Workflow: Workflow

In Open-Systems-Pharmacology/OSPSuite.ReportingEngine: R package to create reports for the Open Systems Pharmacology models

Workflow

Description

R6 class representing Reporting Engine generic Workflow

Public fields

simulationStructures

SimulationStructure R6 class object managing the structure of the workflow output

workflowFolder

path of the folder create by the Workflow

taskNames

Enum of task names

reportFileName

name of the Rmd report file

reportTitle

report title page

createWordReport

logical of option for creating Markdown-Report only but not a Word-Report.

wordConversionTemplate

optional docx template for rendering a tuned Word-Report document

userDefinedTasks

List of user-defined tasks (to update with loadUserDefinedTask)

numberSections

logical defining if the report sections should be numbered

Active bindings

reportFolder

Directory in which workflow report is saved

reportFilePath

Path of workflow report

Methods

Public methods

• Workflow$new()

• Workflow$getAllTasks()

• Workflow$getAllPlotTasks()

• Workflow$getActiveTasks()

• Workflow$getInactiveTasks()

• Workflow$activateTasks()

• Workflow$inactivateTasks()

• Workflow$printReportingEngineInfo()

• Workflow$getWatermark()

• Workflow$setWatermark()

• Workflow$setParameterDisplayPaths()

• Workflow$getParameterDisplayPaths()

• Workflow$setSimulationDescriptor()

• Workflow$getSimulationDescriptor()

• Workflow$print()

• Workflow$clone()

---

Method new()

Create a new Workflow object.

Usage

Workflow$new(
  simulationSets,
  workflowFolder,
  createWordReport = TRUE,
  wordConversionTemplate = NULL,
  watermark = NULL,
  simulationSetDescriptor = NULL,
  numberSections = TRUE,
  reportTitle = NULL,
  theme = NULL
)

Arguments

simulationSets

list of SimulationSet R6 class objects

workflowFolder

path of the output folder created or used by the Workflow.

createWordReport

logical of option for creating Markdown-Report only but not a Word-Report.

wordConversionTemplate

optional docx template for rendering a tuned Word-Report document

watermark

displayed watermark in figures background

simulationSetDescriptor

character Descriptor of simulation sets indicated in reports

numberSections

logical defining if the report sections should be numbered

reportTitle

report title internally added as a cover page If reportTitle is an existing file, it will be merged to the report as cover page.

theme

A Theme object from {tlf} package

Returns

A new Workflow object

---

Method getAllTasks()

Get a vector with all the names of the tasks within the Workflow

Usage

Workflow$getAllTasks()

Returns

Vector of Task names

---

Method getAllPlotTasks()

Get a vector with all the names of the plot tasks within the Workflow

Usage

Workflow$getAllPlotTasks()

Returns

Vector of PlotTask names

---

Method getActiveTasks()

Get a vector with all the names of active tasks within the Workflow

Usage

Workflow$getActiveTasks()

Returns

Vector of active Task names

---

Method getInactiveTasks()

Get a vector with all the names of inactive tasks within the Workflow

Usage

Workflow$getInactiveTasks()

Returns

Vector of inactive Task names

---

Method activateTasks()

Activates a series of Tasks from current Workflow

Usage

Workflow$activateTasks(tasks = self$getAllTasks())

Arguments

tasks

names of the workflow tasks to activate. Default activates all tasks of the workflow using workflow method workflow$getAllTasks()

Returns

Vector of inactive Task names

---

Method inactivateTasks()

Inactivates a series of Tasks from current Workflow

Usage

Workflow$inactivateTasks(tasks = self$getAllTasks())

Arguments

tasks

names of the workflow tasks to inactivate. Default inactivates all tasks of the workflow using workflow method workflow$getAllTasks()

Returns

Vector of inactive Task names

---

Method printReportingEngineInfo()

Print reporting engine information obtained from initializing a Workflow

Usage

Workflow$printReportingEngineInfo()

---

Method getWatermark()

Get the current watermark to be reported on figures background

Usage

Workflow$getWatermark()

---

Method setWatermark()

Set the watermark to be reported on figure background. The default value NULL leads to check if the computer has a validated environment. If the environment is validated, no watermark is reported on the background. If the environment is NOT validated, workflowWatermarkMessage is reported on the background. Any user-defined text will overwrite this default feature and be reported on the figure background.

Usage

Workflow$setWatermark(watermark)

Arguments

watermark

text to be reported on figures background. Default value is NULL, which leads to check if the computer has a validated environment. If the environment is validated, no watermark is reported on the background. If the environment is NOT validated, workflowWatermarkMessage is reported on the background. Any user-defined text will overwrite this default feature and be reported on the figure background.

---

Method setParameterDisplayPaths()

Set mapping between parameters and their display paths in workflow to replace standard display of parameter paths.

Usage

Workflow$setParameterDisplayPaths(parameterDisplayPaths)

Arguments

parameterDisplayPaths

data.frame mapping Parameters with their display paths Variables of the data.frame should include parameter and displayPath.

---

Method getParameterDisplayPaths()

Get mapping between parameters and their display paths in workflow to replace standard display of parameter paths.

Usage

Workflow$getParameterDisplayPaths()

Returns

A data.frame with parameter and displayPath variables.

---

Method setSimulationDescriptor()

Set descriptor of simulation sets indicated in reports

Usage

Workflow$setSimulationDescriptor(text)

Arguments

text

character describing what simulation sets refer to

---

Method getSimulationDescriptor()

Get descriptor of simulation sets indicated in reports

Usage

Workflow$getSimulationDescriptor()

Returns

character Descriptor of simulation sets

---

Method print()

Print workflow list of tasks

Usage

Workflow$print()

Returns

Task list information

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Workflow$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Open-Systems-Pharmacology/OSPSuite.ReportingEngine documentation built on April 13, 2025, 10:37 a.m.