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ghcn-extract.R
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ghcn-extract.R
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#' Setup the global variables for NOOA GHCN data
#'
#' @param dat_flag (character) : "noaa_ghcn_daily" (default) name of the data -
#' will appear as data folder name when data are
#' saved
#' @param data_dl_method (character) : "libcurl" (default) data download method
#' @param metadata_dirname (character) : "metadata" (default) metadata
#' folder name
#' @param url (character) : NULL (default) data url - the default one is encoded
#' in the function body
#'
#' @export
nooa_ghcn_setup_variables <- function(dat_flag = 'noaa_ghcn_daily',
data_dl_method = 'libcurl',
metadata_dirname = 'metadata',
url = NULL){
backburner::setup_global_variables(dat_flag = dat_flag, data_dl_method = data_dl_method,
metadata_dirname = metadata_dirname)
RE_PTRN_ARCHIVE <<- "(zip|gz)$" # generic archive matching pattern
RE_PTRN_YEAR <<- "^\\d{1,4}"
RE_PTRN_CSV_ONLY <<- "csv$"
if (is.null(url)){
url <- "ftp://ftp.ncdc.noaa.gov/pub/data/ghcn/daily/by_year/"
}
noaa_url <<- stringr::str_c(url, sep = "")
}
#' Extracting information on the download URLs forNOOA GHCN data
#'
#' @export
nooa_ghcn_read_data <- function(){
# Getting URL Tibble
hand <- curl::new_handle()
gg <- curl::curl_fetch_memory(url = noaa_url, handle = hand)
gg <- rawToChar(gg$content)
noaa_urls <- readr::read_delim(file = gg, delim = "\\s+", col_names = FALSE) %>%
tibble::as_tibble() %>%
tidyr::separate(data = ., col = X1,
into = c("rw", "group", "ftp", "code", "size",
"month", "dom", "time", "fname"),
sep = "\\s+") %>%
dplyr::mutate(mod_year = base::as.integer(
format(dl_date, "%Y"))) %>%
tidyr::unite(data = ., col = mod_datetime, month, dom, mod_year,
time, sep = " ") %>%
# Modify to a datetime format using lubridate
# Setting the locale to "en_US.UTF-8" is important here
dplyr::mutate(year_data =
base::as.integer(
stringr::str_extract(
string = fname,
pattern = RE_PTRN_YEAR)),
mod_datetime =
lubridate::mdy_hm(mod_datetime,
locale = "en_US.UTF-8"),
size_mb = base::as.double(size),
ind_zip =
base::as.integer(
stringr::str_detect(string = fname,
pattern = RE_PTRN_ARCHIVE)),
# In this case metadata column is the same
# as zip indicator. Duplicated to have consistent
# metadata column names
ind_mtda = base::as.integer(!ind_zip),
ind_csv_only =
base::as.integer(
stringr::str_detect(string = fname,
pattern = RE_PTRN_CSV_ONLY)),
dl_datetime = dl_datetime,
dl_date = dl_date,
dl_user = dl_user,
dl_sysname = dl_sysname,
dat_src_flag = DAT_SRC_FLAG) %>%
dplyr::select(-c("rw", "group", "ftp"))
return(noaa_urls)
}
#' Download full data and metadata information for NOOA GHCN data
#' @param noaa_urls (tibble) : NOOA GHCN URLs tibble
#'
#' @export
nooa_ghcn_metadata<- function(noaa_urls){
noaa_all <- noaa_urls %>%
dplyr::mutate(furl = stringr::str_c(noaa_url,
fname, sep = ""),
outpath =
dplyr::if_else(!base::is.na(year_data),
here::here("data",
DAT_SRC_FLAG,
base::format(dl_date,
"%Y%m%d"),
year_data,
fname),
here::here("data",
DAT_SRC_FLAG,
base::format(dl_date,
"%Y%m%d"),
GLOBAL_MTDA_DIRNAME,
fname)),
ind_mtda = as.integer(base::is.na(year_data)),
