R/read_nml.R

In USGS-R/glmtools: Tools for working with the General Lake Model (GLM)

#'@title read in a GLM simulation *.nml file
#'@description 
#'read in a GLM simulation *.nml file and create a list.  \cr
#'
#'
#'@param nml_file a string with the path to the GLM glm2.nml file, or 
#'\code{'template'} for loading the GLM template nml file with GLM3r (default)
#'@return glm_nml a nml (a list) for GLM config
#'@keywords methods
#'@author
#'Jordan S. Read
#'@seealso \link{get_nml_value}
#'@examples 
#'glm_nml <- read_nml()
#'print(glm_nml)
#'@export
read_nml  <-	function(nml_file = 'template'){

  nml_file <- nml_path_norm(nml_file)
  
  if (!ascii_only(nml_file)){
    stop('non-ASCII characters found in nml file on line ', what_ascii(nml_file))
  }
  # skip all commented lines, return all variables and associated values
  # requires NO return line variables (all variables must be completely defined on a single line)
  c <- file(nml_file,"r") 
  fileLines <- readLines(c)
  close(c)
  lineStart	<-	substr(fileLines,1,1)
  # ignore comment lines or empty lines
  ignoreLn	<-	lineStart=='!' | fileLines==""
  lineStart	<-	lineStart[!ignoreLn]
  fileLines	<-	fileLines[!ignoreLn]
  # find all lines which start with "&" * requires FIRST char to be value
  
  lineIdx		<- seq(1,length(lineStart))
  blckOpen	<-	lineIdx[lineStart=="&"]
  blckClse	<-	lineIdx[lineStart=="/"]
  
  nml <- list()
  for (i in seq_len(length(blckOpen))){
    blckName   <-	substr(fileLines[blckOpen[i]], 
                         2, nchar(fileLines[blckOpen[i]]))
    blckName   <- gsub("\\s", "", blckName) 
    oldNms	   <-	names(nml)
    nml[[i]]   <-	list()
    names(nml) <-	c(oldNms,blckName)
    
    carryover <- ''
    
    for (j in (blckOpen[i]+1):(blckClse[i]-1)){

      textLine	<-	paste(carryover, 
                        gsub("\t", "", gsub(" ", "", fileLines[j])), sep = '')
      
      if(substr(textLine, 1, 1) != '!'){
        # Add a check here, sometimes, if there is a hanging comma, 
        #and only sometimes that means add next row
        if(substr(textLine, nchar(textLine), nchar(textLine)) == ',' && 
           j+1 <= length(fileLines) && 
           !any(grep("=", fileLines[j + 1])) && 
           !any(grep("/", fileLines[j + 1]))){
          
          carryover = textLine
          next
        }else{
          carryover = ''
        }
        # else, line is commented out
        lineVal	  <-	buildVal(textLine, lineNum = j, blckName)
        nml[[i]]	<-	c(nml[[i]], lineVal)
      }
    }
  }
  nml <- .nml(nml)
  return(nml)
}

#' @importFrom GLM3r nml_template_path
nml_path_norm <- function(nml_file){
  if (nml_file == "template"){
    nml_file <- GLM3r::nml_template_path()
  }
  if (!is_nml_file(nml_file)){
    stop(nml_file, ' is not of file type *.nml')
  }

  return(nml_file)
}