def init_test_env():
"""
This method prepares all necessary data for tests execution
"""
# Set a default test profile, for when running tests from dev-env.
from tvb.basic.profile import TvbProfile
if TvbProfile.CURRENT_PROFILE_NAME is None:
profile = TvbProfile.TEST_SQLITE_PROFILE
if len(sys.argv) > 1:
for i in range(1, len(sys.argv) - 1):
if "--profile=" in sys.argv[i]:
profile = sys.argv[i].split("=")[1]
TvbProfile.set_profile(profile)
print("Not expected to happen except from PyCharm: setting profile",
TvbProfile.CURRENT_PROFILE_NAME)
db_file = TvbProfile.current.db.DB_URL.replace('sqlite:///', '')
if os.path.exists(db_file):
os.remove(db_file)
from tvb.config.init.model_manager import reset_database
from tvb.config.init.initializer import initialize
reset_database()
initialize(skip_import=True)
# Add Dummy DataType
REGISTRY.register_datatype(DummyDataType, DummyDataTypeH5,
DummyDataTypeIndex)
REGISTRY.register_datatype(None, None, DummyDataType2Index)
def __init__(self,
trait_attribute,
form,
name=None,
conditions=None,
draw_dynamic_conditions_buttons=True,
dynamic_conditions=None,
has_all_option=False,
show_only_all_option=False):
super(TraitDataTypeSelectField, self).__init__(trait_attribute, form,
name)
if issubclass(type(trait_attribute), DataTypeGidAttr):
type_to_query = trait_attribute.linked_datatype
else:
type_to_query = trait_attribute.field_type
if issubclass(type_to_query, HasTraitsIndex):
self.datatype_index = type_to_query
else:
self.datatype_index = REGISTRY.get_index_for_datatype(
type_to_query)
self.conditions = conditions
self.draw_dynamic_conditions_buttons = draw_dynamic_conditions_buttons
self.dynamic_conditions = dynamic_conditions
self.has_all_option = has_all_option
self.show_only_all_option = show_only_all_option
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 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)
for idx in range(len(filters_dict['fields'])):
if filters_dict['values'][idx] in ['True', 'False']:
filters_dict['values'][idx] = string2bool(
filters_dict['values'][idx])
filter = FilterChain(fields=filters_dict['fields'],
operations=filters_dict['operations'],
values=filters_dict['values'])
project = common.get_current_project()
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,
conditions=filter,
has_all_option=string2bool(has_all_option))
self.algorithm_service.fill_selectfield_with_datatypes(
select_field, project.id)
return {'options': select_field.options()}
def populate_datatypes_registry():
REGISTRY.register_datatype(Connectivity, ConnectivityH5, ConnectivityIndex)
REGISTRY.register_datatype(None, BurstConfigurationH5, BurstConfiguration)
REGISTRY.register_datatype(LocalConnectivity, LocalConnectivityH5,
LocalConnectivityIndex)
REGISTRY.register_datatype(ProjectionMatrix, ProjectionMatrixH5,
ProjectionMatrixIndex, make_proj_matrix,
ProjectionsTypeEnum)
REGISTRY.register_datatype(RegionVolumeMapping, RegionVolumeMappingH5,
RegionVolumeMappingIndex)
REGISTRY.register_datatype(RegionMapping, RegionMappingH5,
RegionMappingIndex)
REGISTRY.register_datatype(Sensors, SensorsH5, SensorsIndex, make_sensors,
SensorTypesEnum)
REGISTRY.register_datatype(SimulationHistory, SimulationHistoryH5,
SimulationHistoryIndex)
REGISTRY.register_datatype(CoherenceSpectrum, CoherenceSpectrumH5,
CoherenceSpectrumIndex)
REGISTRY.register_datatype(ComplexCoherenceSpectrum,
ComplexCoherenceSpectrumH5,
ComplexCoherenceSpectrumIndex)
REGISTRY.register_datatype(FourierSpectrum, FourierSpectrumH5,
FourierSpectrumIndex)
REGISTRY.register_datatype(WaveletCoefficients, WaveletCoefficientsH5,
WaveletCoefficientsIndex)
REGISTRY.register_datatype(StructuralMRI, StructuralMRIH5,
StructuralMRIIndex)
REGISTRY.register_datatype(Surface, SurfaceH5, SurfaceIndex, make_surface,
SurfaceTypesEnum)
REGISTRY.register_datatype(CrossCorrelation, CrossCorrelationH5,
CrossCorrelationIndex)
REGISTRY.register_datatype(TimeSeries, TimeSeriesH5, TimeSeriesIndex)
REGISTRY.register_datatype(TimeSeriesRegion, TimeSeriesRegionH5,
TimeSeriesRegionIndex)
REGISTRY.register_datatype(TimeSeriesSurface, TimeSeriesSurfaceH5,
TimeSeriesSurfaceIndex)
REGISTRY.register_datatype(TimeSeriesVolume, TimeSeriesVolumeH5,
TimeSeriesVolumeIndex)
REGISTRY.register_datatype(TimeSeriesEEG, TimeSeriesEEGH5,
TimeSeriesEEGIndex)
REGISTRY.register_datatype(TimeSeriesMEG, TimeSeriesMEGH5,
TimeSeriesMEGIndex)
REGISTRY.register_datatype(TimeSeriesSEEG, TimeSeriesSEEGH5,
TimeSeriesSEEGIndex)
REGISTRY.register_datatype(Tracts, TractsH5, TractsIndex)
REGISTRY.register_datatype(Volume, VolumeH5, VolumeIndex)
REGISTRY.register_datatype(PrincipalComponents, PrincipalComponentsH5,
PrincipalComponentsIndex)
REGISTRY.register_datatype(IndependentComponents, IndependentComponentsH5,
IndependentComponentsIndex)
REGISTRY.register_datatype(ConnectivityMeasure, ConnectivityMeasureH5,
ConnectivityMeasureIndex)
REGISTRY.register_datatype(CorrelationCoefficients,
CorrelationCoefficientsH5,
CorrelationCoefficientsIndex)
REGISTRY.register_datatype(Covariance, CovarianceH5, CovarianceIndex)
REGISTRY.register_datatype(Fcd, FcdH5, FcdIndex)
REGISTRY.register_datatype(SpatioTemporalPattern, None,
SpatioTemporalPatternIndex)
REGISTRY.register_datatype(StimuliRegion, StimuliRegionH5,
StimuliRegionIndex)
REGISTRY.register_datatype(StimuliSurface, StimuliSurfaceH5,
StimuliSurfaceIndex)
REGISTRY.register_datatype(DatatypeMeasure, DatatypeMeasureH5,
DatatypeMeasureIndex)
REGISTRY.register_datatype(ConnectivityAnnotations,
ConnectivityAnnotationsH5,
ConnectivityAnnotationsIndex)
REGISTRY.register_datatype(ValueWrapper, ValueWrapperH5, ValueWrapperIndex)
