Run a workflow via it's YAML specification.

Attempts to run a single assessment (lWorkflow) using shared data (lData) and metadata (lMapping). Calls RunStep for each item in lWorkflow$workflow and saves the results to lWorkflow.

Usage

RunWorkflow(
  lWorkflow,
  lData = NULL,
  lConfig = NULL,
  bReturnResult = TRUE,
  bKeepInputData = TRUE
)

Arguments

lWorkflow

list A named list of metadata defining how the workflow should be run.

lData

list A named list of domain-level data frames.

lConfig

list A configuration object with two methods:

• LoadData: A function that loads data specified in lWorkflow$spec.

• SaveData: A function that saves data returned by the last step in lWorkflow$steps.

bReturnResult

boolean should only the result from the last step (lResults) be returned? If false, the full workflow (including lResults) is returned. Default is TRUE.

bKeepInputData

boolean should the input data be included in lData after the workflow is run? Only relevant when bReturnResult is FALSE. Default is TRUE.

Value

Object containing the results of the workflow's last step (if bLastResult is TRUE) or the full workflow object (if bReturnResults is TRUE) or the full workflow object (if bReturnResults is FALSE).

list contains just lData if bReturnData is TRUE, otherwise returns the full lWorkflow object.

Examples

if (FALSE) { # \dontrun{
# ----
# Workflow using in-memory data.

lRawData <- list(
  Raw_AE = clindata::rawplus_ae,
  Raw_SUBJ = clindata::rawplus_dm
)

# Generate mapped input data to metric workflow.
lMappingWorkflows <- MakeWorkflowList(
  c("AE", "SUBJ"),
  bExact = TRUE
)

lMappedData <- RunWorkflows(
  lMappingWorkflows,
  lRawData
)

# Run the metric workflow.
lMetricWorkflow <- MakeWorkflowList("kri0001")$kri0001
lMetricOutput <- RunWorkflow(
  lMetricWorkflow,
  lMappedData
)

# ----
# Workflow using data read/write functions.

# Define a function that loads data.
LoadData <- function(lWorkflow, lConfig, lData) {
  lData <- lData
  purrr::imap(
    lWorkflow$spec,
    ~ {
      input <- lConfig$Domains[[.y]]

      if (is.function(input)) {
        data <- input()
      } else if (is.character(input)) {
        data <- read.csv(input)
      }

      lData[[.y]] <- ApplySpec(data, .x)
    }
  )
  return(lData)
}

# Define a function that saves data to .csv.
SaveData <- function(lWorkflow, lConfig) {
  domain <- paste0(lWorkflow$meta$Type, "_", lWorkflow$meta$ID)
  if (domain %in% names(lConfig$Domains)) {
    output <- lConfig$Domains[[domain]]

    write.csv(
      lWorkflow$lResult,
      output
    )
  }
}

# Define a configuration object with LoadData/SaveData functions and a list of named data sources.
lConfig <- list(
  LoadData = LoadData,
  SaveData = SaveData,
  Domains = c(
    Raw_AE = function() {
      clindata::rawplus_ae
    },
    Raw_SUBJ = function() {
      clindata::rawplus_dm
    },
    Mapped_AE = file.path(tempdir(), "mapped-ae.csv"),
    Mapped_SUBJ = file.path(tempdir(), "mapped-subj.csv")
  )
)

# Generate mapped input data to metric workflow.
lMappingWorkflows <- MakeWorkflowList(
  c("AE", "SUBJ"),
  bExact = TRUE
)

lMappedData <- RunWorkflows(
  lMappingWorkflows,
  lConfig = lConfig
)

# Run the metric workflow.
lMetricWorkflow <- MakeWorkflowList("kri0001")$kri0001
lMetricOutput <- RunWorkflow(
  lMetricWorkflow,
  lConfig = lConfig
)
} # }