DAGWorkflow: DAG Workflow Class

In uptake/updraft: An R Based Workflow Manager

Description

Directed Acyclic Graph (DAG) workflow implementation

Usage

DAGWorkflow

Format

An object of class R6ClassGenerator of length 25.

Class Constructor

new(name = "")

• name: character string that identifies this workflow

Public

addConnections(connections)

• Adds a list of connection to a workflow.

• connection: list of implementation ConnectionInterface object.

• Returns: NULL

addModules(modules)

• Adds a list of modules to a workflow.

• modules: list of implementation ModuleInterface objects.

• Returns: NULL

errorCheck(executionCheck = FALSE, ...)

• Runs error checking on the internal state of a workflow.

• executionCheck: when set to TRUE, runs additional checks to determine if ready for execution.

• ...: character vectors of additional argument names from sources outside of connections, such as an enviroment.

• Returns: NULL, will raise a fatal error if an error is found

getWorkflowInputs()

• Gets a named logical vector where names are the possible inputs into the workflow and the values indicate if an input is required.

• Returns: logical vector

getModuleInputs(module)

• Gets a named logical vector where the names are the inputs, excluding those provided by connections from upstream modules, into a module and the values indicate if an input is required.

• module: implementation obj of ModuleInterface or a character string of a module in a workflow.

• Returns: logical vector

getConnections(module1, module2)

• Gets a list of connections between module1 and module2.

• module1: implementation obj of ModuleInterface or a character string of a module in a workflow. Because this is a directed implementation class, module1 is the head module.

• module2: implementation obj of ModuleInterface or a character string of a module in a workflow. Because this is a directed implementation class, module1 is the tail module.

• Returns: vector of character strings

getDownstreamModules(module)

• Gets a list of modules downstream of module.

• module: valid implementation ModuleInterface obj or name of module that is present in a workflow.

• Returns: list of downstream modules

getEndingModules()

• Gets a list of ending modules in a workflow.

• Returns: a list of ending modules

getAllModules()

• gets a list of all modules in a workflow.

• Returns: a list of all modules

getName()

• Gets the name of a workflow.

• Returns: character string

getSaveInfo()

• DOES NOT APPLY TO WORKFLOWS.

• Returns: NULL

getStartingModules()

• Gets a list of starting modules in a workflow.

• Returns: a list of starting modules

getUpstreamModules(module)

• Gets a list of modules upstream of module.

• module: valid implementation ModuleInterface obj or name of module that is present in a workflow.

• Returns: list of downstream modules

removeConnection(connection)

• Removes a connection from a workflow.

• connection: implementation object of ConnectionInterface, or a character vector of connection names

• Returns: NULL

removeModule(module)

• Removes a modules from a workflow. Also, removes associated connections with module.

• module: implementation object of ModuleInterface, or a character vector of module names

• Returns: NULL

save(filename)

• Saves a workflow onto disk at filename.

• filename: location to store file

• Returns: NULL

visualize()

• Visualizes a workflow.

• Returns: NULL. Output will be on a plot, etc.

Private

connections

• Stores a workflow's connections.

graph

• Stores a workflow's internal graph representation.

modules

• Stores a workflow's modules.

name

• Stores a workflow's name.

getNeighbors(graph, module, direction)

• Gets a list of the neighbor modules of module in graph.

• graph: valid igraph object.

• module: module obj or module name.

• direction: "in" for upstream neighbors or "out" for downstream neighbors.

• Returns: a list of neighbor modules.

getRevertState()

• Gets a list of data that can be used with the revert method to revert a workflow to the state outputted from this method.

• Returns: a list that contains revert state data.

revert(previousState)

• Returns a workflow to the state stored in previousState.

• Returns: NULL.

Static Class Methods

DAGWorkflow-cash-initFromFile

uptake/updraft documentation built on Oct. 17, 2019, 11:59 a.m.