model Package

Gather together all model classes, for easy import and usage.

model_burst

class tvb.core.entities.model.model_burst.BurstConfiguration(project_id, status='running', name=None)

Bases: tvb.core.neotraits.db.HasTraitsIndex

BURST_CANCELED = 'canceled'

BURST_ERROR = 'error'

BURST_FINISHED = 'finished'

BURST_RUNNING = 'running'

clone()

create_date

datatypes_number

dynamic_ids

error_message

finish_time

fk_metric_operation_group

fk_operation_group

fk_project

fk_simulation

gid

id

is_finished

is_group = False

is_pse_burst()

metric_operation_group

name

operation_group

operation_info_for_burst_removal

Return operation id for whole burst removal and a flag specifying whether the current burst is a group.

parent_burst_object = None

process_time

project

range1

range2

ranges

selected_tab = -1

simulator_gid

start_time

status

title

type_

class tvb.core.entities.model.model_burst.Dynamic(name, user_id, model_class, model_parameters, integrator_class, integrator_parameters)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

code_version

fk_user

id

integrator_class

integrator_parameters

model_class

model_parameters

name

model_datatype

Entities for Generic DataTypes, Links and Groups of DataTypes are defined here.

class tvb.core.entities.model.model_datatype.DataType(gid=None, **kwargs)

Bases: tvb.core.neotraits.db.HasTraitsIndex

Base class for DB storage of Types. DataTypes, are the common language between Visualizers, Simulator and Analyzers.

LINKS

static accepted_filters()

Return accepted UI filters for current DataType.

after_store()

Put here code (as a trigger after storage) to be executed by ABCAdapter after the current DT is stored in DB

create_date

disk_size

display_name

To be implemented in each sub-class which is about to be displayed in UI, and return the text to appear.

display_type

fill_from_generic_attributes(attrs)

fill_from_h5(h5_file)

fill_from_has_traits(has_traits)

fixed_generic_attributes = False

fk_datatype_group

fk_from_operation

fk_parent_burst

get_extra_info()

gid

id

invalid

is_nan

module

parent_operation

state

subject

summary_info

title

type

type_

user_tag_1

user_tag_2

user_tag_3

user_tag_4

user_tag_5

visible

class tvb.core.entities.model.model_datatype.DataTypeGroup(operation_group, **kwargs)

Bases: tvb.core.entities.model.model_datatype.DataType

All the DataTypes resulted from an operation group will be part from a DataType group.

LINKS

count_results

create_date

disk_size

fk_datatype_group

fk_from_operation

fk_operation_group

fk_parent_burst

gid

id

invalid

is_nan

module

no_of_ranges

parent_operation

parent_operation_group

state

subject

title

type

type_

user_tag_1

user_tag_2

user_tag_3

user_tag_4

user_tag_5

visible

class tvb.core.entities.model.model_datatype.DataTypeMatrix(gid=None, **kwargs)

Bases: tvb.core.entities.model.model_datatype.DataType

LINKS

array_data_max

array_data_mean

array_data_min

array_has_complex

array_is_finite

create_date

disk_size

fill_from_has_traits(datatype)

fk_datatype_group

fk_from_operation

fk_parent_burst

gid

has_valid_time_series

has_volume_mapping

id

invalid

is_nan

module

ndim

parent_operation

parsed_shape

shape

state

subject

subtype

title

type

type_

user_tag_1

user_tag_2

user_tag_3

user_tag_4

user_tag_5

visible

class tvb.core.entities.model.model_datatype.Links(from_datatype, to_project)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Class used to handle shortcuts from one DataType to another project.

fk_from_datatype

fk_to_project

id

referenced_datatype

referenced_project

class tvb.core.entities.model.model_datatype.MeasurePointsSelection(ui_name, selected_nodes, datatype_gid, project_id)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Interest area. A subset of nodes from a Connectivity or Sensors.

fk_datatype_gid

fk_in_project

id

selected_nodes

ui_name

class tvb.core.entities.model.model_datatype.StoredPSEFilter(ui_name, datatype_gid, threshold_value, applied_on)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Interest Area PSE Viewer Filter tool, specific filter configuration user inputs to be stored from multiple elements

applied_on

fk_datatype_gid

id

threshold_value

ui_name

model_operation

Here we define entities for Operations and Algorithms.

class tvb.core.entities.model.model_operation.Algorithm(module, classname, category_key, group_name=None, group_description=None, display_name='', description='', subsection_name=None, last_introspection_check=None)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

algorithm_category

classname

datatype_filter

description

displayname

fk_category

group_description

group_name

id

last_introspection_check

module

outputlist

parameter_name

removed

required_datatype

subsection_name

class tvb.core.entities.model.model_operation.AlgorithmCategory(displayname, launchable=False, rawinput=False, display=False, defaultdatastate='', order_nr='999', last_introspection_check=None)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

A category that will have different boolean attributes e.g.: launchable|rawinput| display, a displayName and a default state for data.

