensorTypesEnum
 from tvb.simulator.monitors import DefaultMasks
 
+PROJECTION_TYPE_KEY = '.projection_type'
+SENSORS_TYPE_KEY = '.sensors_type'
+
 
 def get_monitor_to_form_dict():
     monitor_class_to_form = {
@@ -167,10 +170,10 @@ class EEGMonitorForm(ProjectionMonitorForm):
     def __init__(self, session_stored_simulator=None, is_period_disabled=False):
         super(EEGMonitorForm, self).__init__(session_stored_simulator, is_period_disabled)
 
-        sensor_filter = FilterChain(fields=[FilterChain.datatype + '.sensors_type'], operations=["=="],
+        sensor_filter = FilterChain(fields=[FilterChain.datatype + SENSORS_TYPE_KEY], operations=["=="],
                                     values=[SensorTypesEnum.TYPE_EEG.value])
 
-        projection_filter = FilterChain(fields=[FilterChain.datatype + '.projection_type'], operations=["=="],
+        projection_filter = FilterChain(fields=[FilterChain.datatype + PROJECTION_TYPE_KEY], operations=["=="],
                                         values=[ProjectionsTypeEnum.EEG.value])
 
         self.projection = TraitDataTypeSelectField(EEGViewModel.projection, name='projection',
@@ -185,10 +188,10 @@ class MEGMonitorForm(ProjectionMonitorForm):
     def __init__(self, session_stored_simulator=None, is_period_disabled=False):
         super(MEGMonitorForm, self).__init__(session_stored_simulator, is_period_disabled)
 
-        sensor_filter = FilterChain(fields=[FilterChain.datatype + '.sensors_type'], operations=["=="],
+        sensor_filter = FilterChain(fields=[FilterChain.datatype + SENSORS_TYPE_KEY], operations=["=="],
                                     values=[SensorTypesEnum.TYPE_MEG.value])
 
-        projection_filter = FilterChain(fields=[FilterChain.datatype + '.projection_type'], operations=["=="],
+        projection_filter = FilterChain(fields=[FilterChain.datatype + PROJECTION_TYPE_KEY], operations=["=="],
                                         values=[ProjectionsTypeEnum.MEG.value])
 
         self.projection = TraitDataTypeSelectField(MEGViewModel.projection, name='projection',
@@ -201,10 +204,10 @@ class iEEGMonitorForm(ProjectionMonitorForm):
     def __init__(self, session_stored_simulator=None, is_period_disabled=False):
         super(iEEGMonitorForm, self).__init__(session_stored_simulator, is_period_disabled)
 
-        sensor_filter = FilterChain(fields=[FilterChain.datatype + '.sensors_type'], operations=["=="],
+        sensor_filter = FilterChain(fields=[FilterChain.datatype + SENSORS_TYPE_KEY], operations=["=="],
                                     values=[SensorTypesEnum.TYPE_INTERNAL.value])
 
-        projection_filter = FilterChain(fields=[FilterChain.datatype + '.projection_type'], operations=["=="],
+        projection_filter = FilterChain(fields=[FilterChain.datatype + PROJECTION_TYPE_KEY], operations=["=="],
                                         values=[ProjectionsTypeEnum.SEEG.value])
 
         self.projection = TraitDataTypeSelectField(iEEGViewModel.projection, name='projection',

tvb_framework/tvb/adapters/visualizers/eeg_monitor.py

@@ -41,26 +41,28 @@
 from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr, replace_nan_values
 from tvb.datatypes.time_series import TimeSeries
 
+TIME_SERIES_TO_DISPLAY_ = 'Time series to display.'
+
 
 class EegMonitorModel(ViewModel):
     input_data = DataTypeGidAttr(
         linked_datatype=TimeSeries,
         label='Input Data',
-        doc='Time series to display.'
+        doc=TIME_SERIES_TO_DISPLAY_
     )
 
     data_2 = DataTypeGidAttr(
         linked_datatype=TimeSeries,
         required=False,
         label='Input Data 2',
-        doc='Time series to display.'
+        doc=TIME_SERIES_TO_DISPLAY_
     )
 
     data_3 = DataTypeGidAttr(
         linked_datatype=TimeSeries,
         required=False,
         label='Input Data 3',
-        doc='Time series to display.'
+        doc=TIME_SERIES_TO_DISPLAY_
     )
 
 

tvb_framework/tvb/adapters/visualizers/region_volume_mapping.py

@@ -54,6 +54,10 @@
 from tvb.datatypes.region_mapping import RegionVolumeMapping
 from tvb.datatypes.structural import StructuralMRI
 
