R/post_meta.R

In USGS-R/mda.streams: Data Preparation, Access, and Analysis Functions for the Powell Center Continental Stream Metabolism Project

#' Post new metadata file[s] to SB
#' 
#' If a file with the same name already exists in Sites_meta, the
#' \code{on_exists} argument specifies how to manage the conflict.
#' 
#' @param files character one or more files to post to SB
#' @param on_exists character. what should be done when an item already exists?
#' @param verbose logical. Should status messages be given?
#' @return an item list
#' @author Alison Appling
#' @import sbtools
#' @importFrom stats setNames
#' @export
#' @examples 
#' \dontrun{
#' login_sb()
#' set_scheme("mda_streams_dev")
#' metafile <- stage_meta(sites=list_sites(), folder="temp")
#' post_meta(metafile, on_exists="stop", verbose=TRUE)
#' set_scheme("mda_streams")
#' }
post_meta <- function(files, on_exists=c("stop", "skip", "replace", "merge"), verbose=TRUE) {
  # handle inputs
  on_exists <- match.arg(on_exists)
  sb_require_login("stop")
  
  meta_ids <- sapply(setNames(files, files), function(metafile) {
    
    # look for an existing ts and respond appropriately
    metapath <- parse_meta_path(metafile)
    meta_id <- locate_meta(metapath$type, by="either")
    if(!is.na(meta_id)) {
      if(verbose) message('the metadata item ', metapath$meta_type, ' already exists on SB')
      switch(
        on_exists,
        "stop"={ 
          stop('the metadata item already exists and on_exists="stop"') },
        "skip"={ 
          if(isTRUE(verbose)) message("skipping posting of the metadata item") 
          return(NA) # na is signal that doesn't need new tags
        },
        "replace"={ 
          if(verbose) message("deleting metadata before replacement: ", meta_id)
          delete_meta(metapath$type, files_only=TRUE, verbose=verbose)
        },
        "merge"={ 
          if(verbose) message("merging new metadata with old: ", meta_id)
          stop("merge not yet implemented")
          #pre_merge_dir <- file.path(ts_path$dir_name, "pre_merge_temp")
          #dir.create(pre_merge_dir, showWarnings=FALSE)
          #meta_old <- read_meta(download_meta(var_src=ts_path$var_src, site_name=ts_path$site_name, folder=pre_merge_dir, on_local_exists="replace"))
          #meta_old <- read.table(download_meta(...))
          #meta_new <- read_meta(...)
          # join.
          #meta_merged <- full_join(meta_old, meta_new, by=names(meta_old))
          #if(verbose) message("num rows before & after merge: old=", nrow(meta_old), ", new=", nrow(meta_new), ", merged=", nrow(meta_merged))
          # replace the input file, but write to a nearby directory so we don't overwrite the user's file
          #merge_dir <- file.path(metapath$dir_name, "post_merge_temp")
          #dir.create(merge_dir, showWarnings=FALSE)
          #fpath <- file.path(metapath$file_name, merge_dir)
          #files[i] <- write.table(meta_merged, fpath, sep="\t", row.names=FALSE)
          # delete the old one in preparation for overwriting
          #delete_meta(metapath$type, files_only=TRUE, verbose=verbose)
        })
    } else {
      # create the item
      meta_id <- item_create(locate_folder("sites_meta"), title=metapath$meta_type)$id
    }

    # attach data file to ts item. SB quirk: must be done before tagging with 
    # identifiers, or identifiers will be lost
    if(verbose) message("posting metadata file ", metapath$file_name)
    item_append_files(meta_id, files = metafile)
    
    # check/repair identifiers
    repair_meta(metapath$type)

    return(meta_id)  
  })
  
  # re-tagging files seems to be unnecessary for the current options, but keep an eye on this.
  
  invisible(meta_ids)
}