R/getConfigFile.R

In alberto-rodriguezizquierdo/airen_r: A R package to optimize the performance of Restriction digestion to improve the resolution of GBS

#' @title ConfigFileGet
#' @name getConfigFile
#' @param root Root path
#' @description QC of all data
#'
#' @import dplyr
#' @import XML
#' @import tidyverse
#' @import SimRAD
#' @import data.table
#' @import phylotools
#' @import biomartr
#' @return configFile
#'
#' @author Alberto Rodriguez-Izquierdo, 2021

getConfigFile <- function(root){

  #loginfo('Reading configFile...')
  configFile <- readConfigFile(root)


  #####-------------------Validations----------------------######

  #loginfo('Validating configFile...')


  #------------------Validation nodes----------------------#

  configFile <- nodesValidation(configFile)


  ######--------------Validation nodes content --------------######

#  error <- FALSE

  #Validate generalParameters

###-----------------------Validation data-----------------------###

  validateDataPath          <- validateCharacter(configFile$data$dataPath)

  configFile$data$dataPath  <- validateDataPath

  validateGenome            <- validateCharacter(configFile$data$genome)

  configFile$data$genome    <- validateGenome

  validateEnzymeDB          <- validateCharacter(configFile$data$enzyme_db)

  configFile$data$enzyme_db <- validateEnzymeDB


  ###----------------------Validation parameters---------------###

  validateTypeAnalysis                                              <- validateCharacter(configFile$parameters$typeAnalysis)

  configFile$parameters$typeAnalysis                                <- validateTypeAnalysis

  validateIfRestriction                                             <- validateCharacter(configFile$parameters$ifRestriction)

  configFile$parameters$ifRestriction                               <- validateIfRestriction

  validateEnzymeSelection                                           <- validateCharacter(configFile$parameters$combination$enzyme_selection)

  validateEnzymeSelection                                           <- unlist(strsplit(validateEnzymeSelection, ','))

  configFile$parameters$combination$enzyme_selection                <- validateEnzymeSelection

  validateUseRepEnzyme                                              <- validateCharacter(configFile$parameters$replicate_enzyme$use_replicate)

  configFile$parameters$replicate_enzyme$use_replicate              <- validateUseRepEnzyme

  validateRepEnzymeSel                                              <- validateCharacter(configFile$parameters$replicate_enzyme$enzyme_selection)

  configFile$parameters$replicate_enzyme$enzyme_selection           <- validateRepEnzymeSel

  validateRepEnzymeNb                                               <- validateNumber(configFile$parameters$replicate_enzyme$nb_repeat)

  configFile$parameters$replicate_enzyme$nb_repeat                  <- validateRepEnzymeNb

  validateRandomNb                                                  <- validateNumber(configFile$parameters$random_genome_fragmentation$nb_fragments)

  configFile$parameters$random_genome_fragmentation$nb_fragments    <- validateRandomNb

  validateRandomRepe                                                <- validateNumber(configFile$parameters$random_genome_fragmentation$nb_repeat)

  configFile$parameters$random_genome_fragmentation$nb_repeat       <- validateRandomRepe

  validateUseCalculate                                              <- validateCharacter(configFile$parameters$calculatePosition$use_calculate)

  configFile$parameters$calculatePosition$use_calculate             <- validateUseCalculate

  validateAlignmentPath                                             <- validateCharacter(configFile$parameters$calculatePosition$alignment_path)

  configFile$parameters$calculatePosition$alignment_path            <- validateAlignmentPath

  validateGffFile                                                   <- validateCharacter(configFile$parameters$calculatePosition$gffFile)

  configFile$parameters$calculatePosition$gffFile                   <- validateGffFile

  validateOutputPath                                                <- validateCharacter(configFile$parameters$calculatePosition$outputPath)

  configFile$parameters$calculatePosition$outputPath                <- validateOutputPath

  validateCategory                                                  <- validateCharacter(configFile$parameters$calculatePosition$category)

  configFile$parameters$calculatePosition$category                  <- validateCategory

  validateMinSize                                                   <- validateNumber(configFile$parameters$min.size)

  configFile$parameters$min.size                                    <- validateMinSize

  validateMaxSize                                                   <- validateNumber(configFile$parameters$max.size)

  configFile$parameters$max.size                                    <- validateMaxSize