ALGORITHMS

defaultdatastate

display

displayname

id

last_introspection_check

launchable

order_nr

rawinput

removed

class tvb.core.entities.model.model_operation.AlgorithmTransientGroup(name, description, subsection=None)

Bases: builtins.object

class tvb.core.entities.model.model_operation.Operation(view_model_gid, fk_launched_by, fk_launched_in, fk_from_algo, status='4-PENDING', start_date=None, completion_date=None, op_group_id=None, additional_info='', user_group=None, range_values=None, estimated_disk_size=0)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase, tvb.core.entities.exportable.Exportable

The class used to log any action executed in Projects.

DATA_TYPES

OPERATION_PROCESS_IDENTIFIERS

additional_info

algorithm

completion_date

create_date

estimated_disk_size

fk_from_algo

fk_launched_by

fk_launched_in

fk_operation_group

from_dict(dictionary, dao, user_id=None, project_gid=None)

Add specific attributes from a input dictionary.

gid

has_finished

id

mark_complete(status, additional_info=None)

Update Operation fields on completion: Status and Date

operation_group

project

queue_full

range_values

start_date

start_now()

Update Operation fields at startup: Status and Date

status

to_dict()

Overwrite superclass method to add required changes.

user

user_group

view_model_disk_size

view_model_gid

visible

class tvb.core.entities.model.model_operation.OperationGroup(project_id, name='incomplete', ranges=None, gid=None)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase, tvb.core.entities.exportable.Exportable

We use this group entity, to map in DB a group of operations started in the same time by the user

DATA_TYPES_GROUPS

fill_operationgroup_name(entities_in_group)

Display name for UI.

fk_launched_in

gid

id

name

project

range1

range2

range3

range_references

Memorized range starter

class tvb.core.entities.model.model_operation.OperationProcessIdentifier(operation_id, pid=None, job_id=None)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Class for storing for each operation the process identifier under which it was launched so any operation can be stopped from tvb.

fk_from_operation

id

job_id

operation

pid

class tvb.core.entities.model.model_operation.ResultFigure(user_id, project_id, session_name, name, path, file_format='PNG')

Bases: sqlalchemy.orm.decl_api.DeclarativeBase, tvb.core.entities.exportable.Exportable

Class for storing figures from results, visualize them eventually next to each other. A group of results, with the same session_name will be displayed

file_format

file_path

fk_for_user

fk_in_project

from_dict(dictionary)

Add specific attributes from a input dictionary.

id

name

project

session_name

to_dict()

Overwrite superclass method with required additional data.

tvb.core.entities.model.model_operation.has_finished(status)

Is the given status indicating a finished operation?

model_project

Here we define entities related to user and project.

class tvb.core.entities.model.model_project.Project(name, fk_admin, description='')

Bases: sqlalchemy.orm.decl_api.DeclarativeBase, tvb.core.entities.exportable.Exportable

Contains the Projects informations and who is the administrator.

BurstConfiguration

LINKS

OPERATIONS

OPERATION_GROUPS

RESULT_FIGURES

administrator

description

fk_admin

from_dict(dictionary, user_id)

Add specific attributes from a input dictionary.

gid

id

last_updated

members = []

name

operations_canceled = 0

operations_error = 0

operations_finished = 0

operations_pending = 0

operations_started = 0

refresh_update_date()

Mark entity as being changed NOW. (last_update field)

to_dict()

Overwrite superclass method to add required changes.

version

class tvb.core.entities.model.model_project.User(login, display_name, password, email=None, validated=True, role='RESEARCHER', gid=None)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Contains the users informations.

display_name

email

get_project_structure_grouping()

get_viewers_color_scheme()

gid

id

is_administrator()

Return a boolean, saying if current user has role Administrator

is_online_help_active()

This method returns True if this user should see online help.

password

preferences = ColumnAssociationProxyInstance(AssociationProxy('user_preferences', 'value'))

role

selected_project

set_project_structure_grouping(first, second)

set_viewers_color_scheme(color_scheme)

switch_online_help_state()

This method changes the state of the OnlineHelp Active flag.

user_preferences

username

validated

class tvb.core.entities.model.model_project.UserPreferences(**kwargs)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Contains the user preferences data.

ONLINE_HELP_ACTIVE = 'online_help_active'

PROJECT_STRUCTURE_GROUPING = 'project_structure_grouping'

VIEWERS_COLOR_SCHEME = 'viewers_color_scheme'

fk_user

key

user

value

class tvb.core.entities.model.model_project.User_to_Project(user, case)

Bases: sqlalchemy.orm.decl_api.DeclarativeBase

Multiple Users can be members of a given Project.

fk_project

fk_user

id