Fixes Open-Systems-Pharmacology#755 add new function adjustTitlePage

I named the object QualificationVersionInfo instead of VersionInfo.
I felt that VersionInfo was too vague

NAMESPACE

@@ -16,6 +16,7 @@ export(PopulationSimulationSet)
 export(PopulationWorkflow)
 export(PopulationWorkflowTypes)
 export(QualificationTask)
+export(QualificationVersionInfo)
 export(QualificationWorkflow)
 export(ResidualScales)
 export(SensitivityPlotSettings)
@@ -34,6 +35,7 @@ export(addXParametersForDemogrpahyPlot)
 export(addXParametersForPkParametersPlot)
 export(addYParametersForDemogrpahyPlot)
 export(addYParametersForPkParametersPlot)
+export(adjustTitlePage)
 export(analyzeCoreSensitivity)
 export(analyzeSensitivity)
 export(calculateArithmeticErrorRange)

R/qualification-version-info.R

@@ -0,0 +1,141 @@
+#' @title QualificationVersionInfo
+#' @description Object defining Qualification Version Information to be displayed on title page
+#' @field qualificationPlanRelease Qualification Plan Release Version (string, e.g. `"1.1"`)
+#' @field osp OSP version (string, e.g. `"10.0"`)
+#' @field qualificationFramework Qualification Framework version (string, e.g. `"3.0"`)
+#' @export
+#' @import ospsuite.utils
+QualificationVersionInfo <- R6::R6Class(
+  "QualificationVersionInfo",
+  public = list(
+    qualificationPlanRelease = NULL,
+    osp = NULL,
+    qualificationFramework = NULL,
+
+    #' @description
+    #' Create a new `QualificationVersionInfo` object.
+    #' @param qualificationPlanRelease Qualification Plan Release Version (string, e.g. `"1.1"`)
+    #' @param osp OSP version (string, e.g. `"10.0"`)
+    #' @param qualificationFramework Qualification Framework version (string, e.g. `"3.0"`)
+    #' @return A new `QualificationVersionInfo` object
+    initialize = function(qualificationPlanRelease = NULL,
+                              osp = NULL,
+                              qualificationFramework = NULL) {
+      validateIsString(qualificationPlanRelease, nullAllowed = TRUE)
+      validateIsString(osp, nullAllowed = TRUE)
+      validateIsString(qualificationFramework, nullAllowed = TRUE)
+
+      # In gsub, character "." has a special meaning
+      # and needs to be escaped in the expression using "\\"
+      private$.qualificationPlanReleasePattern <- "x\\.x"
+      private$.ospPattern <- "y\\.y"
+      private$.qualificationFrameworkPattern <- "z\\.z"
+
+      self$qualificationPlanRelease <- qualificationPlanRelease
+      self$osp <- osp
+      self$qualificationFramework <- qualificationFramework
+    },
+
+    #' @description
+    #' Print version information
+    #' @return A text with system information
+    print = function() {
+      infoPrint <- c(
+        sprintf("Qualification Plan Release Version: %s", self$qualificationPlanRelease %||% ""),
+        sprintf("OSP version: %s", self$osp %||% ""),
+        sprintf("Qualification Framework version: %s", self$qualificationFramework %||% "")
+      )
+      cat(infoPrint, sep = "\n")
+      return(invisible(infoPrint))
+    },
+
+    #' @description
+    #' Update `text` if patterns of version info are found
+    #' @param text character string
+    #' @return Updated character string
+    updateText = function(text) {
+      eval(private$.updateExpression(c("qualificationPlanRelease", "osp", "qualificationFramework")))
+      return(text)
+    },
+
+    #' @description
+    #' Get the Qualification Plan Release Version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern**
+    #' **Escape characters may be included in the pattern**
+    #' @return A character
+    getQualificationPlanReleasePattern = function() {
+      return(private$.getPattern("qualificationPlanRelease"))
+    },
+
+    #' @description
+    #' Get the OSP version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern**
+    #' **Escape characters may be included in the pattern**
+    #' @return A character
+    getOSPPattern = function() {
+      return(private$.getPattern("osp"))
+    },
+
+    #' @description
+    #' Get the Qualification Framework version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern**
+    #' **Escape characters may be included in the pattern**
+    #' @return A character
+    getQualificationFrameworkPattern = function() {
+      return(private$.getPattern("qualificationFramework"))
+    },
+
+    #' @description
+    #' Set the Qualification Plan Release Version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern.**
+    #' **You may need to include escape characters in `pattern`**
+    #' @param pattern characters to be replaced in title page
+    setQualificationPlanReleasePattern = function(pattern) {
+      validateIsString(pattern)
+      private$.qualificationPlanRelease <- pattern
+      return(invisible())
+    },
+
+    #' @description
+    #' Set the OSP version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern.**
+    #' **You may need to include escape characters in `pattern`**
+    #' @param pattern characters to be replaced in title page
+    setOSPPattern = function(pattern) {
+      validateIsString(pattern)
+      private$.osp <- pattern
+      return(invisible())
+    },
+
+    #' @description
+    #' Set the Qualification Framework version pattern to be replaced in title page
+    #' **Caution, the function `gsub` is used to replace the pattern.**
+    #' **You may need to include escape characters in `pattern`**
+    #' @param pattern characters to be replaced in title page
+    setQualificationFrameworkPattern = function(pattern) {
+      validateIsString(pattern)
+      private$.qualificationFrameworkPattern <- pattern
+      return(invisible())
+    }
+  ),
+
+  private = list(
+    .qualificationPlanReleasePattern = NULL,
+    .ospPattern = NULL,
+    .qualificationFrameworkPattern = NULL,
+
+    .getPattern = function(field) {
+      # Return the value of a field to be passed on gsub pattern input
+      return(eval(parse(text = paste0("private$.", field, "Pattern"))))
+    },
+
+    .updateExpression = function(field) {
+      # Return expression to be evaluated that updates text based on version info
+      return(parse(text = paste0(
+        "if(!isEmpty(self$", field, ")){",
+        "text <- gsub(pattern = private$.", field, "Pattern, replacement = self$", field, ", x = text)",
+        "}"
+      )))
+    }
+  )
+)

R/utilities-writing-report.R

@@ -445,3 +445,23 @@ getSimulationDescriptor <- function(workflow) {
   validateIsOfType(workflow, "Workflow")
   return(workflow$getSimulationDescriptor())
 }
+
+#' @title adjustTitlePage
+#' @description Adust Qualification Version Information to be displayed on title page 
+#' @param fileName name of .md file to update
+#' @param qualificationVersionInfo A `QualificationVersionInfo`object defining Qualification Version Information to be displayed on title page
+#' @export
+adjustTitlePage <- function(fileName, qualificationVersionInfo = NULL) {
+  validateIsOfType(qualificationVersionInfo, "QualificationVersionInfo", nullAllowed = TRUE)
+  # Does not adust title page if no QualificationVersionInfo
+  if(isEmpty(qualificationVersionInfo)){
+    return(invisible())
+  }
+  fileContent <- readLines(fileName, encoding = "UTF-8")
+  fileContent <- qualificationVersionInfo$updateText(fileContent)
+
+  fileObject <- file(fileName, encoding = "UTF-8")
+  write(fileContent, file = fileObject, sep = "\n")
+  close(fileObject)
+  return(invisible())
+}