Run a single step in a workflow.

Runs a single step of an assessment workflow. This function is called by RunWorkflow for each step in the workflow. It prepares the parameters for the function call, including the metadata, mapping, and data inputs. It then calls the function specified in lStep$name with the prepared parameters.

Usage

RunStep(lStep, lData, lMeta)

Arguments

lStep: list single workflow step (typically defined in lWorkflow$workflow). Should include the name of the function to run (lStep$name), data inputs (lStep$inputs), name of output (lStep$output) and configurable parameters (lStep$params) (if any)
lData: list a named list of domain level data frames.
lMeta: list a named list of meta data.

Value

list containing the results of the lStep$name function call should contain .$checks parameter with results from is_mapping_vald for each domain in lStep$inputs.

Examples

wf_mapping <- MakeWorkflowList("mapping")
lStep <- MakeWorkflowList("kri0001")[["kri0001"]][["steps"]][[1]]
lMeta <- MakeWorkflowList("kri0001")[["kri0001"]][["meta"]]
lData <- list(
  dfSUBJ = clindata::rawplus_dm,
  dfAE = clindata::rawplus_ae,
  dfPD = clindata::ctms_protdev,
  dfCONSENT = clindata::rawplus_consent,
  dfIE = clindata::rawplus_ie
)
lMapped <- RunWorkflow(wf_mapping, lData)$lData
#> 
#> ── Initializing `` Workflow ────────────────────────────────────────────────────
#> → Colnames: dfSUBJ, dfAE, dfPD, dfCONSENT, and dfIE
#> → Workflow `` has no `steps` property.
#> → Workflow `` has no `meta` property.
#> ℹ Returning workflow outputs: 
#> 
#> ── Completed `` Workflow ───────────────────────────────────────────────────────

ae_step <- RunStep(lStep = lStep, lData = lMapped, lMeta = lMeta)
#> 
#> ── Evaluating 1 parameter(s) for `ParseThreshold()` 
#> ✔ strThreshold = Threshold: Passing lMeta$Threshold.
#> 
#> ── Calling `ParseThreshold()` 
#> ✔ Parsed -2,-1,2,3 to numeric vector: -2, -1, 2, and 3