ProtocolModel - gws_core

Base abstract class for Process and Protocol

:param Viewable: [description] :type Viewable: [type]

Attributes

config: Configdata: Dict[str, Any]error_info: ProcessErrorInfolayout: ProtocolLayoutprogress_bar: ProgressBarscenario: Scenariostatus: ProcessStatusstyle: TypingStyle

Functions

__INIT__

Constructor

ADD_CONNECTOR

Adds a connector to the pfrotocol.

Parameters:

Name	Type	Default value	Description
from_process_name	`str`
from_port_name	`str`
to_process_name	`str`
to_port_name	`str`

Return type:

Connector

ADD_CONNECTORS

Parameters:

Name	Type	Default value	Description
connectors	`List`

ADD_INTERFACE

Parameters:

Name	Type	Default value	Description
name	`str`
process_name	`str`
port_name	`str`

Return type:

IOface

ADD_INTERFACES

Parameters:

Name	Type	Default value	Description
interfaces	`Dict`

ADD_INTERFACES_FROM_DTO

Parameters:

Name	Type	Default value	Description
interfaces	`Dict`

ADD_OUTERFACE

Parameters:

Name	Type	Default value	Description
name	`str`
process_name	`str`
port_name	`str`

Return type:

IOface

ADD_OUTERFACES

Parameters:

Name	Type	Default value	Description
outerfaces	`Dict`

ADD_OUTERFACES_FROM_DTO

Parameters:

Name	Type	Default value	Description
outerfaces	`Dict`

ADD_PROCESS_MODEL

Adds a process to the protocol.

Parameters:

Name	Type	Default value	Description
process_model	`ProcessModel`
instance_name	`str`		Unique name of the process. if none, the name is generated

ALL_PROCESSES_ARE_DRAFT

Return True if all the processes are in draft

Return type:

bool

ALL_PROCESSES_ARE_SUCCESS

Return True if all the processes are in success

Return type:

bool

ARCHIVE

CHECK_IS_UPDATABLE

Parameters:

Name	Type	Default value	Description
error_if_finished	`bool`	True

CLONE

COERCE

Parameters:

Name	Type	Default value	Description
_coerce	`bool`	True

DELETE_CONNECTOR_FROM_RIGHT

remove the connector which right side is connected to the specified port of the specified process return the list of deleted connectors

Parameters:

Name	Type	Default value	Description
right_process_name	`str`
right_process_port_name	`str`

Return type:

Optional

DELETE_CONNECTORS_FROM_LEFT

remove the connector which left side is connected to the specified port of the specified process It can remove multiple connectors if there are multiple connectors connected to the same port Return the list of deleted connectors

Parameters:

Name	Type	Default value	Description
left_process_name	`str`
left_process_port_name	`str`

DELETE_INSTANCE

DEPENDENCIES

Parameters:

Name	Type	Default value	Description
search_nullable	`bool`	False

GENERATE_INTERFACE_NAME

Generate a unique interface name

Return type:

str

GENERATE_OUTERFACE_NAME

Generate a unique outerface name

Return type:

str

GENERATE_UNIQUE_INSTANCE_NAME

Generate a unique instance name from an instance_name by adding _1 or _2... to the end of the instance name

Parameters:

Name	Type	Default value	Description
instance_name	`str`

Return type:

str

GET_ALL_NEXT_PROCESSES

Returns all the next processes of a process in this protocol and parent protocols.

Parameters:

Name	Type	Default value	Description
process_name	`str`
check_parent_protocol	`bool`	True	If true, the next processes of the parent protocol are also returned
check_circular_connexion	`bool`	False	If true, check if there is a circular connexion and raise an exception

Return type:

Set

GET_ALL_PROCESSES_FLATTEN_SORT_BY_START_DATE

Return all the processes of the protocol and its sub protocols, sorted by start date

Return type:

List

GET_CONNECTOR_FROM_RIGHT

Returns a connector by the destination process and port

Parameters:

Name	Type	Default value	Description
right_process_name	`str`
right_process_port_name	`str`

Return type:

Optional

GET_CONNECTORS_FROM_LEFT

Returns a connector by the destination process and port

Parameters:

Name	Type	Default value	Description
left_process_name	`str`
left_process_port_name	`str`

Return type:

List

GET_DIRECT_NEXT_PROCESSES

Returns the next processes of a process.

