Safety Outlier Explorer Workflow

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This example runs the Safety Outlier Explorer report through a workr YAML workflow: inst/workflow/3_reports/safety_outlier_explorer.yaml. The YAML stores the widget settings, initializes the widget when a safetyCharts init_* helper is available, and writes the rendered HTML report with gsm.safety::RenderSafetyChartsWidget().

workflow_path <- system.file(
  "workflow", "3_reports", "safety_outlier_explorer.yaml",
  package = "gsm.safety"
)
if (!nzchar(workflow_path)) {
  workflow_path <- file.path("inst", "workflow", "3_reports", "safety_outlier_explorer.yaml")
}

lWorkflow <- yaml::read_yaml(workflow_path)
lData <- gsm.safety::MakeExampleData()

The workflow YAML is the report contract:

Workflow YAML

meta:
  Type: Report
  ID: safety_outlier_explorer
  Output: html
  Name: Safety Outlier Explorer Report
  Description: Safety Outlier Explorer report scaffold for SafetyCharts lab review
  ParentIssue: 23
  domains:
    dm: Mapped_SUBJ
    labs: Mapped_LB
  widgetName: safetyOutlierExplorer
  widgetSettings:
    dm:
      id_col: subjid
      age_col: age
      sex_col: sex
      race_col: race
    labs:
      id_col: subjid
      visit_col: visit
      visitn_col: visitn
      studyday_col: studyday
      measure_col: measure
      value_col: value
      normal_col_low: normal_low
      normal_col_high: normal_high
      group_by: sex
      group_cols:
        - value_col: sex
          label: Sex
spec:
  Mapped_SUBJ:
    _all:
      required: true
    subjid:
      type: character
    age:
      type: integer
      required: false
    sex:
      type: character
      required: false
    race:
      type: character
      required: false
  Mapped_LB:
    _all:
      required: true
    subjid:
      type: character
    visit:
      type: character
    visitn:
      type: integer
    studyday:
      type: integer
    measure:
      type: character
    value:
      type: numeric
    unit:
      type: character
      required: false
    normal_low:
      type: numeric
      required: false
    normal_high:
      type: numeric
      required: false
    baseline_flag:
      type: character
      required: false
steps:
  - output: WidgetData
    name: list
    params:
      dm: Mapped_SUBJ
      labs: Mapped_LB
  - output: InitializedWidget
    name: safetyCharts::init_safetyOutlierExplorer
    params:
      data: WidgetData
      settings: widgetSettings
  - output: strOutputDir
    name: getwd
  - output: Report
    name: gsm.safety::RenderSafetyChartsWidget
    params:
      lInitialized: InitializedWidget
      strWidgetName: widgetName
      strOutputDir: strOutputDir
      strOutputFile: ID

Run the workflow with the example mapped data:

lReport <- workr::RunWorkflow(
  lWorkflow = lWorkflow,
  lData = lData,
  bReturnResult = TRUE
)
#> [INFO] Initializing `Report_safety_outlier_explorer` Workflow
#> [INFO] Checking data against spec
#> [INFO] Workflow Step 1 of 4: `list`
#> [INFO] Evaluating 2 parameter(s) for `list`
#> [INFO] dm = Mapped_SUBJ: Passing lData$Mapped_SUBJ.
#> [INFO] labs = Mapped_LB: Passing lData$Mapped_LB.
#> [INFO] Calling `list`
#> [INFO] list of length 2 saved as `lData$WidgetData`.
#> [INFO] Workflow Step 2 of 4: `safetyCharts::init_safetyOutlierExplorer`
#> [INFO] Evaluating 2 parameter(s) for `safetyCharts::init_safetyOutlierExplorer`
#> [INFO] data = WidgetData: Passing lData$WidgetData.
#> [INFO] settings = widgetSettings: Passing lMeta$widgetSettings.
#> [INFO] Calling `safetyCharts::init_safetyOutlierExplorer`
#> [INFO] list of length 2 saved as `lData$InitializedWidget`.
#> [INFO] Workflow Step 3 of 4: `getwd`
#> [INFO] Evaluating 0 parameter(s) for `getwd`
#> [INFO] Calling `getwd`
#> [INFO] character of length 1 saved as `lData$strOutputDir`.
#> [INFO] Workflow Step 4 of 4: `gsm.safety::RenderSafetyChartsWidget`
#> [INFO] Evaluating 4 parameter(s) for `gsm.safety::RenderSafetyChartsWidget`
#> [INFO] lInitialized = InitializedWidget: Passing lData$InitializedWidget.
#> [INFO] strWidgetName = widgetName: Passing lMeta$widgetName.
#> [INFO] strOutputDir = strOutputDir: Passing lData$strOutputDir.
#> [INFO] strOutputFile = ID: Passing lMeta$ID.
#> [INFO] Calling `gsm.safety::RenderSafetyChartsWidget`
#> [INFO] list of length 3 saved as `lData$Report`.
#> [INFO] Returning results from final step: list of length 3`.
#> [INFO] Completed `Report_safety_outlier_explorer` Workflow

lReport$path
#> [1] "/home/runner/work/gsm.safety/gsm.safety/pkgdown/menus/examples/safety_outlier_explorer.html"