R/set_sols_param_xml.R

In SticsRFiles: Read and Modify 'STICS' Input/Output Files

#' @title Setting soil parameter(s) value(s) in a sols xml_document
#' @param xml_doc an xml_document object (created from an xml sols file)
#'
#' @param sols_param soils parameters (data.frame)
#' @param overwrite replace existing soil (TRUE) or not,
#' updating existing ones (FALSE)
#'
#'
#' @examples
#' \dontrun{
#' xml_path <- file.path(get_examples_path(file_type = "xml"), "sols.xml")
#' sols_doc <- xmldocument(xml_path)
#'
#' xl_path <- file.path(get_examples_path(file_type = "xl"),
#'                     "inputs_stics_example.xlsx")
#' sols_df <- read_excel(xl_path, sheet = "Soils")
#'
#' # For updating an existing xml doc (using existing soils names)
#' # Creating a fake existing_doc
#' existing_doc <- gen_usms_sols_doc("sols", nodes_nb = 3)
#' set_param_value(existing_doc,
#'   param_name = "sol",
#'   param_value = sols_df$Soil_name[c(3, 1, 5)]
#' )
#'
#' set_sols_param_xml(existing_doc, sols_df)
#'
#'
#' # For a new xml doc
#' # In that case: sols_df must contain all the soils parameters !)
#' soils_nb <- dim(sols_df)[1]
#' new_doc <- gen_usms_sols_doc("sols", nodes_nb = soils_nb)
#'
#' set_sols_param_xml(new_doc, sols_df, overwrite = TRUE)
#' }
#'
#' @keywords internal
#'
#' @noRd
#'

set_sols_param_xml <- function(xml_doc, sols_param, overwrite = FALSE) {
  if (!"data.frame" %in% class(sols_param)) {
    stop("sols_param do not belong to data.frame class/type")
  }

  if (!is.xml_document(xml_doc)) {
    stop("xml_doc is not an xml_document object")
  }


  # detecting soils names column
  in_params <- names(sols_param)
  col_id <- grep("^soil", tolower(in_params))
  if (!length(col_id)) {
    stop("The column for identifying soil names has not been found !")
  }
  sol_col <- in_params[col_id]

  # Checking parameter names from param_table against xml ones
  check_param_names(
    param_names = in_params[-col_id],
    ref_names = get_param_names(xml_object = xml_doc)
  )

  # TODO: evaluate if this use case is relevant !
  # checking soils based on names if overwrite == FALSE
  if (!overwrite) {
    # getting soils names
    xml_sols <- as.vector(get_param_value(xml_doc, "sol"))


    ###############################################
    # TODO : see adding sols not in xml file ?
    ###############################################

    # checking xl names against xml names
    xl_in_xml <- sols_param[[sol_col]] %in% xml_sols

    if (!any(xl_in_xml)) {
      stop("Not any sol name in sols_param table is in xml doc !")
    }

    # xl sols idx in xml doc to be updated
    sols_xml_idx <- which(xml_sols %in% sols_param[[sol_col]])

    # Selecting data & ordering upon xml
    # order
    sols_param <- sols_param[xl_in_xml, ]
    sols_param <-
      sols_param[match(xml_sols[sols_xml_idx], sols_param[[sol_col]]), ]
  } else {
    # setting soils names
    set_param_value(xml_doc, "sol", sols_param[[sol_col]])
  }


  # Managing parameter values replacement from sols_param
  # data.frame

  # Treating Layers params
  # reshape them to set values for all soils
  # select epc_1 to epc_5 in df and as.vector to
  # set_sols_param

  layers_params <- grep("_[0-9]*$", in_params, value = TRUE)
  layers_params_names <- unique(gsub("_[0-9]*$", "", layers_params))



  for (i in 1:5) {
    for (p in layers_params_names) {
      # column name
      par <- paste0(p, "_", i)

      layer <- paste("layer", as.character(i))
      par_values <- sols_param[[par]]

      # Taking into account values to be filtered 999 or NA
      # except for epc
      sols_idx <- as.vector(
        !grepl(pattern = "^999", par_values) & !is.na(par_values)
        )

      # Filtering all parameters
      if (!any(sols_idx)) next

      # Selecting parameters values according to
      # valid values to set
      par_values <- par_values[sols_idx]

      # Setting parameters values in doc
      if (is.element(par, layers_params)) {
        set_param_value(xml_doc, p, par_values, layer, which(sols_idx))
      }
    }
  }

  # Treating other params (simple ones and options ones)
  other_params <- setdiff(in_params, c(layers_params, sol_col))

  # No other parameters than layer dependent ones to set
  if (!length(other_params)) {
    return(xml_doc)
  }

  # Setting param values
  for (p in other_params) {
    set_param_value(xml_doc, p, sols_param[[p]])
  }

}