outdir = fs::path_dir(path = outpath)) %>%
# Reorder dataset
dplyr::select(fname, furl, year_data, size_mb, mod_datetime,
ind_zip, ind_mtda, ind_csv_only,
dl_datetime, dl_date, dl_sysname,
dat_src_flag, outpath, ind_mtda, outdir)
return(noaa_all)
}
#' Download data for NOOA GHCN data
#' @param noaa_all (tibble) : Data and Metadata info
#' @param year_periods (numeric) : 1800:1800 (default) array of years to be
#' downloaded
#' @param data_folder (character) : "data" (default) data folder name
#' @param remove (logical) : FALSE (default) remove .zip file after extraction
#'
#' @export
noaa_ghcn_data_download <- function(noaa_all, year_periods = 1800:1800,
data_folder = 'data', remove = FALSE){
outpath_mtda <- here::here(data_folder, DAT_SRC_FLAG, base::format(dl_date,
"%Y%m%d"),
stringr::str_c(DAT_SRC_FLAG,
"metadata.csv",
sep = "_"))
outpath_mtda_all <- here::here(data_folder, DAT_SRC_FLAG, base::format(dl_date,
"%Y%m%d"),
stringr::str_c(DAT_SRC_FLAG,
"metadata_all.csv",
sep = "_"))
outdir_mtda <- outpath_mtda %>% fs::path_dir(path = .)
outdir_mtda_all <- outpath_mtda_all %>% fs::path_dir(path = .)
fs::dir_create(path = outdir_mtda)
# I've got a problem here as apparently R archive does not really
# work with gzip
# https://github.com/omnisci/omniscidb/blob/master/Archive/Archive.h LINE 75
# https://github.com/libarchive/libarchive/issues/586
noaa_all %T>%
readr::write_csv(x = ., file = outpath_mtda_all, col_names = TRUE) %>%
dplyr::filter(year_data %in% year_periods) %>%
dplyr::select(furl, outpath, ind_zip, outdir) %>%
dplyr::mutate(extr = base::as.logical(ind_zip),
remove = base::as.logical(remove)) %>%
dplyr::select(-ind_zip) %T>%
readr::write_csv(x = ., file = outpath_mtda, col_names = TRUE) %>%
purrr::pwalk(dl_extract_file)
}
#' Wrapper for NOOA GCHN data extraction pipeline.
#' This function will setup global variables, gather information and urls on
#' data and metadata and download the data.
#' @param dat_flag (character) : "noaa_ghcn_daily" (default) name of the data -
#' will appear as data folder name when data are
#' saved
#' @param data_dl_method (character) : "libcurl" (default) data download method
#' @param metadata_dirname (character) : "metadata" (default) metadata
#' folder name
#' @param url (character) : NULL (default) data url - the default one is encoded
#' in the function body
#' @param year_periods (numeric) : 1800:1800 (default) array of years to be
#' downloaded
#' @param data_folder (character) : "data" (default) data folder name
#' @param remove (logical) : FALSE (default) remove .zip file after extraction
#'
#' @examples
#' \dontrun{
#' noaa_ghcn_extract(year_periods = 1800:1801)
#' }
#' @export
noaa_ghcn_extract <- function(year_periods = 1800:1800, data_folder = 'data',
dat_flag = 'noaa_ghcn_daily', remove = FALSE,
data_dl_method = 'libcurl', url = NULL,
metadata_dirname = 'metadata'){
nooa_ghcn_setup_variables(dat_flag = dat_flag,
data_dl_method = data_dl_method,
url = url, metadata_dirname=metadata_dirname)
noaa_urls <- nooa_ghcn_read_data()
noaa_all <- nooa_ghcn_metadata(noaa_urls = noaa_urls)
noaa_ghcn_data_download(noaa_all = noaa_all, year_periods = year_periods,
data_folder = data_folder, remove = remove)
}