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#This file contains functions related to managing data.dir (create, set, read contents, etc.)
#' Creates a data.dir
#'
#' @param folder.path
#' @param raw_str_map.file
#' @param metadata
#'
#' @return TRUE if created succesfully; FALSE otherwise. It return in invisible mode.
#' @export
#'
#' @examples
create.data.dir = function(folder.path,
metadata = "{\n'description': 'No Description Provided',\n'created-by':'',\n'created-at':''\n}") {
if(file.exists(folder.path)) {
#if it is already a data.dir, exit
if(check.data.dir.structure(folder.path)) {
cat("This is already a data.dir structure. Doing nothing.\n")
return(invisible(FALSE));
}
}
else { #if folder does not exist, create it
if(!dir.create(folder.path)) {print("Could not create folder."); return(invisible(FALSE));}
}
#create fadnUtils.metadata ----
cat(metadata, file=paste0(folder.path,"/fadnUtils.metadata.json"))
#create DIR>csv ----
dir.create(paste0(folder.path,"/csv"))
#create DIR>rds ----
dir.create(paste0(folder.path,"/rds"))
#create DIR>spool ----
dir.create(paste0(folder.path,"/spool"))
cat(
"In this folder you can save project related files",
file = paste0(folder.path,"/spool/readme.txt")
)
return(invisible(TRUE));
}
#' Sets the data.dir
#'
#' @param new.data.dir the full path to the folder where the data.dir will be. Ending slash "/" shall not be present
#'
#' @return TRUE if succesfully set the data.dir; FALSE otherwise. Returns in invisible mode.
#' @export
#'
#' @examples
set.data.dir = function(new.data.dir) {
#check that it is a valid data.dir ----
if(!check.data.dir.structure(new.data.dir, silent = F)) {
cat("Not a valid data.dir. cannot set the folder provided.\n");
return(invisible(FALSE));
}
#set option for fadnUtils.data.dir ----
options("fadnUtils.data.dir" = new.data.dir)
#load stored.rds.env ----
stored.rds.env.path = paste0(new.data.dir,"/stored.rds.data.RData")
if(file.exists(stored.rds.env.path)) {
load(stored.rds.env.path,envir = env.stored.rds)
}
return(invisible(TRUE));
}
#' Gets the data.dir
#'
#' data.dir is the folder where data is stored
#' r package will create two subfolders:
#' csv = location to store the csv files of th DG-AGRI (fadn.raw.csv)
#' rds = location to store rds files (fadn.raw.rds, fadn.str.rds, etc.)
#'
#' @return the value of option("fadnUtils.data.dir")
#' @export
#'
#' @examples
get.data.dir = function() {
ret = getOption("fadnUtils.data.dir")
if(is.null(ret)) {
return(NULL)
} else {
if(ret=="") {
return(NULL)
} else {
return(ret)
}
}
}
#' Show the contents of data.dir
#'
#' @param data.dir a specific directory to show contents, otherwise it will read the fadnUtils.data.dir
#' @param return.list if T, returns a list, otherwise print the results
#'
#' @return returns a list containing: {description: "the description of the data dir",
#' DT of fadn.raw.rds (Country-Year) and of fadn.str.rds (country-Year)
#' @export
#'
#' @examples
show.data.dir.contents = function(data.dir=NULL, return.list=F) {
if(is.null(data.dir)) {
data.dir=get.data.dir()
}
if(!check.data.dir.structure(data.dir)) {
warning("Not a valid data.dir. Exiting ....")