Parameters:

Name	Type	Default value	Description
process_name	`str`

Return type:

Set

GET_DIRECT_PREVIOUS_PROCESSES

Returns the previous processes of a process.

Parameters:

Name	Type	Default value	Description
process_name	`str`

Return type:

Set

GET_ERROR_INFO

Return type:

Optional[ProcessErrorInfo]

GET_ERROR_TASKS

Return type:

List

GET_EXECUTION_TIME

Return the execution time of the process

Return type:

float

GET_GRAPH

Return the graph json object

Return type:

ProtocolMinimumDTO

GET_ID

GET_INPUT_RESOURCE_IDS

Return type:

Set

GET_INSTANCE_NAME_CONTEXT

return the instance name in the context

Return type:

str

GET_INSTANCE_PATH

Return the instance path

Return type:

str

GET_INTERFACES_LINKED_TO_PROCESS

Returns the interfaces linked to a process

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`

Return type:

List

GET_LAST_MESSAGE

Return the last message of the process

Return type:

Optional[ProgressBarMessageDTO]

GET_NAME

Return the name of the process

Return type:

str

GET_OUTERFACE_LINKED_TO_PROCESS

Returns the outerface linked to the process with the given name

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`

Return type:

List

GET_PROCESS

Returns a process by its name.

Parameters:

Name	Type	Default value	Description
name	`str`

Return type:

ProcessModel

GET_PROCESS_BY_INSTANCE_PATH

Returns a process by its instance path.

Parameters:

Name	Type	Default value	Description
instance_path	`str`

Return type:

ProcessModel

GET_PROCESS_TYPE

Return type:

Type[Process]

GET_PROCESS_TYPING

Return type:

Typing

GET_PROGRESS_VALUE

Return the last message of the process

Return type:

float

GET_PROTOCOL_CHAIN_INFO

return a string with the information up to the main protocol

Return type:

str

GET_RUNNING_TASK

Return the running process, go through all the sub protocols

Return type:

Optional

GET_STYLE

Return the style of the process

Return type:

TypingStyle

HAS_FINISHED_PROCESSES

Return True if the protocol has finished processes (except the auto run processes)

Return type:

bool

IN_PORT

Returns the port of the inputs by its name.

Parameters:

Name	Type	Default value	Description
port_name	`str`

Return type:

InPort

INIT_CONNECTORS_FROM_GRAPH

Parameters:

Name	Type	Default value	Description
links	`List`
check_compatiblity	`bool`	True

INIT_PROCESSES_FROM_GRAPH

Parameters:

Name	Type	Default value	Description
sub_process_factory	`ProtocolSubProcessBuilder`

IS_ALIAS

IS_AUTO_RUN

Return true if the process is automatically run when added to a protocol

Return type:

bool

IS_DIRTY

IS_ENABLE_IN_SUB_PROTOCOL

Return true if the process is enable in sub protocol

Return type:

bool

IS_INPUT_TASK

return true if the process is of type InputTask

Return type:

bool

IS_INTERFACED_WITH

Returns True if the input poort the process is an interface of the protocol

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`

Return type:

bool

IS_OUTERFACED_WITH

Returns True if the input poort the process is an outerface of the protocol

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`

Return type:

bool

IS_OUTPUT_TASK

return true if the process is of type OutputTask

Return type:

bool

IS_PROTOCOL

Return type:

bool

IS_ROOT_PROCESS

Return type:

bool

IS_SAVED

Returns True if the model is saved in db, False otherwise

Return type:

bool

MARK_AS_DRAFT

MARK_AS_ERROR

Parameters:

Name	Type	Default value	Description
error_info	`ProcessErrorInfo`

MARK_AS_ERROR_AND_PARENT

Parameters:

Name	Type	Default value	Description
process_error	`ProcessRunException`
context	`str`

MARK_AS_STARTED

MARK_AS_SUCCESS

MARK_AS_WAITING_FOR_CLI_PROCESS

OUT_PORT

Returns the port of the outputs by its name.

