Run a single step in a workflow.

RunStep() has moved to workr::RunStep(). This wrapper remains for backward compatibility in {gsm.core}.

Usage

RunStep(lStep, lData, lMeta, lSpec = NULL)

Arguments

lStep

list single workflow step (typically pulled from lWorkflow$steps). Should include the name of the function to run (lStep$name), name of the object where the function result should be saved (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.

lSpec

list a data specification containing required columns. See the gsm Extensions article.

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 <- workr::MakeWorkflowList(
  strNames = c("AE", "SUBJ"),
  strPath = "example_workflow/1_mappings",
  strPackage = "gsm.core",
  bExact = TRUE
)
lWorkflow <- workr::MakeWorkflowList(
  strPath = "example_workflow/2_metrics",
  strNames = c("kri0001", "kri0002"),
  strPackage = "gsm.core"
)
lStep <- lWorkflow[["kri0001"]][["steps"]][[1]]
lMeta <- lWorkflow[["kri0001"]][["meta"]]

lRaw <- list(
  Raw_SUBJ = gsm.core::lSource$Raw_SUBJ,
  Raw_AE = gsm.core::lSource$Raw_AE
)

mapped <- workr::RunWorkflows(wf_mapping, lRaw)
#> [INFO] Running 2 Workflows
#> [INFO] Initializing `Mapped_AE` Workflow
#> [INFO] Checking data against spec
#> [INFO] Workflow Step 1 of 1: `=`
#> [INFO] Evaluating 2 parameter(s) for `=`
#> [INFO] lhs = Mapped_AE: No matching data found. Passing 'Mapped_AE' as a string.
#> [INFO] rhs = Raw_AE: Passing lData$Raw_AE.
#> [INFO] Calling `=`
#> [INFO] 3000x11 data.frame saved as `lData$Mapped_AE`.
#> [INFO] Returning results from final step: 3000x11 data.frame`.
#> [INFO] Completed `Mapped_AE` Workflow
#> [INFO] Initializing `Mapped_SUBJ` Workflow
#> [INFO] Checking data against spec
#> [INFO] Workflow Step 1 of 1: `gsm.core::RunQuery`
#> [INFO] Evaluating 2 parameter(s) for `gsm.core::RunQuery`
#> [INFO] df = Raw_SUBJ: Passing lData$Raw_SUBJ.
#> [INFO] strQuery = SELECT * FROM df WHERE enrollyn == 'Y': No matching data found. Passing 'SELECT * FROM df WHERE enrollyn == 'Y'' as a string.
#> [INFO] Calling `gsm.core::RunQuery`
#> Warning: `RunQuery()` was deprecated in gsm.core 1.3.0.
#> ℹ Please use `workr::RunQuery()` instead.
#> ℹ The deprecated feature was likely used in the workr package.
#>   Please report the issue to the authors.
#> [INFO] Creating a new temporary DuckDB connection.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmpvj3eea/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> [INFO] SQL Query complete: 762 rows returned.
#> [INFO] Disconnected from temporary DuckDB connection.
#> [INFO] 762x15 data.frame saved as `lData$Mapped_SUBJ`.
#> [INFO] Returning results from final step: 762x15 data.frame`.
#> [INFO] Completed `Mapped_SUBJ` Workflow
ae_step <- workr::RunStep(lStep = lStep, lData = mapped, lMeta = lMeta)
#> [INFO] Evaluating 1 parameter(s) for `gsm.core::ParseThreshold`
#> [INFO] strThreshold = Threshold: Passing lMeta$Threshold.
#> [INFO] Calling `gsm.core::ParseThreshold`
#> Parsed -2,-1,2,3 to numeric vector: -2, -1, 2, 3