R/taxa_tbl.R

In cboettig/taxadb: A High-Performance Local Taxonomic Database Interface

#' Return a reference to a given table in the taxadb database
#'
#' @importFrom dplyr tbl
#' @inheritParams filter_by
#' @export
#' @examples
#' \donttest{
#'   \dontshow{
#'    ## All examples use a temporary directory
#'    Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))
#'    options("taxadb_default_provider"="itis_test")
#'   }
#'
#'   ## default schema is the dwc table
#'   taxa_tbl()
#'
#'   ## common names table
#'   taxa_tbl(schema = "common")
#'
#'
#'
#' }

taxa_tbl <- function(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc","common"),
  version = latest_version(),
  db = td_connect()){

  schema <- match.arg(schema)
  tbl_name <- paste0("v", version, "_", schema, "_", provider)

  if (is.null(db)){
    warning("NULL db not supported")
    db = td_connect()
  }
  if (!has_table(tbl_name, db)){
    td_create(provider = provider, schema = schema, version = version, db = db)
  }
  dplyr::tbl(db, tbl_name, check_from = FALSE)
}


has_table <- function(table = NULL, db = td_connect()){
  if (is.null(db)) return(FALSE)
  else if (table %in% DBI::dbListTables(db)) return(TRUE)
  else FALSE
}