+HAS_VOLUME_MAPPING_FILTER_ATTR = '.has_volume_mapping'
+NDIM_FILTER_ATTR = '.ndim'
+REGION_MAPPING_LABEL = 'Region mapping'
+
 
 @add_metaclass(ABCMeta)
 class _MappedArrayVolumeBase(ABCDisplayer):
@@ -293,7 +297,7 @@ class VolumeVisualizerModel(BaseVolumeVisualizerModel):
     region_mapping_volume = DataTypeGidAttr(
         linked_datatype=RegionVolumeMapping,
         required=False,
-        label='Region mapping'
+        label=REGION_MAPPING_LABEL
     )
 
     data_slice = Attr(
@@ -319,8 +323,8 @@ def get_view_model():
 
     @staticmethod
     def get_filters():
-        return FilterChain(fields=[FilterChain.datatype + '.ndim',
-                                   FilterChain.datatype + '.has_volume_mapping',
+        return FilterChain(fields=[FilterChain.datatype + NDIM_FILTER_ATTR,
+                                   FilterChain.datatype + HAS_VOLUME_MAPPING_FILTER_ATTR,
                                    FilterChain.datatype + '.subtype'],
                            operations=[">=", "==", "not in"],
                            values=[2, True, ["RegionVolumeMapping", "StructuralMRI"]])
@@ -372,7 +376,7 @@ class ConnectivityMeasureVolumeVisualizerModel(BaseVolumeVisualizerModel):
     region_mapping_volume = DataTypeGidAttr(
         linked_datatype=RegionVolumeMapping,
         required=False,
-        label='Region mapping'
+        label=REGION_MAPPING_LABEL
     )
 
 
@@ -400,7 +404,7 @@ def get_input_name():
 
     @staticmethod
     def get_filters():
-        return FilterChain(fields=[FilterChain.datatype + '.ndim', FilterChain.datatype + '.has_volume_mapping'],
+        return FilterChain(fields=[FilterChain.datatype + NDIM_FILTER_ATTR, FilterChain.datatype + HAS_VOLUME_MAPPING_FILTER_ATTR],
                            operations=["==", "=="], values=[1, True])
 
 
@@ -434,7 +438,7 @@ def launch(self, view_model):
 class RegionVolumeMappingVisualiserModel(BaseVolumeVisualizerModel):
     region_mapping_volume = DataTypeGidAttr(
         linked_datatype=RegionVolumeMapping,
-        label='Region mapping'
+        label=REGION_MAPPING_LABEL
     )
 
     connectivity_measure = DataTypeGidAttr(
@@ -454,7 +458,7 @@ def __init__(self):
                                                               conditions=self.get_filters())
 
         cm_conditions = FilterChain(
-            fields=[FilterChain.datatype + '.ndim', FilterChain.datatype + '.has_volume_mapping'],
+            fields=[FilterChain.datatype + NDIM_FILTER_ATTR, FilterChain.datatype + HAS_VOLUME_MAPPING_FILTER_ATTR],
             operations=["==", "=="], values=[1, True])
         self.connectivity_measure = TraitDataTypeSelectField(RegionVolumeMappingVisualiserModel.connectivity_measure,
                                                              name='connectivity_measure', conditions=cm_conditions)

tvb_framework/tvb/adapters/visualizers/sensors.py

@@ -43,6 +43,8 @@
 from tvb.datatypes.sensors import SensorsInternal, SensorsEEG, SensorsMEG, Sensors
 from tvb.datatypes.surfaces import Surface, SurfaceTypesEnum
 
+SENSORS_CONTROLS_PAGE = "sensors/sensors_controls"
+
 LOG = get_logger(__name__)
 
 
@@ -207,7 +209,7 @@ def _params_internal_sensors(self, internal_sensors, shell_surface=None):
         params['shellObject'] = self.prepare_shell_surface_params(shell_surface, SurfaceURLGenerator)
 
         return self.build_display_result('sensors/sensors_internal', params,
-                                         pages={"controlPage": "sensors/sensors_controls"})
+                                         pages={"controlPage": SENSORS_CONTROLS_PAGE})
 
     def _params_eeg_sensors(self, eeg_sensors, eeg_cap=None, shell_surface=None):
 
@@ -228,7 +230,7 @@ def _params_eeg_sensors(self, eeg_sensors, eeg_cap=None, shell_surface=None):
                 params.update(self._compute_surface_params(eeg_cap_h5))
 
         return self.build_display_result("sensors/sensors_eeg", params,
-                                         pages={"controlPage": "sensors/sensors_controls"})
+                                         pages={"controlPage": SENSORS_CONTROLS_PAGE})
 
     def _params_meg_sensors(self, meg_sensors, projection_surface=None, shell_surface=None):
 
