R/create_entity_all.R

In atn38/metabase-to-eml-R: Create Ecological Metadata Language From LTER Core Metabase

#' @title Quickly create all EML entity list objects.
#'
#' @description. Use to quickly create EML entity list objects from all entities listed in dataset.
#' @param meta_list (character) A list of dataframes containing metadata returned by \code{\link{get_meta}}.
#' @param file_dir (character) Path to directory containing flat files (data files). Defaults to current R working directory.
#' @param dataset_id (numeric) A dataset ID.
#' @param entity_numbers (numeric) Vector of entity numbers to include. Defaults to all of them. Use only when you need to delibrately exclude a couple entities.
#' @param skip_checks (logical) Whether to skip checking for attribute congruence. Defaults to FALSE. 

#'
#' @return (list) A list containing all data entities from dataset. Use this in the `entity_list` argument for \code{\link{create_EML}}.
#' First level list elements are grouped by entity types present in dataset and named accordingly.
#' Each first level element is a list of unnamed lists; the number of elements correspond to how many entities of each type are present in dataset.
#' Second level elements are analogous to output from \code{\link{create_entity}}.
#'
#' @examples
#' \dontrun{
#' # continued from \code{\link{get_meta}}
#' entities <- create_entity_all(meta_list = metadata, dataset_id = 1)
#' }
#'
#' @export
#'


create_entity_all <- function(meta_list, file_dir = getwd(), dataset_id, entity_numbers = NULL, skip_checks = FALSE) {
  entities <- subset_dataset(meta_list, "entities", dataset_id)
  factors <- subset_dataset(meta_list, "factors", dataset_id)
  attributes <- subset_dataset(meta_list, "attributes", dataset_id)
  missing <- subset_dataset(meta_list, "missing", dataset_id)
  
  if (is.null(entity_numbers)) {
    e_nos <- entities[["entity_position"]]
    names(e_nos) <- entities[["entitytype"]]
  } else {
    e_nos <- entity_numbers
    names(e_nos) <- entities[["entitytype"]][entity_numbers]
  }
  
  all <-
    lapply(e_nos,
      create_entity,
      meta_list = meta_list,
      file_dir = file_dir,
      dataset_id = dataset_id,
      skip_checks = skip_checks
    )

  all2 <- list(
    data_tables = all[which(names(all) %in% c("dataTable", "data table"))],
    other_entities = all[which(FALSE == (names(all) %in% c("dataTable", "data table")))]
  )
  names(all2[["other_entities"]]) <- NULL
  names(all2[["data_tables"]]) <- NULL

  return(all2)
}