R/refactoring_fns.R

In mariyad/openbiodiving: Linking the Open Biodiversity Knowledge Management System With BOLD Systems to Retrieve Specimen Voucher Metadata

#' @export
get_author_label = function(node, mongo_key){
  label = paste0(xml2::xml_text(xml2::xml_find_all(node, mongo_key[1])), " ", xml2::xml_text(xml2::xml_find_all(node, mongo_key[2])))
  return(label)
}

#' @export
get_author_orcid = function(node){
  orcid = xml2::xml_text(xml2::xml_find_first(node, "./uri[@content-type='orcid']"))
  orcid = gsub("^(.*)orcid.org\\/", "", orcid)
  return(orcid)
}

#' @export
get_taxon_label = function(node, mongo_key){
  b=NULL
  x = sapply(mongo_key, function(i){
    label = xml2::xml_text(xml2::xml_find_all(node, i))
    if(length(label) > 0 && label!="" && label!=" "){
      b = c(b, label)
      b
    }
  })
  
  tolit = do.call(get_scientific_name_or_tcl, x)
  label = tolit
  label
}

#' @export
get_figure_label = function(node, mongo_key, id_num)
{
  caption_xpath = paste0("//fig[@id='",fig_number,"']","|//fig-group[@id='",fig_number,"']")
  label = xml2::xml_text(xml2::xml_find_first(node, caption_xpath))
  label
}

#' @export
set_component_frame = function(label, mongo_key, type, orcid){
  df = data.frame(label = label, mongo_key = mongo_key, type = type, orcid = orcid)
  df
}

#' @export
process_author = function(node, mongo_key){
  label = get_author_label(node, mongo_key)
  orcid = get_author_orcid(node)
  df = set_component_frame(label = label, mongo_key = c(author=""), type = names(mongo_key), orcid = orcid )
  return(df)
}

#' @export
process_tnu = function(node, mongo_key)
{
  label = get_taxon_label(node, mongo_key)
  df = set_component_frame(label = label, mongo_key = c(taxonomic_name=""), type = names(mongo_key), orcid = NA )
  return(df)
}

#' @export
process_figure =  function(node, mongo_key)
{
  fig_number = xml2::xml_attr(node, "id")
  label = get_figure_label(node, mongo_key, fig_number)
  type = paste0(names(mongo_key), " ", fig_number)
  df = set_component_frame(label = label, mongo_key = mongo_key, type = type, orcid = NA )
  return(df)
}

#' @export
process_general_component = function(node, mongo_key){
  label = xml2::xml_text(xml2::xml_find_first(node, mongo_key))
  df = set_component_frame(label = label, mongo_key = mongo_key, type = names(mongo_key), orcid = NA)
  return(df)
}

#' @export
process_schema_component = function(node, mongo_key)
{
  if (is.author(mongo_key) == TRUE){
    df = process_author(node, mongo_key)
  } else if (is.tnu(mongo_key) == TRUE){
    df = process_tnu(node, mongo_key)
  } else if (is.figure(mongo_key) == TRUE){
    df = process_figure(node, mongo_key)
  }
  else{
    df = process_general_component(node, mongo_key)
  }
  df
}

#' @export
get_or_set_mongoid = function(df, schema_name, mongo_key){
  general_collection = mongolite::mongo("new_collection")
  
  if (!(is.na(df$orcid))){
    key = check_mongo_via_orcid(df$orcid, general_collection)
    if (is.null(key) == TRUE){
      id = paste0(schema_name,"/", names(mongo_key), "/", df$orcid)
      save_to_mongo(key = id, value = df$label, type = df$type, collection = general_collection)
    }
    else
      id = key
  }else{

    key = check_mongo(value = df$label, type = df$type, collection = general_collection, regex = FALSE)
    if (is.null(key) == TRUE)
    {
      key = set_obkms(schema_name, df$type)
      save_to_mongo(key = key, value = df$label, type = df$type, collection = general_collection)
    }
    id = key
  }
  return(id)
}