R/getOMLRun.R

In openml/r: Open Machine Learning and Open Data Platform

#' @title Get an OpenML run.
#'
#' @description
#' Given an run id, the corresponding \code{\link{OMLRun}} including all server
#' and user computed metrics is downloaded if not already available in cache.
#'
#' @param run.id [\code{integer(1)}]\cr
#'   The run ID.
#' @template arg_cache_only
#' @param only.xml [\code{logical(1)}]\cr
#'   Should only the XML be downloaded?
#' @template arg_verbosity
#' @return [\code{\link{OMLRun}}].
#' @family downloading functions
#' @family run-related functions
#' @example inst/examples/getOMLRun.R
#' @export
getOMLRun = function(run.id, cache.only = FALSE, only.xml = FALSE, verbosity = NULL) {
  id = asCount(run.id)
  assertFlag(cache.only)

  down = downloadOMLObject(id, object = "run", cache.only = cache.only, only.xml = only.xml, verbosity = verbosity)
  f = down$files
  doc = down$doc

  run.args = filterNull(list(
    run.id = xmlREValI(doc, "/oml:run/oml:run_id"),
    uploader = xmlREValI(doc, "/oml:run/oml:uploader"),
    uploader.name = xmlOValS(doc, "/oml:run/oml:uploader.name"),
    task.id = xmlREValI(doc, "/oml:run/oml:task_id"),
    task.type = xmlOValS(doc, "/oml:run/oml:task_type"),
    task.evaluation.measure = xmlOValS(doc, "/oml:run/oml:task_evaluation_measure"),
    flow.id = xmlRValI(doc, "/oml:run/oml:flow_id"),
    flow.name = xmlOValS(doc, "/oml:run/oml:flow_name"),
    setup.id = xmlREValI(doc, "/oml:run/oml:setup_id"),
    setup.string = xmlOValS(doc, "/oml:run/oml:setup_string"),
    error.message = xmlOValS(doc, "/oml:run/oml:error_message"),
    tags = xmlOValsMultNsS(doc, "/oml:run/oml:tag"),
    input.data = parseData(doc, "/oml:run/oml:input_data"),
    output.data = parseData(doc, "/oml:run/oml:output_data"),
    parameter.setting = list()
  ))

  # parse parameters
  ns.pars = getNodeSet(doc, "/oml:run/oml:parameter_setting")
  run.args[["parameter.setting"]] = lapply(seq_along(ns.pars), function(i) {
    args = filterNull(list(
      name = xmlRValS(doc, paste("/oml:run/oml:parameter_setting[", i, "]/oml:name", sep = "")),
      value = xmlRValS(doc, paste("/oml:run/oml:parameter_setting[", i, "]/oml:value", sep = "")),
      component = xmlOValS(doc, paste("/oml:run/oml:parameter_setting[", i, "]/oml:component", sep = ""))
    ))
    do.call(makeOMLRunParameter, args)
  })
  par.names = vcapply(run.args[["parameter.setting"]], function(x) x$name)
  run.args[["parameter.setting"]] = setNames(run.args[["parameter.setting"]], par.names)
  #setClasses(run.args[["parameter.setting"]], "OMLRunParList")

  # get the predictions
  f = findCachedRun(run.args$run.id)

  if (!f$predictions.arff$found) {
    showInfo(verbosity, "No ARFF file containing the predictions found.")
    pred = NULL
  } else {
    #showInfo(verbosity, "Predictions found in cache.")
    pred = arff.reader(f$predictions.arff$path)
  }
  run.args[["predictions"]] = pred

  return(do.call(makeOMLRun, run.args))
}

parseData = function(doc, path) {
  # parse datasets
  path.ds = paste(path, "oml:dataset", sep = "/")
  ns.datasets = getNodeSet(doc, path.ds)
  datasets = lapply(seq_along(ns.datasets), function(i) {
    list(
      data.id = xmlRValR(doc, paste(path.ds, "[", i, "]/oml:did", sep = "")),
      name = xmlRValS(doc, paste(path.ds, "[", i, "]/oml:name", sep = "")),
      url = xmlRValS(doc, paste(path.ds, "[", i, "]/oml:url", sep = ""))
    )})
  datasets = convertListOfRowsToDataFrame(datasets, strings.as.factors = FALSE)

  # parse files
  path.fls = paste(path, "oml:file", sep = "/")
  ns.fls = getNodeSet(doc, path.fls)
  files = lapply(seq_along(ns.fls), function(i) {
    list(
      data.id = xmlRValR(doc, paste(path.fls, "[", i, "]/oml:did", sep = "")),
      name = xmlRValS(doc, paste(path.fls, "[", i, "]/oml:name", sep = "")),
      url = xmlRValS(doc, paste(path.fls, "[", i, "]/oml:url", sep = ""))
    )})
  files = convertListOfRowsToDataFrame(files, strings.as.factors = FALSE)

  # parse evaluations
  path.evals = paste(path, "oml:evaluation", sep = "/")
  ns.evals = getNodeSet(doc, path.evals)

  evals = setDF(rbindlist(lapply(ns.evals, function(node) {
    children = xmlChildren(node)
    row = list(
      as.integer(xmlValue(children[["did"]])),
      xmlValue(children[["name"]]),
      xmlValue(children[["flow_id"]]),
      xmlValue(children[["label"]]),
      as.numeric(xmlValue(children[["value"]])),
      as.numeric(xmlValue(children[["stdev"]])),
      xmlValue(children[["array_data"]]),
      as.integer(xmlValue(children[["sample_size"]]))
    )
    cv.info = xmlAttrs(node)[c("repeat", "fold")]
    if (is.null(cv.info)) cv.info = c(NA, NA)
    row = c(row, cv.info)
    names(row) = c("data.id", "name", "flow_id", "label", "value", "stdev", "array.data", "sample.size", "repeat", "fold")
    row
  }), fill = TRUE))
  makeOMLIOData(datasets = datasets, files = files, evaluations = evals)
}