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', simulator_configuration=None, name=None)

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase, tvb.core.entities.exportable.Exportable

Contains information required to rebuild the interface of a burst that was already launched.

• simulator_configuration - hold a dictionary with what entries were displayed in the simulator part
• dynamic_ids - A list of dynamic id’s associated with the connectivity nodes. Used by the region parameters page

BURST_CANCELED = 'canceled'

BURST_ERROR = 'error'

BURST_FINISHED = 'finished'

BURST_RUNNING = 'running'

DEFAULT_PORTLET_CONFIGURATION = [[[-1, 'None'], [-1, 'None'], [-1, 'None'], [-1, 'None']], [[-1, 'None'], [-1, 'None'], [-1, 'None'], [-1, 'None']], [[-1, 'None'], [-1, 'None'], [-1, 'None'], [-1, 'None']]]

clone()

Return an exact copy of the entity with the exception than none of it’s sub-entities (tabs, portlets, workflow steps) are persisted in db.

datatypes_number

error_message

finish_time

fk_project

from_dict(dictionary)

get_all_simulator_values()

Returns:dictionary {simulator_attribute_name: value}

get_simulation_parameter_value(param_name)

Read value set for simulation parameter. Return None, when no previous value was set.

id

is_group

Returns:True, when current burst configuration will generate a group.

name

nr_of_tabs = 3

parent

prepare_after_load()

Load Simulator configuration from JSON string, as it was stored in DB.

prepare_before_save()

From dictionary, compose JSON string for DB storage of burst configuration parameters.

process_time

reset_tabs()

Set all tabs to default configuration (empty constructor).

selected_tab = 0

set_portlet(tab_index, index_in_tab, portlet_configuration)

Set in the select with index ‘index_in_tab’ from the tab with index ‘tab_index’ the given ‘portlet_configuration’.

simulator_configuration = {}

start_time

status

update_selected_portlets()

Update the DEFAULT_PORTLET_CONFIGURATION with the selected entries from the current burst config.

update_simulation_parameter(param_name, param_value, specific_key='value')

Update single simulator parameter value or checked state.

update_simulator_configuration(new_values)

Update the stored simulator configuration given the input dictionary :param new_values: new values

workflows_number

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

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase

code_version

fk_user

id

integrator_class

integrator_parameters

model_class

model_parameters

name

class tvb.core.entities.model.model_burst.TabConfiguration

Bases: builtins.object

Helper entity to hold data that is currently being configured in a new burst page.

clone()

Return an exact copy of the entity with the exception than none of it’s sub-entities (portlets, workflow steps) are persisted in db.

get_portlet(portlet_id)

Returns:a PortletConfiguration entity.

reset()

Set to None all portlets in current TAB.

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.

static accepted_filters()

Return accepted UI filters for current DataType.

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_has_traits(has_traits)

fk_datatype_group

fk_from_operation

fk_parent_burst

gid

id

invalid

is_nan

module

parent_operation

persist_full_metadata()

Do nothing here. We will implement this only in MappedType.

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.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.

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

create_date

disk_size

fk_datatype_group

fk_from_operation

fk_parent_burst

gid

id

invalid

is_nan

module

ndim

parent_operation

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.Links(from_datatype, to_project)

Bases: sqlalchemy.ext.declarative.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.ext.declarative.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.ext.declarative.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.ext.declarative.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.ext.declarative.api.DeclarativeBase

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

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(fk_launched_by, fk_launched_in, fk_from_algo, parameters, meta='', 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.ext.declarative.api.DeclarativeBase, tvb.core.entities.exportable.Exportable

The class used to log any action executed in Projects.

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

meta_data

operation_group

parameters

project

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

visible

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

Bases: sqlalchemy.ext.declarative.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

fill_operationgroup_name(entities_in_group)

Display name for UI.

fk_launched_in

gid

id

static load_range_numbers(range_value)

Parse the range values for a given json-like string.