Parameters:

Name	Type	Default value	Description
port_name	`str`

Return type:

OutPort

PORT_IS_INTERFACE

Return True if the port of the process is an interface of the protocol

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`
port_name	`Any`

Return type:

bool

PROCESS_IS_READY

Parameters:

Name	Type	Default value	Description
process	`ProcessModel`

Return type:

bool

PROPAGATE_RESOURCES

REFRESH

Return type:

ModelType

REFRESH_GRAPH_FROM_DUMP

Refresh the graph json object inside the data from the dump method

REFRESH_STATUS

Refresh the status of the protocol based on the status of its processes

Parameters:

Name	Type	Default value	Description
refresh_parent	`bool`	True

REMOVE_INTERFACE

Remove an interface

:raises BadRequestException: description

Parameters:

Name	Type	Default value	Description
name	`str`		_description_

REMOVE_INTERFACES_BY_PROCESS_NAME

Remove the interface linked the process with the given name

Parameters:

Name	Type	Default value	Description
process_name	`str`

REMOVE_OUTERFACE

Parameters:

Name	Type	Default value	Description
name	`str`

REMOVE_OUTERFACES_BY_PROCESS_NAME

Remove the outerfaces linked to the process with the given name

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`

REMOVE_PROCESS

Parameters:

Name	Type	Default value	Description
name	`str`

REPLACE_IO_PROCESS_WITH_IOFACE

Method to replace each Input process with an interface and each Output process with an outerface. It does not replace on sub protocols

RESET

RUN

Run the process and save its state in the database.

RUN_AUTO_RUN_PROCESSES

Run all the auto run processes of the protocol

RUN_PROCESS

Method to run a single process of the protocol

Parameters:

Name	Type	Default value	Description
process_instance_name	`str`		Process to run

SAVE

Override save to save the inputs and outputs

Return type:

'ProcessModel'

SAVE_FULL

SAVE_GRAPH

Return type:

ProtocolModel

SET_CONFIG

Set the config object

Parameters:

Name	Type	Default value	Description
config	`Config`		[description] paramsdict

SET_CONFIG_VALUE

Set a value of the config

Parameters:

Name	Type	Default value	Description
param_name	`str`		[description]
value	`Any`		[description]

SET_CONFIG_VALUES

Set the config values

Parameters:

Name	Type	Default value	Description
config_values	`ConfigParamsDict`		[description] dict[str, any]

SET_ERROR_INFO

Parameters:

Name	Type	Default value	Description
error_info	`ProcessErrorInfo`

SET_INPUTS_FROM_DTO

Set the inputs from a DTO

Parameters:

Name	Type	Default value	Description
inputs_dto	`IODTO`
reset	`bool`	False

SET_INPUTS_FROM_SPECS

Set the inputs from specs

Parameters:

Name	Type	Default value	Description
inputs_specs	`IOSpecs`

SET_OUTPUTS_FROM_DTO

Set the outputs from a DTO

Parameters:

Name	Type	Default value	Description
outputs_dto	`IODTO`
reset	`bool`	False

SET_OUTPUTS_FROM_SPECS

Set the outputs from specs

Parameters:

Name	Type	Default value	Description
outputs_specs	`IOSpecs`

SET_PARENT_PROTOCOL

Sets the parent protocol of the process

Parameters:

Name	Type	Default value	Description
parent_protocol	`ProtocolModel`

SET_PROCESS_TYPE

Parameters:

