R/fake_lotus.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Fake LOTUS
#'
#' @description This function fakes LOTUS in case the download failed
#'
#' @param export Path to save the file to
#'
#' @return NULL
#'
#' @export
#'
#' @examples NULL
fake_lotus <- function(export) {
  log_debug("External failure. Returning empty file instead.")
  tidytable::tidytable() |>
    tidytable::mutate(
      structure_wikidata = NA,
      structure_inchikey = NA,
      structure_inchi = NA,
      structure_smiles = NA,
      structure_molecular_formula = NA,
      structure_exact_mass = NA,
      structure_xlogp = NA,
      structure_smiles_2D = NA,
      structure_cid = NA,
      structure_nameIupac = NA,
      structure_nameTraditional = NA,
      structure_stereocenters_total = NA,
      structure_stereocenters_unspecified = NA,
      structure_taxonomy_npclassifier_01pathway = NA,
      structure_taxonomy_npclassifier_02superclass = NA,
      structure_taxonomy_npclassifier_03class = NA,
      structure_taxonomy_classyfire_chemontid = NA,
      structure_taxonomy_classyfire_01kingdom = NA,
      structure_taxonomy_classyfire_02superclass = NA,
      structure_taxonomy_classyfire_03class = NA,
      structure_taxonomy_classyfire_04directparent = NA,
      organism_wikidata = NA,
      organism_name = NA,
      organism_taxonomy_gbifid = NA,
      organism_taxonomy_ncbiid = NA,
      organism_taxonomy_ottid = NA,
      organism_taxonomy_01domain = NA,
      organism_taxonomy_02kingdom = NA,
      organism_taxonomy_03phylum = NA,
      organism_taxonomy_04class = NA,
      organism_taxonomy_05order = NA,
      organism_taxonomy_06family = NA,
      organism_taxonomy_07tribe = NA,
      organism_taxonomy_08genus = NA,
      organism_taxonomy_09species = NA,
      organism_taxonomy_10varietas = NA,
      reference_wikidata = NA,
      reference_doi = NA,
      manual_validation = NA
    ) |>
    tidytable::fwrite(export)
  return(export)
}

## See https://github.com/markfairbanks/tidytable/issues/269
.datatable.aware <- TRUE