@@ -246,7 +248,7 @@ def _params_meg_sensors(self, meg_sensors, projection_surface=None, shell_surfac
                 params.update(self._compute_surface_params(projection_surface_h5))
 
         return self.build_display_result("sensors/sensors_eeg", params,
-                                         pages={"controlPage": "sensors/sensors_controls"})
+                                         pages={"controlPage": SENSORS_CONTROLS_PAGE})
 
     @staticmethod
     def _compute_surface_params(surface_h5):

tvb_framework/tvb/core/entities/model/model_datatype.py

@@ -46,6 +46,7 @@
 from tvb.core.entities.model.model_burst import BurstConfiguration
 from tvb.core.neotraits.db import HasTraitsIndex, Base, from_ndarray
 
+DATATYPE_ID_KEY = 'DataType.id'
 
 LOG = get_logger(__name__)
 
@@ -108,7 +109,7 @@ class DataType(HasTraitsIndex):
     # it should be a reference to a DataTypeGroup, but we can not create that FK
     # because this two tables (DATA_TYPES, DATA_TYPES_GROUPS) will reference each
     # other mutually and SQL-Alchemy complains about that.
-    fk_datatype_group = Column(Integer, ForeignKey('DataType.id'))
+    fk_datatype_group = Column(Integer, ForeignKey(DATATYPE_ID_KEY))
 
     fk_from_operation = Column(Integer, ForeignKey('OPERATIONS.id', ondelete="CASCADE"))
     parent_operation = relationship(Operation, backref=backref("DATA_TYPES", order_by=id, cascade="all,delete"))
@@ -284,7 +285,7 @@ class DataTypeGroup(DataType):
     """
     __tablename__ = 'DATA_TYPES_GROUPS'
 
-    id = Column('id', Integer, ForeignKey('DataType.id', ondelete="CASCADE"), primary_key=True)
+    id = Column('id', Integer, ForeignKey(DATATYPE_ID_KEY, ondelete="CASCADE"), primary_key=True)
     count_results = Column(Integer)
     no_of_ranges = Column(Integer, default=0)  # Number of ranged parameters
     fk_operation_group = Column(Integer, ForeignKey('OPERATION_GROUPS.id', ondelete="CASCADE"))
@@ -322,7 +323,7 @@ class Links(Base):
 
     id = Column(Integer, primary_key=True)
     fk_to_project = Column(Integer, ForeignKey('PROJECTS.id', ondelete="CASCADE"))
-    fk_from_datatype = Column(Integer, ForeignKey('DataType.id', ondelete="CASCADE"))
+    fk_from_datatype = Column(Integer, ForeignKey(DATATYPE_ID_KEY, ondelete="CASCADE"))
 
     referenced_project = relationship(Project, backref=backref('LINKS', order_by=id, cascade="delete, all"))
     referenced_datatype = relationship(DataType, backref=backref('LINKS', order_by=id, cascade="delete, all"))

tvb_framework/tvb/core/entities/model/model_operation.py

@@ -44,6 +44,8 @@
 from tvb.core.neotraits.db import Base
 from tvb.core.utils import generate_guid, string2date, string2bool, date2string, LESS_COMPLEX_TIME_FORMAT
 
+PROJECTS_ID_KEY = 'PROJECTS.id'
+
 LOG = get_logger(__name__)
 
 
@@ -165,7 +167,7 @@ class OperationGroup(Base, Exportable):
     range2 = Column(String)
     range3 = Column(String)
     gid = Column(String)
-    fk_launched_in = Column(Integer, ForeignKey('PROJECTS.id', ondelete="CASCADE"))
+    fk_launched_in = Column(Integer, ForeignKey(PROJECTS_ID_KEY, ondelete="CASCADE"))
     project = relationship(Project, backref=backref('OPERATION_GROUPS', order_by=id, cascade="all,delete"))
 
     def __init__(self, project_id, name='incomplete', ranges=None, gid=None):
@@ -235,7 +237,7 @@ class Operation(Base, Exportable):
 
     id = Column(Integer, primary_key=True)
     fk_launched_by = Column(Integer, ForeignKey('USERS.id'))
-    fk_launched_in = Column(Integer, ForeignKey('PROJECTS.id', ondelete="CASCADE"))
+    fk_launched_in = Column(Integer, ForeignKey(PROJECTS_ID_KEY, ondelete="CASCADE"))
     fk_from_algo = Column(Integer, ForeignKey('ALGORITHMS.id'))
     fk_operation_group = Column(Integer, ForeignKey('OPERATION_GROUPS.id', ondelete="CASCADE"), default=None)
     gid = Column(String)
@@ -435,7 +437,7 @@ class ResultFigure(Base, Exportable):
 