Name	Type	Default value	Description
process_type	`Type[Process]`

SET_SCENARIO

Parameters:

Name	Type	Default value	Description
scenario	`Any`

TO_CONFIG_DTO

Return the config DTO

Parameters:

Name	Type	Default value	Description
ignore_source_config	`bool`	False

Return type:

ProcessConfigDTO

TO_DTO

Return type:

ProcessDTO

TO_MINIMUM_DTO

Return the minium json to recognize this process

Return type:

ProcessMinimumDTO

TO_PROTOCOL_CONFIG_DTO

Parameters:

Name	Type	Default value	Description
ignore_source_config	`bool`	False

Return type:

ProtocolGraphConfigDTO

TO_PROTOCOL_DTO

Return type:

ProtocolDTO

TO_PROTOCOL_FULL_DTO

Return type:

ProtocolFullDTO

TO_PROTOCOL_MINIMUM_DTO

Return type:

ProtocolMinimumDTO

UNWRAP

ADD_INDEX - @classmethod

Parameters:

Name	Type	Default value	Description
fields	`Any`

AFTER_ALL_TABLES_INIT - @classmethod

Method call after all the table are inited

Useful when use DeferredForeignKey to create the foreign key manually latter

AFTER_TABLE_CREATION - @classmethod

Method call after the table is created

Usefull to create the full text indexes

ALIAS - @classmethod

Parameters:

Name	Type	Default value	Description
alias	`Any`

BIND - @classmethod

Parameters:

Name	Type	Default value
database	`Any`
bind_refs	`bool`	True
bind_backrefs	`bool`	True
_exclude	`Any`

BIND_CTX - @classmethod

Parameters:

Name	Type	Default value
database	`Any`
bind_refs	`bool`	True
bind_backrefs	`bool`	True

BULK_CREATE - @classmethod

Parameters:

Name	Type	Default value	Description
model_list	`Any`
batch_size	`Any`

BULK_UPDATE - @classmethod

Parameters:

Name	Type	Default value	Description
model_list	`Any`
fields	`Any`
batch_size	`Any`

CLASSNAME - @classmethod

Returns the name of the class

Parameters:

Name	Type	Default value	Description
slugify	`bool`	False	True to slugify the class name if true, defaults to false , optional
snakefy	`bool`	False	True to snakefy the class name if true, defaults to false , optional
replace_uppercase	`bool`	False	Replace upper cases by "-" if true, defaults to false , optional

Return type:

str

COLUMN_EXISTS - @classmethod

Returns True if the column exists in the table

Parameters:

Name	Type	Default value	Description
column_name	`str`		The column name ``

Return type:

bool

CREATE - @classmethod

Parameters:

Name	Type	Default value	Description
query	`Any`

CREATE_FOREIGN_KEY_IF_NOT_EXIST - @classmethod

Create a foreign key for a Foreign key field only if the foreign key does not exists

Parameters:

Name	Type	Default value	Description
field	`ForeignKeyField`		[description]

CREATE_FULL_TEXT_INDEX - @classmethod

Method to create a full text index

Parameters:

Name	Type	Default value	Description
columns	`List`		[description] [str]
index_name	`str`

CREATE_TABLE - @classmethod

Create model table

DECORATED_METHOD_NAMES - @classmethod

Parameters:

Name	Type	Default value	Description
decorator_name	`Any`

DELETE - @classmethod

DELETE_BY_ID - @classmethod

Parameters:

Name	Type	Default value	Description
pk	`Any`

DROP_TABLE - @classmethod

Drop model table

EXECUTE_SQL - @classmethod

Execute a raw SQL query. Can use the [TABLE_NAME] to replace by the table name

Parameters:

Name	Type	Default value	Description
query	`str`		The query to execute ``

FILTER - @classmethod

Parameters:

Name	Type	Default value	Description
dq_nodes	`Any`
filters	`Any`

FOREIGN_KEY_EXISTS - @classmethod

Parameters:

