R/reference_db.R

In adamryczkowski/ONWebDUALSimport: Routines for importing and merging databases for the ONWebDUALS project

#' Returns empty reference database that is ready to accept new rows
#'
#' @param row_length The database may come pre-filled with the
#'        \code{row_length} empty rows. All data will be \code{NA}
#' @param reference_source Path to the reference source. Defaults
#'        to the reference shipped with the library.

read_ref<-function(row_length=0, reference_source=NULL, flag_ALSFRS_as_integers=TRUE) {
  if(is.null(reference_source)) {
    reference_source<-system.file(getOption('onwebduals.dbtemplate'),package='ONWebDUALSimport')
  }
#	debugonce(danesurowe::readDaneSurowe4)
	tmpl<-danesurowe::readDaneSurowe(reference_source)
	template<-gen_blank_df(tmpl, row_length)
	# template<-tmpl[integer(0),]
	# template<-danesurowe::copy_dt_attributes(dt_source = tmpl, dt_dest=template)
	# if(row_length>0) {
	# 	template<-rbind(template, lp=seq(length.out=row_length), fill=TRUE)
	# 	template<-danesurowe::copy_dt_attributes(dt_source = tmpl, dt_dest=template)
	# }
  if(flag_ALSFRS_as_integers==TRUE) {
    template<-recode_ALSFRS(template)
  }
	return(template)
}

#' Gets the structure of the reference database (The One That Can Store Them All)
#' @param outputfile Where the structure shall be saved (in Excel format)
#' @param reference_source Path to the reference source. Defaults
#'        to the reference shipped with the library.
#' @return Nothing
get_reference_structure<-function(outputfile='webstruct.xlsx', reference_source=NULL) {
  if(is.null(reference_source)) {
    reference_source<-system.file(getOption('onwebduals.dbtemplate'),package='ONWebDUALSimport')
  }
  dtall_struct<-danesurowe::create_df_from_df_structure(dtall)
  savedb(dtall_struct,'webstruct.xlsx')
}


#' Gets the dictionary that translates web database (in its raw form) into the
#' reference database.
#'
#' @param filename Path to the dictionary (if different than the included in the library)
#' @return Returns the dictionary in the form of the data.frame
#' @export
get_dict<-function(filename) {
  dict<-xlsx::read.xlsx(file=filename, sheetName = 1, colClasses = 'character')
  var<-dict$ExistingSourceName
  valid_rows<-!is.na(var)
  dict<-dict[valid_rows,]
  dict$ExistingSourceName<-as.character(dict$ExistingSourceName)
  dict$colname<-as.character(dict$colname)
  dict$Type_of_conversion_1<-as.character(dict$Type_of_conversion_1)
  dict$Par_1<-as.character(dict$Par_1)
  dict$Type_of_conversion_2<-as.character(dict$Type_of_conversion_2)
  dict$Par_2<-as.character(dict$Par_2)
  dict<-dplyr::select(dict, in_colname=colname, out_colname=ExistingSourceName,
                      convtype1=Type_of_conversion_1, par1=Par_1,
                      convtype2=Type_of_conversion_2, par2=Par_2)
  return(dict)
}