R/fname_sites.R

Defines functions fname_cross_marker fname_module fname_dictionary fname_material_lists fname_program_stage fname_programs fname_fieldbooks fname_crops fname_sites get_base_dir

Documented in fname_crops fname_cross_marker fname_dictionary fname_fieldbooks fname_material_lists fname_module fname_programs fname_program_stage fname_sites get_base_dir

#' Base path
#'
#' @param amode mode of data: Local, Demo, BrAPI, ...
#' @param is_server logical, default = FALSE
#' @author Reinhard Simon
#' @return character file.path or NULL
#' @export
get_base_dir <- function(amode = "Default", is_server = FALSE){
  #default to Linux server susing wwww subir in wd as starting point
  if(is_server) {
    dbName = Sys.getenv("BRAPI_DBNAME")
    fp = file.path("www", "xdata", "brapi", dbName)
    print(fp)
    if(!dir.exists(fp)) dir.create(fp)
    return(fp)
  }
  hddir = "www"

  sbdir = file.path("HIDAP", "xdata", amode)
  hddir = file.path(hddir, sbdir)

  locos = Sys.getenv("R_HOME")
  if(stringr::str_detect(locos, ":")){ # Only on Windows!
    hddir = file.path(Sys.getenv("LOCALAPPDATA"), sbdir)
  }

  if(stringr::str_detect(locos, "Frameworks/R.framework")) { #assume MACOS
    hddir = file.path("/Users", Sys.getenv("USER"),"Documents", sbdir)
  }
  if(!dir.exists(hddir)) {
    dir.create(hddir, recursive = TRUE)
    if(amode == "Default") {
      # copy over default datasets from fbglobal dir
      dd = system.file("xdata/Default", package = "fbglobal")
      file.copy(from = dd, to = get_base_dir(""), recursive = TRUE)
    }
  }
  hddir
}

#' Fieldbook Sites path
#'
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_sites <- function() {
  file.path(get_base_dir(), "table_sites.rds")
}


#' Fieldbook crops path
#'
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_crops <- function(){
  file.path(get_base_dir(), "table_crops.rda")
}

#' Fieldbook crops path
#'
#' @param crop a crop name
#' @param amode a source path
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_fieldbooks <- function(crop, amode = "Default"){
  file.path(get_base_dir(amode), crop, "fieldbooks")
}


#' Breeding program data path
#'
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_programs <- function(){
  file.path(get_base_dir(), "table_programs.rda")
}

#' Breeding program data path
#'
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_program_stage <- function(){
  file.path(get_base_dir(), "table_program_stages.rda")
}

#' Path to lists of plant materials
#'
#' @param crop character a crop
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_material_lists <- function(crop = NULL){
  if(is.null(crop)) {
    lf  = list.files(get_base_dir(), recursive = TRUE, full.names = TRUE)
    lf = lf[stringr::str_detect(lf, "material_lists")]
    dn = unique(dirname(lf))
    return(dn)
  }
  file.path(get_base_dir(), crop, "material_lists")
}


#' Dictionary path
#'
#' @param crop string
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_dictionary <- function(crop = NULL) {
  if ( is.null(crop) ) return( NULL )
  fp <- file.path(get_base_dir(), crop, "dictionary", paste0("table_dictionary_", crop, ".rda"))
  #if ( !file.exists(fp) ) file.create(fp, recursive = TRUE)
  fp
}

#' Module path
#'
#' @param crop string
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_module <- function(crop = NULL) {
  if ( is.null(crop) ) return( NULL )
  fp <- file.path(get_base_dir(), crop, "dictionary", paste0("table_module_", crop, ".rda"))
  fp
}

#' Cross marker path
#'
#' @param crop string
#' @author Reinhard Simon
#' @return character file.path
#' @export
fname_cross_marker <- function(crop = NULL) {
  if ( is.null(crop) ) return( NULL )
  fp <- file.path(get_base_dir(), crop, "cross_marker")
  fp
}
c5sire/fbglobal documentation built on June 27, 2017, 11:54 a.m.