Name	Type	Default value	Description
column_name	`str`

Return type:

bool

FULL_CLASSNAME - @classmethod

Returns the full name of the class

Parameters:

Name	Type	Default value	Description
slugify	`bool`	False	Slugify the returned class name if true, defaults to false , optional
snakefy	`bool`	False	Snakefy the returned class name if true, defaults to false ``

Return type:

str

GET - @classmethod

Parameters:

Name	Type	Default value	Description
query	`Any`
filters	`Any`

GET_BY_ID - @classmethod

Parameters:

Name	Type	Default value	Description
id	`str`

Return type:

Optional

GET_BY_ID_AND_CHECK - @classmethod

Get by ID and throw 404 error if object not found

Parameters:

Name	Type	Default value	Description
id	`str`		[description]

Return type:

ModelType

GET_BY_IDS - @classmethod

Parameters:

Name	Type	Default value	Description
ids	`List`

Return type:

List

GET_DB - @classmethod

Return type:

DatabaseProxy

GET_DB_MANAGER - @classmethod

Returns the (current) DbManager of this model

Return type:

Type

GET_OR_CREATE - @classmethod

GET_OR_NONE - @classmethod

Parameters:

Name	Type	Default value	Description
query	`Any`
filters	`Any`

GET_TABLE_NAME - @classmethod

Returns the table name of this class

Return type:

str

INDEX - @classmethod

Parameters:

Name	Type	Default value	Description
fields	`Any`

INDEX_EXISTS - @classmethod

Returns True if the index exists in the table

Parameters:

Name	Type	Default value	Description
index_name	`str`		The index name ``

Return type:

bool

INHERITORS - @classmethod

Get all the classes that inherit this class

Return type:

List

INSERT - @classmethod

Parameters:

Name	Type	Default value	Description
_Model__data	`Any`
insert	`Any`

INSERT_FROM - @classmethod

Parameters:

Name	Type	Default value	Description
query	`Any`
fields	`Any`

INSERT_MANY - @classmethod

Parameters:

Name	Type	Default value	Description
rows	`Any`
fields	`Any`

IS_MYSQL_ENGINE - @classmethod

METHOD_NAMES - @classmethod

Returns the list of the methods

Return type:

List

MODULE_NAME - @classmethod

Returns the module name of the class

Return type:

str

NOOP - @classmethod

PROPERTY_METHOD_NAMES - @classmethod

PROPERTY_NAMES - @classmethod

Retrieves the property names

Parameters:

Name	Type	Default value	Description
instance	`type`		The s of the properties to retrieve. set `none` to retrieve all. `type` or `union[type]`
exclude	`type`

Return type:

List

RAW - @classmethod

Parameters:

Name	Type	Default value	Description
sql	`Any`
params	`Any`

REPLACE - @classmethod

Parameters:

Name	Type	Default value	Description
_Model__data	`Any`
insert	`Any`

REPLACE_MANY - @classmethod

Parameters:

Name	Type	Default value	Description
rows	`Any`
fields	`Any`

SAVE_ALL - @classmethod

SEARCH - @classmethod

Performs full-text search on the field. Must be overrided by child class to work

Parameters:

Name	Type	Default value	Description
phrase	`str`		The phrase to search ``
modifier	`str`

Return type:

ModelSelect

SELECT - @classmethod

Parameters:

Name	Type	Default value	Description
fields	`Any`

SET_BY_ID - @classmethod

Parameters:

Name	Type	Default value	Description
key	`Any`
value	`Any`

TABLE_EXISTS - @classmethod

TRUNCATE_TABLE - @classmethod

Parameters:

Name	Type	Default value	Description
options	`Any`

UPDATE - @classmethod

Parameters:

Name	Type	Default value	Description
_Model__data	`Any`
update	`Any`

VALIDATE_MODEL - @classmethod

COPY - @staticmethod

Parameters:

Name	Type	Default value	Description
method	`Any`