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add overwrite and timeout arguments #115

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Mar 8, 2023
Merged

add overwrite and timeout arguments #115

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21 changes: 17 additions & 4 deletions R/ZenodoRecord.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1082,18 +1082,28 @@ ZenodoRecord <- R6Class("ZenodoRecord",
#' and passed as \code{cl} argument. After downloading all files, the cluster will be stopped automatically.
#' @param cl an optional cluster for cluster-based parallel handlers
#' @param quiet (default is \code{FALSE}) can be set to suppress informative messages (not warnings).
#' @param overwrite (default is \code{TRUE}) can be set to FALSE to avoid re-downloading existing files.
#' @param timeout (default is 60s) see \code{download.file}.
#' @param ... arguments inherited from \code{parallel::mclapply} or the custom \code{parallel_handler}
#' can be added (eg. \code{mc.cores} for \code{mclapply})
#'
#' @note See examples in \code{\link{download_zenodo}} utility function.
#'
downloadFiles = function(path = ".", files = list(),
parallel = FALSE, parallel_handler = NULL, cl = NULL, quiet = FALSE, ...){
parallel = FALSE, parallel_handler = NULL, cl = NULL, quiet = FALSE, overwrite=TRUE, timeout=60, ...){
if(length(self$files)==0){
self$WARN(sprintf("No files to download for record '%s' (doi: '%s')",
self$id, self$doi))
}else{
files.list <- self$files

if(!overwrite){
files.list <- files.list[
which(sapply(files.list, function(x){
!file.exists(file.path(path, x$filename))}))
]
}

if(length(files)>0) files.list <- files.list[sapply(files.list, function(x){x$filename %in% files})]
if(length(files.list)==0){
errMsg <- sprintf("No files available in record '%s' (doi: '%s') for file names [%s]",
Expand All @@ -1107,7 +1117,7 @@ ZenodoRecord <- R6Class("ZenodoRecord",
self$id, self$doi, file))
}
}

files_summary <- sprintf("Will download %s file%s from record '%s' (doi: '%s') - total size: %s",
length(files.list), ifelse(length(files.list)>1,"s",""), self$id, self$doi,
human_filesize(sum(sapply(files.list, function(x){x$filesize}))))
Expand All @@ -1117,10 +1127,13 @@ ZenodoRecord <- R6Class("ZenodoRecord",
file$filename <- substring(file$filename, regexpr("/", file$filename)+1, nchar(file$filename))
if (!quiet) cat(sprintf("[zen4R][INFO] Downloading file '%s' - size: %s\n",
file$filename, human_filesize(file$filesize)))
target_file <-file.path(path, file$filename)
target_file <- file.path(path, file$filename)
timeout_cache <- getOption("timeout")
options(timeout = timeout)
download.file(url = file$links$download, destfile = target_file,
quiet = quiet, mode = "wb")
}
options(timeout = timeout_cache)
}
#check_integrity util
check_integrity <- function(file){
file$filename <- substring(file$filename, regexpr("/", file$filename)+1, nchar(file$filename))
Expand Down