     id = Column(Integer, primary_key=True)
     fk_for_user = Column(Integer, ForeignKey('USERS.id', ondelete="CASCADE"))
-    fk_in_project = Column(Integer, ForeignKey('PROJECTS.id', ondelete="CASCADE"))
+    fk_in_project = Column(Integer, ForeignKey(PROJECTS_ID_KEY, ondelete="CASCADE"))
     project = relationship(Project, backref=backref('RESULT_FIGURES', order_by=id, cascade="delete"))
     session_name = Column(String)
     name = Column(String)

tvb_framework/tvb/core/entities/model/model_project.py

@@ -46,6 +46,8 @@
 from tvb.core.entities.transient.structure_entities import DataTypeMetaData
 from tvb.core.neotraits.db import Base
 
+USERS_ID_KEY = 'USERS.id'
+
 LOG = get_logger(__name__)
 
 # Constants for User Roles.
@@ -152,7 +154,7 @@ class UserPreferences(Base):
     ONLINE_HELP_ACTIVE = "online_help_active"
     VIEWERS_COLOR_SCHEME = "viewers_color_scheme"
     PROJECT_STRUCTURE_GROUPING = "project_structure_grouping"
-    fk_user = Column(Integer, ForeignKey('USERS.id'), primary_key=True)
+    fk_user = Column(Integer, ForeignKey(USERS_ID_KEY), primary_key=True)
     key = Column(String, primary_key=True)
     value = Column(String)
 
@@ -173,7 +175,7 @@ class Project(Base, Exportable):
     name = Column(String, unique=True)
     description = Column(String)
     last_updated = Column(DateTime)
-    fk_admin = Column(Integer, ForeignKey('USERS.id'))
+    fk_admin = Column(Integer, ForeignKey(USERS_ID_KEY))
     gid = Column(String, unique=True)
     version = Column(Integer)
     disable_imports = Column(Boolean, default=False)
@@ -235,7 +237,7 @@ class User_to_Project(Base):
     __tablename__ = 'USERS_TO_PROJECTS'
 
     id = Column(Integer, primary_key=True)
-    fk_user = Column(Integer, ForeignKey('USERS.id', ondelete="CASCADE"))
+    fk_user = Column(Integer, ForeignKey(USERS_ID_KEY, ondelete="CASCADE"))
     fk_project = Column(Integer, ForeignKey('PROJECTS.id', ondelete="CASCADE"))
 
     def __init__(self, user, case):

tvb_framework/tvb/core/neotraits/forms.py

@@ -37,6 +37,9 @@
 from tvb.core.neotraits.db import HasTraitsIndex
 from tvb.core.neotraits.view_model import DataTypeGidAttr
 
+FIELD_REQUIRED_ERROR = 'Field required'
+STR_FIELD_TEMPLATE = 'form_fields/str_field.html'
+
 # This setting is injected.
 # The pattern might be confusing, but it is an interesting alternative to
 # universal tvbprofile imports
@@ -78,7 +81,7 @@ def validate(self):
 
     def _from_post(self):
         if self.required and (self.unvalidated_data is None or len(str(self.unvalidated_data).strip()) == 0):
-            raise ValueError('Field required')
+            raise ValueError(FIELD_REQUIRED_ERROR)
         self.data = self.unvalidated_data
 
     @property
@@ -201,7 +204,7 @@ def _from_post(self):
             self.unvalidated_data = None
 
         if self.required and not self.unvalidated_data:
-            raise ValueError('Field required')
+            raise ValueError(FIELD_REQUIRED_ERROR)
 
         # TODO: ensure is in choices
         try:
@@ -214,11 +217,11 @@ def _from_post(self):
 
 
 class StrField(TraitField):
-    template = 'form_fields/str_field.html'
+    template = STR_FIELD_TEMPLATE
 
 
 class UserSessionStrField(TraitField):
-    template = 'form_fields/str_field.html'
+    template = STR_FIELD_TEMPLATE
 
     def __init__(self, trait_attribute, name=None, disabled=False, key=None):
         # type: (Attr, str, bool, str) -> None
@@ -261,7 +264,7 @@ def _from_post(self):
 
 
 class ArrayField(TraitField):
-    template = 'form_fields/str_field.html'
+    template = STR_FIELD_TEMPLATE
 
     def _from_post(self):
         super(ArrayField, self)._from_post()
@@ -444,7 +447,7 @@ def options(self):
     def _from_post(self):
         if self.unvalidated_data is None:
             if self.required:
-                raise ValueError('Field required')
+                raise ValueError(FIELD_REQUIRED_ERROR)
             else:
                 return None