R/download.R

In kkmann/CENTERTBI: CENTER-TBI Utility Functions

#' Download a single opal dataset as tibble
#'
#' @param username opal username as string
#' @param password opal password as string (do not store in any script!)
#' @param table    opal tablename as string
#' @param version_suffix suffix refering to the db version i.e. 'table' will be
#'   downloaded from 'CENTER-TBIversion_suffix'
#'
#' @value a tibble
#'
#' @export
download <- function(username, password, table, version_suffix = "_versionCurrent") {
  require(opal)
  o <- opal.login(username, password, url = 'https://uda.wbic.cam.ac.uk:9443')
  tryCatch({
      opal.assign(o, 'query', sprintf('CENTER-TBI%s.%s', version_suffix, table), id.name = "ID")
      df <- opal.execute(o, 'query') %>% as_tibble()
    }, error = function(e) {opal.logout(o); print(e)}
  )
  opal.logout(o)
  return(df)
}

#' Download entire CENTER-TBI version
#'
#' @param username opal username as string
#' @param password opal password as string (do not store in any script!)
#' @param outdir (relative) path to store datasets in (as .rds per table)
#' @param version_suffix suffix refering to the db version i.e. tables will be
#'   downloaded from 'CENTER-TBIversion_suffix'
#'#'
#' @export
save_all <- function(username, password, outdir, version_suffix = "_versionCurrent") {
  require(opal)
  dir.create(outdir, showWarnings = FALSE)
  db_name = sprintf('CENTER-TBI%s', version_suffix)
  o <- opal.login(username, password, url = 'https://uda.wbic.cam.ac.uk:9443')
  tables <- tryCatch({
      opal.tables(o, db_name)
    }, error = function(e) {opal.logout(o); print(e)}
  )
  opal.logout(o)
  for (tbl in tables) {
    df_tbl <- download(username, password, tbl$name, version_suffix = version_suffix)
    saveRDS(df_tbl, file = sprintf("%s/df_%s.rds", outdir, tbl$name))
  }
}