R/calculate-pk-parameters-task.R

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

#' @title CalculatePKParametersTask
#' @description  R6 class for defining how pk parameters are calculated and save
#' @keywords internal
CalculatePKParametersTask <- R6::R6Class(
  "CalculatePKParametersTask",
  inherit = SimulationTask,
  public = list(
    #' @field ratioComparison logical defining if a ratio comparison is required
    ratioComparison = FALSE,
    #' @description
    #' Save the task results related to a `structureSet`.
    #' @param structureSet A `SimulationStructure` object defining the properties of a simulation set
    #' @param taskResults list of results from task run.
    saveResults = function(structureSet, taskResults) {
      ospsuite::exportPKAnalysesToCSV(
        taskResults,
        structureSet$pkAnalysisResultsFileNames
      )
      logDebug(paste0(
        "PK parameters for '", structureSet$simulationSet$simulationSetName,
        "' saved in '", structureSet$pkAnalysisResultsFileNames
      ))
      re.tStoreFileMetadata(access = "write", filePath = structureSet$pkAnalysisResultsFileNames)
    },

    #' @description
    #' Run task and save its output results
    #' @param structureSets list of `SimulationStructure` objects
    runTask = function(structureSets) {
      actionToken <- re.tStartAction(actionType = "Analysis", actionNameExtension = self$nameTaskResults)
      logInfo(messages$runStarting(self$message))
      t0 <- tic()
      if (!is.null(self$outputFolder)) {
        dir.create(file.path(self$workflowFolder, self$outputFolder), showWarnings = FALSE, recursive = TRUE)
      }
      if (self$settings$showProgress) {
        loadingProgress <- txtProgressBar(max = length(structureSets), style = 3)
        cat("\n")
        setIndex <- 0
      }
      for (set in structureSets) {
        logInfo(messages$runStarting(self$message, set$simulationSet$simulationSetName))
        if (self$validateStructureSetInput(set)) {
          taskResults <- self$getTaskResults(
            structureSet = set,
            settings = self$settings
          )
          self$saveResults(set, taskResults)
        }
        clearMemory(clearSimulationsCache = TRUE)
        if (self$settings$showProgress) {
          setIndex <- setIndex + 1
          setTxtProgressBar(loadingProgress, value = setIndex)
          cat("\n")
        }
      }
      if (self$settings$showProgress) {
        close(loadingProgress)
      }
      if (!self$ratioComparison) {
        re.tEndAction(actionToken = actionToken)
        logInfo(messages$runCompleted(getElapsedTime(t0), self$message))
        return(invisible())
      }
      # Case of ratio comparison
      calculatePKAnalysesRatio(structureSets = structureSets, settings = self$settings)

      re.tEndAction(actionToken = actionToken)
      logInfo(messages$runCompleted(getElapsedTime(t0), self$message))
    }
  )
)