R/gbif_local.R

In gbifdb: High Performance Interface to 'GBIF'

#' Local connection to a downloaded GBIF Parquet database
#' 
#' @importFrom dplyr tbl any_of
#' @param dir location of downloaded GBIF parquet files
#' @param tblname name for the database table
#' @param backend choose duckdb or arrow. 
#' @param safe logical. Should we exclude columns `mediatype`
#'  and `issue`? (default `TRUE`).  
#' varchar datatype on these columns substantially slows downs queries.
#' @return a remote tibble `tbl_sql` class object
#' @details 
#' A summary of this GBIF data, along with column meanings can be found at 
#' <https://github.com/gbif/occurrence/blob/master/aws-public-data.md>
#' @export
#' @examplesIf interactive()
#' 
#' gbif <- gbif_local(gbif_example_data())
#'
gbif_local <- function(dir = gbif_parquet_dir(version = gbif_version(local=TRUE)),
                       tblname="gbif",
                       backend = c("arrow", "duckdb"),
                       safe = TRUE){
  
  backend <- match.arg(backend)
  gbif <- switch(backend,
         duckdb = duckdb_local(dir),
         arrow = arrow::open_dataset(dir)
         )
  if (safe) {
    gbif <- dplyr::select(gbif, -dplyr::any_of(c("mediatype", "issue")))
  }
  gbif
}

duckdb_local <- function(dir) {
  requireNamespace("duckdbfs")
  duckdbfs::open_dataset(paste0(dir, "/*"), tblname = "gbif")
}