R/zenodo_list.R

In RajLabMSSM/downloadR: echoverse module: Single- and multi-threaded downloading functions

#' List Zenodo files
#' 
#' List all files available in a given Zenodo record.
#' Requires already having a Zenodo account set up and 
#' @param token Zenodo
#'  \href{https://zenodo.org/account/settings/applications/tokens/new/}{
#'  Personal access token}.
#' @param concept_doi Concept DOI of the Zenodo record.
#' @param sandbox Whether to use the Zenodo or Zenodo Sandbox API.
#' @param as_datatable Return file info as a \link[data.table]{data.table}.
#' @param verbose Print messages.
#' @source 
#' \href{https://cran.r-project.org/web/packages/zen4R/vignettes/zen4R.html}{
#' zen4R vignette}
#' \href{https://rpubs.com/antaldaniel/zenodo-sandbox-setup}{
#' zen4R vignette}
#' @returns Nested list of Zenodo file info.
#' 
#' @export
#' @importFrom data.table data.table rbindlist :=
#' @examples 
#' \dontrun{
#' zen_dat <- zenodo_list(token="<token>",
#'                        concept_doi="10.5281/zenodo.7062237")
#' }
zenodo_list <- function(concept_doi,
                        token=Sys.getenv("zenodo_token"),
                        sandbox=FALSE,
                        as_datatable=TRUE,
                        verbose=TRUE){  
    
    requireNamespace("zen4R")
    filename <- url <- NULL;
    
    doi_num <- rev(strsplit(concept_doi,"[.]")[[1]])[1]
    zenodo <- zen4R::ZenodoManager$new( 
        url = if(isTRUE(sandbox)) {
            "https://sandbox.zenodo.org/api"
        } else {
            "https://zenodo.org/api"
        },
        token = token, 
        logger = "INFO" 
    )  
    myrec <- zenodo$getDepositionByConceptDOI(concept_doi) 
    zen_files <- zenodo$getFiles(myrec$id)
    #### Report ####
    messager(formatC(length(zen_files),big.mark = ","),
             "files found.", v=verbose) 
    #### Return ####
    if(isTRUE(as_datatable)){ 
        zen_dat <- lapply(zen_files, function(x){
            data.table::data.table(
                filename=x$filename, 
                filesize=x$filesize,
                id=x$id, 
                download_link=x$links$download,
                self_link=x$links$self
            )
        }) |> data.table::rbindlist() 
        zen_dat[,url:=paste0("https://zenodo.org/record/",
                             doi_num,"/files/",
                             filename,"?download=1")]
        return(zen_dat)
    } else {
        return(zen_files)
    } 
}