OCTOPUS: OCTOPUS

##### COPYRIGHT #############################################################################################################
#
# Copyright (C) 2018 JANSSEN RESEARCH & DEVELOPMENT, LLC
# This package is governed by the JRD OCTOPUS License, which is the
# GNU General Public License V3 with additional terms. The precise license terms are located in the files
# LICENSE and GPL.
#
#############################################################################################################################.


## This funciton is not needed as the borrow of patients is at an ISA level not the trial level - this was from a previous verison

#' #' @export
#' RunTrialAnalysis.IncludeAllControl <- function( cISADesigns, cEnrolledPats,  vISAStatus, dCurrentTime,  vRunISAAnalysis, vISAAnalysisIndx, vIsFinalISAAnalysis  )
#' {
#'     nQtyISA <- length( cISADesigns )
#'
#'     if( all( vRunISAAnalysis  == 0 ) )
#'     {
#'         #None of the ISAs are ready or need an analysis run
#'         for( iISA in 1:nQtyISA )
#'         {
#'             lISARes <- list( nGo = 1, nNoGo = 0, nPause = 0)
#'         }
#'
#'     }
#'     lDataAna <-  CreateDataSetForAnalysis( cEnrolledPats, dCurrentTime )
#'
#'
#'
#'     lResISA <- list()
#'     nISA <- 1
#'
#'     for( nISA in 1:nQtyISA)
#'     {
#'         lISARes <- list()
#'         print( paste( "RunTrialAna - ISA ", nISA,  " vISAStatus", vISAStatus[nISA]))
#'
#'         #TODO: Should we run the Analysis for an ISA anytime the vRunISAAnalysis = 1?
#'
#'
#'         if( vRunISAAnalysis[ nISA ] == 1 &&  vISAStatus[ nISA ] <=2 )   #If the minimum is met and the ISA is open then do the analysis
#'         {
#'             #print( paste( ".....Case 1 - Running analysis for ISA ", nISA, " ISAStatus ", vISAStatus[ nISA ]))
#'             cISAAnalysis <- cISADesigns[[ nISA ]]$cISAAnalysis
#'             #print( paste( "Data for trial "))
#'             #print( lDataAna )
#'             lDataTmp <- SubsetDataAllControls( lDataAna, nISA ) #cISAAnalysis$nISA )
#'             #lDataTmp<<- lDataTmp
#'             #print( paste( "Data for ISA ", cISAAnalysis$nISA ))
#'             #print( lDataTmp)
#'             #if( vIsFinalISAAnalysis[ nISA] )
#'             #    print( sprintf( "FINAL ANALYSIS for ISA %f ", nISA))
#'
#'
#'             ###########################
#'             #####  TODO(Kyle) - This use to have vIsFinalISA which has been replaced by index but may not do all that is necessary steps
#'
#'             # print( paste( ".....IndependentISA vISAAnalysisIndx ", vISAAnalysisIndx[ nISA], " IsFinalISA ", vIsFinalISAAnalysis[ nISA ], sep =""))
#'             lISARes <- RunISAAnalysis( cISAAnalysis, lDataTmp, vISAAnalysisIndx[ nISA],  vIsFinalISAAnalysis[ nISA ]  )
#'
#'             vISAAnalysisIndx[ nISA ] <- vISAAnalysisIndx[ nISA ] + 1
#'
#'         }
#'         else if(  vISAStatus[ nISA ] <= 1  )
#'         {
#'             #  print( ".....Case 2 - Analysis not being run for ISA ", nISA )
#'
#'             cISAAnalysis <- cISADesigns[[ nISA ]]$cISAAnalysis
#'
#'             nQtyAna <- length( cISAAnalysis$vAnalysis )
#'             iAna    <- 1
#'             lISARes <- list()
#'             repeat
#'             {
#'                 lISARes[[paste("lAnalysis", iAna, sep="")]] <- list( nGo = 0, nNoGo = 0, nPause = 1)
#'
#'                 if( iAna == nQtyAna )
#'                     break
#'                 iAna <- iAna + 1
#'             }
#'
#'         }
#'         else
#'         {
#'
#'             #print( "Case 3")
#'         }
#'         lISARes$bISAAnalysisRun <- (vRunISAAnalysis[ nISA ] == 1)
#'         lResISA[[paste("lResISA", nISA, sep="")]] <- lISARes
#'
#'
#'
#'     }
#'     lRet <- list( lResISA = lResISA, vISAAnalysisIndx = vISAAnalysisIndx )
#'     return( lRet )
#'
#' }