R/utils.R

In RGLab/AnalyteExplorer: Analyte Explorer

get_url_base <- function() {
  mget("labkey.url.base", envir = .GlobalEnv, ifnotfound = "https://datatools.immunespace.org")[[1]]
}

get_url_path <- function() {
  mget("labkey.url.path", envir = .GlobalEnv, ifnotfound = "/AnalyteExplorer/")[[1]]
}

msg <- function(txt) {
  message(sprintf("[%s] %s", Sys.time(), txt))
}

labkey.importData <- function(baseUrl, folderPath, schemaName, queryName, toImport) {
  temp_file <- tempfile(fileext = ".csv")
  data.table::fwrite(toImport, temp_file)

  url <- paste(baseUrl, "query", folderPath, "import.api", sep = "")
  config <- Rlabkey::labkey.getRequestOptions(method = "POST")
  body <- list(
    schemaName = schemaName,
    queryName = queryName,
    file = httr::upload_file(temp_file)
  )
  header <- httr::add_headers(`Content-Type` = "multipart/form-data")

  response <- httr::POST(url = url, config = config, body = body, header)
  parsed <- Rlabkey:::processResponse(response, haltOnError = TRUE)

  parsed
}

fix_types <- function(types) {
  sapply(types, function(x) {
    switch(
      x,
      "Integer" = "numeric",
      "Number (Double)" = "numeric",
      "Text (String)" = "character",
      stop(sprintf("%s is an unknown type!", x))
    )
  }, USE.NAMES = FALSE)
}

save_debug <- function(object, name) {
  debug_dir <- getOption("debug_dir")
  if (!is.null(debug_dir)) {
    file <- sprintf("%s/%s.rds", debug_dir, name)
    msg(sprintf("Saving to %s", file))
    saveRDS(object, file)
  }
}

add_attributes <- function(data, data_name) {
  class(data) <- c("AnalyteExplorer", class(data))
  attr(data, "type") <- data_name
  attr(data, "version") <- paste0("v", utils::packageVersion("AnalyteExplorer"))
  hash <- utils::packageDescription("AnalyteExplorer")[["GithubSHA1"]]
  attr(data, "hash") <- ifelse(is.null(hash), "", hash)

  data
}