  ###-----------------------Validate Output--------------------###

  validateUseOutput                      <- validateCharacter(configFile$output$use_output)

  configFile$output$use_output         <- validateUseOutput

  validateOutput                      <- validateCharacter(configFile$output$outputDir)

  configFile$output$outputDir         <- validateOutput


  return (configFile)
}


#' @title ConfigReading
#' @name readConfigFile
#' @param root working directory
#' @description App to start geoapp
#'
#' @import XML
#' @return configFile
#'
#' @author Alberto Rodriguez-Izquierdo, 2021

readConfigFile <- function(root){

  require(XML)

  myDirectoryConfigFile <- paste0(root, 'config/')

  if (!file.exists(paste0(myDirectoryConfigFile,"configFile.xml"))){

    #log_error <- 'File path does not exist! Please review the path'
    #logerror(log_error)

    #stop(log_error)
  }

  configFile <- xmlParse(file = paste0(myDirectoryConfigFile,"configFile.xml"))
  configFile <- xmlToList(configFile)
#  configFile <- data.frame(configFile)

  return (configFile)
}



#' @title ConfigValidationsNodes
#' @name nodesValidation
#' @param configFile configFile
#' @return configFile
#'
#' @author Alberto Rodriguez-Izquierdo, 2021


nodesValidation <- function(configFile){

  #Building list with principal and secondary nodes for validation

  principalNodes              <- c('data','parameters','output')

  dataNodes                   <- c('dataPath','genome', 'enzyme_db')

  parametersNodes             <- c('typeAnalysis',
                                   'ifRestriction',
                                   'combination',
                                   'replicate_enzyme',
                                   'random_genome_fragmentation',
                                   'calculatePosition',
                                   'max.size',
                                   'min.size')

  combinationNodes            <- c('enzyme_selection')

  replicateNodes              <- c('enzyme_selection', 'nb_repeat')

  randomGenNodes              <- c('nb_fragments', 'nb_repeat')

  calculatePositionNodes      <- c('alignment_path','gffFile','outputPath', 'category')

  outputNodes                 <- c('use_output','outputDir')

  #Validation principal nodes

  generalParametersNodes        <- validateConfigNodes(principalNodes, configFile)

  ValDataNodes                  <- validateConfigNodes(dataNodes, configFile$data)

  ValParametersNodes            <- validateConfigNodes(parametersNodes, configFile$parameters)

  ValCombinationNodes           <- validateConfigNodes(combinationNodes, configFile$parameters$combination)

  ValReplicateNodes             <- validateConfigNodes(replicateNodes, configFile$parameters$replicate_enzyme)

  valRandomGenNodes             <- validateConfigNodes(randomGenNodes, configFile$parameters$random_genome_fragmentation)

  valCalculatePositionNodes     <- validateConfigNodes(calculatePositionNodes, configFile$parameters$calculatePosition)

  ValOutputNodes                <- validateConfigNodes(outputNodes, configFile$output)


  return(configFile)
  #loginfo('Nodes validation success!')
}




#' @title ConfigValidations
#' @name validateConfigNodes
#' @param configFile configFile
#' @description App to start geoapp
#'
#' @import XML
#' @return configFile
#'
#' @author Alberto Rodríguez Izquierdo, 2021


validateConfigNodes <- function (nodes, configFile){

  if (!is.list(nodes)){
    for (x in nodes){
      if (!(x %in% names(configFile))){
        if (!(x %in% configFile)){

#         log_error <- paste0('Node ',x,' does not exist! Please review configFile.xml')
#         logerror(log_error)
          print(paste0('Warning: Node ', nodes,' does not exist'))
#         stop(log_error)
        }
      }
    }
  }else{
    for (x in names(nodes)){
      if (!(x %in% names(configFile))){

        #       log_error <- paste0('Node ',x,' does not exist! Please review configFile.xml')
        #       logerror(log_error)
        print(paste0('Warning: Node ', nodes,' does not exist'))
        #       stop(log_error)
      }
    }
  }
}