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get_file.R
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get_file.R
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#' @rdname files
#' @title Download File(s)
#' @description Download Dataverse File(s)
#' @details This function provides access to data files from a Dataverse entry.
#' @param file An integer specifying a file identifier; or, if \code{doi} is specified, a character string specifying a file name within the DOI-identified dataset; or an object of class \dQuote{dataverse_file} as returned by \code{\link{dataset_files}}.
#' @template ds
#' @param format A character string specifying a file format. For \code{get_file}: by default, this is \dQuote{original} (the original file format). If \dQuote{RData} or \dQuote{prep} is used, an alternative is returned. If \dQuote{bundle}, a compressed directory containing a bundle of file formats is returned. For \code{get_file_metadata}, this is \dQuote{ddi}.
#' @param vars A character vector specifying one or more variable names, used to extract a subset of the data.
#' @template envvars
#' @template dots
#' @return \code{get_file_metadata} returns a character vector containing a DDI metadata file. \code{get_file} returns a raw vector (or list of raw vectors, if \code{length(file) > 1}).
#' @examples
#' \dontrun{
#' # download file from:
#' # https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/ARKOTI
#' monogan <- get_dataverse("monogan")
#' monogan_data <- dataverse_contents(monogan)
#' d1 <- get_dataset("doi:10.7910/DVN/ARKOTI")
#' f <- get_file(d1$files$datafile$id[3])
#'
#' # check file metadata
#' m1 <- get_file_metadata("constructionData.tab", "doi:10.7910/DVN/ARKOTI")
#' m2 <- get_file_metadata(2437257)
#'
#' # retrieve file based on DOI and filename
#' f2 <- get_file("constructionData.tab", "doi:10.7910/DVN/ARKOTI")
#' f2 <- get_file(2692202)
#'
#' # retrieve file based on "dataverse_file" object
#' flist <- dataset_files(2692151)
#' get_file(flist[[2]])
#'
#' # read file as data.frame
#' if (require("rio")) {
#' tmp <- tempfile(fileext = ".dta")
#' writeBin(f, tmp)
#' str(dat <- rio::import(tmp, haven = FALSE))
#'
#' # check UNF match
#' #if (require("UNF")) {
#' # unf(dat) %unf% d1$files$datafile$UNF[3]
#' #}
#' }
#' }
#' @importFrom utils unzip
#' @export
get_file <-
function(file,
dataset = NULL,
format = c("original", "RData", "prep", "bundle"),
# thumb = TRUE,
vars = NULL,
key = Sys.getenv("DATAVERSE_KEY"),
server = Sys.getenv("DATAVERSE_SERVER"),
...) {
format <- match.arg(format)
# get file ID from 'dataset'
if (!is.numeric(file)) {
if (inherits(file, "dataverse_file")) {
file <- get_fileid(file, key = key, server = server)
} else if (is.null(dataset)) {
stop("When 'file' is a character string, dataset must be specified. Or, use a global fileid instead.")
} else {
file <- get_fileid(dataset, file, key = key, server = server, ...)
}
}
if (length(file) > 1) {
file <- paste0(file, collapse = ",")
u <- paste0(api_url(server), "access/datafiles/", file)
r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), ...)
httr::stop_for_status(r)
tempf <- tempfile(fileext = ".zip")
tempd <- tempfile()
dir.create(tempd)
on.exit(unlink(tempf), add = TRUE)
on.exit(unlink(tempd), add = TRUE)
writeBin(httr::content(r, as = "raw"), tempf)
to_extract <- utils::unzip(tempf, list = TRUE)
out <- lapply(to_extract$Name[to_extract$Name != "MANIFEST.TXT"], function(zipf) {
utils::unzip(zipfile = tempf, files = zipf, exdir = tempd)
readBin(file.path(tempd, zipf), "raw", n = 1e8)
})
return(out)
} else {
if (format == "bundle") {
u <- paste0(api_url(server), "access/datafile/bundle/", file)
r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), ...)
} else {
u <- paste0(api_url(server), "access/datafile/", file)
query <- list()
if (!is.null(vars)) {
query$vars <- paste0(vars, collapse = ",")
}
if (!is.null(format)) {
query$format <- match.arg(format)
}
# request
if (length(query)) {
r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), query = query, ...)
} else {
r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), ...)
}
}
httr::stop_for_status(r)
return(httr::content(r, as = "raw"))
}
}
get_file_name_from_header <- function(x) {
gsub("\"", "", strsplit(httr::headers(x)[["content-type"]], "name=")[[1]][2])
}
#' @rdname files
#' @import xml2
#' @export
get_file_metadata <-
function(file,
dataset = NULL,
format = c("ddi", "preprocessed"),
key = Sys.getenv("DATAVERSE_KEY"),
server = Sys.getenv("DATAVERSE_SERVER"),
...) {
# get file ID from doi
if (!is.numeric(file)) {
if (inherits(file, "dataverse_file")) {
file <- get_fileid(file)
} else if(is.null(dataset)) {
stop("When 'file' is a character string, dataset must be specified. Or, use a global fileid instead.")
} else {
file <- get_fileid(dataset, file, key = key, server = server, ...)
}
}
format <- match.arg(format)
u <- paste0(api_url(server), "access/datafile/", file, "/metadata/", format)
r <- httr::GET(u, httr::add_headers("X-Dataverse-key" = key), ...)
httr::stop_for_status(r)
out <- httr::content(r, as = "text", encoding = "UTF-8")
return(out)
}