return(NULL)
}
#store the results in a list
ret=list()
#get descriptio
ret[['description']]=paste(readLines(paste0(data.dir,'/fadnUtils.metadata.json'),warn = F),collapse = " ")
#get raw data
ret[["raw"]] = get.available.fadn.raw.rds()
#get extracted data
ret[["extractions"]]=list();
extr.dirs = list.dirs(path = paste0(data.dir,"/rds"), full.names = F, recursive = F)
for(d in extr.dirs) {
ret[["extractions"]][[d]]=list()
ret[["extractions"]][[d]][["contents"]] = get.available.fadn.str.rds(extract_dir = d)
}
if(return.list==T) {
return(invisible(ret));
} else {
cat("\n","Description: \n", ret[['description']])
cat("\n\nRaw data: \n")
print(dcast(ret[["raw"]] ,COUNTRY~YEAR,value.var = "COUNTRY",fun.aggregate = length))
cat("\n\nExtracted data : \n")
for(d in extr.dirs) {
cat("\n---- Extracted dir: ", d, "\n")
if(nrow(ret[["extractions"]][[d]][["contents"]])>0 ) {
print(dcast(ret[["extractions"]][[d]][["contents"]] ,COUNTRY~YEAR,value.var = "COUNTRY",fun.aggregate = length))
} else {
cat("No data present")
}
}
cat("\n\n")
}
}
#' Checks if the structure of the fadnUtils.data.dir is ok
#'
#' @param data.dir a specific directory to show contents, otherwise it will read the fadnUtils.data.dir
#' @param silent if TRUE, do not print any message
#'
#' @return TRUe if everything is ok; FALSE otherwise
#' @export
#'
#' @examples
check.data.dir.structure = function(data.dir=NULL, silent=T) {
messages = c()
if(is.null(data.dir)) {data.dir = get.data.dir()}
if(!file.exists(data.dir)) {
messages=c(messages,"Folder provided as data.dir does not exit.");
}
if(!file.exists(paste0(data.dir,"/fadnUtils.metadata.json"))) {
messages=c(messages,"Problem with data.dir: fadnUtils.metadata.json does not exist.")
}
if(!file.exists(paste0(data.dir,"/csv"))) {
messages=c(messages,"Problem with data.dir: 'csv' directory does not exist.")
}
if(!file.exists(paste0(data.dir,"/rds"))) {
messages=c(messages,"Problem with data.dir: 'rds' directory does not exist.")
}
if(length(messages)==0) {return(invisible(TRUE))}
if(!silent) {
cat(messages,sep = "\n")
}
return(invisible(FALSE))
}
#' Returns the available YEAR-COUNTRY fadn.raw.rds
#'
#' @return a DT of the available YEAR-COUNTRY fadn.raw.rds
#'
#' @export
#'
#' @examples
get.available.fadn.raw.rds = function(data.dir=NULL) {
if(is.null(data.dir)) {data.dir=get.data.dir()}
if(is.null(data.dir)) {
warning("Either provide explicitly a fadnUtils.data.dir to the function orfirst to set the fadnUtils.data.dir using set.data.dir function. Exiting ....")
return(FALSE)
}
rds.dir = paste0(data.dir,"/rds/")
rds.avail.files = list.files(rds.dir,pattern = "fadn.raw.*.rds")
pattern = "fadn[.]raw[.](\\d*)[.](\\S*)[.]rds"
fadn.raw.rds.avail = data.table(
YEAR = gsub(pattern,"\\1",rds.avail.files),
COUNTRY = sub(pattern,"\\2",rds.avail.files)
)
return(fadn.raw.rds.avail)
}
#' Returns the available YEAR-COUNTRY fadn.str.rds, for each str.folder
#'
#' @return DT of the available YEAR-COUNTRY fadn.str.rds
#' @param extract_dir The name of the extraction dir
#'
#' @export
#'
#' @examples
get.available.fadn.str.rds = function(data.dir=NULL,extract_dir) {
if(is.null(data.dir)) {data.dir=get.data.dir()}
if(is.null(data.dir)) {
warning("Either provide explicitly a fadnUtils.data.dir or set the fadnUtils.data.dir using set.data.dir function. Exiting ....")
return(FALSE)
}
rds.dir = paste0(data.dir,"/rds/",extract_dir)
rds.avail.files = list.files(rds.dir,pattern = "fadn.str.*.rds")
pattern = "fadn[.]str[.](\\d+)[.](\\S+)[.]rds"
fadn.str.rds.avail = data.table(
YEAR = gsub(pattern,"\\1",rds.avail.files),
COUNTRY = gsub(pattern,"\\2",rds.avail.files)
)
return(fadn.str.rds.avail)
}