Returns:Boolean_are_all_numbers, range_field_name, array_range_values)

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.ext.declarative.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(operation_id, user_id, project_id, session_name, name, path, file_format='PNG')

Bases: sqlalchemy.ext.declarative.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_from_operation

fk_in_project

from_dict(dictionary)

Add specific attributes from a input dictionary.

id

name

operation

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.ext.declarative.api.DeclarativeBase, tvb.core.entities.exportable.Exportable

Contains the Projects informations and who is the administrator.

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, password, email=None, validated=True, role='RESEARCHER')

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase

Contains the users informations.

email

get_project_structure_grouping()

get_viewers_color_scheme()

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

A descriptor that presents a read/write view of an object attribute.

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.

username

validated

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

Bases: sqlalchemy.ext.declarative.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.ext.declarative.api.DeclarativeBase

Multiple Users can be members of a given Project.

fk_project

fk_user

id

model_workflow

Here we define entities related to workflows and portlets.

class tvb.core.entities.model.model_workflow.Portlet(algorithm_identifier, xml_path, name='TVB Portlet')

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase

Store the Portlet entities. One entity will hold: - portlet id; - path to the XML file that declares it; - a name given in the XML - an unique identifier (also from XML) - last date of introspection.

algorithm_identifier

id

last_introspection_check

name

xml_path

class tvb.core.entities.model.model_workflow.Workflow(project_id, burst_id, status='started')

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase, tvb.core.entities.exportable.Exportable

Main Workflow class. One Burst can have multiple Workflow entities associated (when launching a range).

STATUS_FINISHED = 'finished'

STATUS_STARTED = 'started'

burst

fk_burst

fk_project

from_dict(info_dict)

id

project

status

class tvb.core.entities.model.model_workflow.WorkflowStep(algorithm_id, static_param=None, dynamic_param=None, user_dynamic_param=None, workflow_id=None, step_index=None, tab_index=None, index_in_tab=None)

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase, tvb.core.entities.model.model_workflow._BaseWorkflowStep

Analyze/Simulate step inside a workflow. This type of step will generate an operation to be scheduled for execution.

• step_index - the index of the step into the workflow;
• fk_operation - the operation that resulted from this workflow step.

algorithm

clone()

Return clone - not linked to any DB session or Operation.

fk_algorithm

Column attributes with Foreign Keys can not be declared directly in SqlAlchemy

fk_operation

fk_workflow

Column attributes with Foreign Keys can not be declared directly in SqlAlchemy

from_dict(data)

id

index_in_tab

step_index

tab_index

user_dynamic_param

workflow

class tvb.core.entities.model.model_workflow.WorkflowStepView(algorithm_id, static_param=None, dynamic_param=None, user_dynamic_param=None, workflow_id=None, portlet_id=-1, tab_index=None, index_in_tab=None, ui_name='Default')

Bases: sqlalchemy.ext.declarative.api.DeclarativeBase, tvb.core.entities.model.model_workflow._BaseWorkflowStep

View Step inside a workflow.

• portlet_id - the id of the portlet (or -1 if simulator or result measure);
• ui_name - custom title given by the user when selecting a portlet.

algorithm

clone()

Return clone - not linked to any DB session or Operation.

fk_algorithm

Column attributes with Foreign Keys can not be declared directly in SqlAlchemy

fk_portlet

fk_workflow

Column attributes with Foreign Keys can not be declared directly in SqlAlchemy

from_dict(data)

id

index_in_tab

portlet

tab_index

ui_name

user_dynamic_param

workflow

Subpackages

• db_update_scripts Package
  • 001_update_db
  • 002_update_db
  • 003_update_db
  • 004_update_db
  • 005_update_db
  • 006_update_db
  • 007_update_db
  • 008_update_db
  • 009_update_db
  • 010_update_db
  • 011_update_db
  • 012_update_db
  • 013_update_db
  • 014_update_db
  • 015_update_db
  • 016_update_db
  • 017_update_db
  • 018_update_db
  • helper
• simulator Package
  • burst_configuration
  • simulator