Create a workflow template environment from an existing workflow
createWorkflowTemplateEnv.RdExtracts all steps, relationships, parameters, and files from the workflow and builds a reusable workflow template environment.
Value
An environment representing the workflow template with the following methods:
- addStepTemplate(stepTemplate, name=NULL)
Adds a step template to the workflow template.
- createExecutionPlan()
Creates a data.frame describing the execution plan for the workflow.
- df()
Returns a data.frame with metadata for all steps in the template.
- executePlan(executionPlan)
Executes a given execution plan data.frame.
- listParameters()
Returns a data frame of all defined parameters.
- parameterizeStep(paramName, stepPattern, property, target=NULL, required=TRUE, defaultValue=NULL)
Registers a parameter to modify steps before realisation.
- paramName
Name of the parameter.
- stepPattern
Pattern to match steps. Three matching modes are supported:
"*"matches all steps in the workflow template.Prefix pattern ending with
*(e.g.,"analysisTree1/*") matches all steps whose fullName starts with the prefix.Exact match (e.g.,
"import data") first tries to match the step's fullName, then falls back to matching the step's description.
- property
The property to parameterize: "remoteFile", "localFile", "treeIdent", "gridArgument.
", "description", "rationale", or "stepName". - target
(Optional) Target within the property, e.g., the path of a remote file.
- required
(Optional) Whether this parameter must be set before realization (default: TRUE).
- defaultValue
(Optional) Default value if not set.
- realise()
Executes the plan, applying parameters and creating the workflow steps.
- setParameter(paramName, value)
Sets a value for a defined parameter.
- setWorkflowTreeIdent(treeIdent, from=pwd())
Sets the ident of the location/analysis tree where the workflow template should be created, i.e., realised. If not defined, the new workflow will be located in the same location(s) where the step(s) of the template workflow are located.
- setWorkflowTreeName(treeName)
Sets the name of the location/analysis tree where the workflow template should be created, i.e., realised. If not defined, the new workflow will be located in the same location(s) where the step(s) of the template workflow are located.
- setWorkflowTreeRootFolder(rootFolder)
Sets the root folder path for the workflow tree where the template is realised to.
- toJSON(filepath, pretty=TRUE)
Saves the template definition to a JSON file.
- validateParameters()
Checks if all required parameters are set, throwing an error if not.
Examples
if (FALSE) { # \dontrun{
# Get a step and load its dependencies
step <- getStep("/myProject/workflow/analysisTree/Step 1")
step$dependencies$load()
# Create a workflow template from the step's workflow
workflowTemplate <- createWorkflowTemplateEnv(step$workflow)
# View the steps in the template
workflowTemplate$df()
# Define a parameter to modify the description of a specific step
workflowTemplate$parameterizeStep(
stepPattern = "import data", #pattern that matches the name or the description of the step which the paramter should target
paramName = "inputDescription", #name of the parameter to which a value will be asigned to
property = "description" #the property of the targeted step which will be modified by the parameter
)
# Define a parameter that applies to all steps
workflowTemplate$parameterizeStep(
stepPattern = "*",
paramName = "allStepsRationale",
property = "rationale"
)
# Set the parameter values
workflowTemplate$setParameter("inputDescription", "Load input dataset")
workflowTemplate$setParameter("allStepsRationale", "Automated workflow execution")
# Review parameters before realisation
workflowTemplate$listParameters()
# Optionally set a new target tree for the realised workflow
workflowTemplate$setWorkflowTreeName("newAnalysisTree")
# Realise the template (creates actual steps)
realisedWorkflow <- workflowTemplate$realise()
} # }