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Querying Web Resources

Packages that rely on access to web resources need to be written carefully. Web resources can change location, can be temporarily unavailable, or can be very slow to access and retrieve. Functions that query web resources, should anticipate and handle such situations gracefully – failing quickly and clearly when the resource is not available in a reasonable time frame. Some avoidable problems seen in Bioconductor package code include infinite loops, use of all available R connections, and unclear error messages.

Guiding Principles

Remember the Bioconductor packages are built nightly across multiple operating systems, and that users benefit from easy-to-run vignettes and examples.

  1. Download files of reasonable size. Use system.time() to estimate the download time. Remember the package should require less than 5 minutes to run R CMD check --no-build-vignettes.

  2. Set a limit on the number of times the function tries a URL. Avoid while() statements that have no guaranteed termination. These become infinite loops and eventually result in build-system TIMEOUTs.

  3. Supply an informative error message.

Template for Resource Queries

This function can serve as a template for appropriate resource retrieval. It tries to retrieve the resource one or several times before failing, and takes as arguments:

  • URL, the resource to be queried, typically character(1) or url().
  • FUN, the function to be used to query the resource. Examples might include readLines(), download.file(), httr::GET(), RCurl::getURL().
  • ...: additional arguments used by FUN.
  • N.TRIES: the number of times the URL will be attempted; only under exceptional circumstances might this differ from its default value.

The return value is the retrieved resource. If resource retrieval fails, the function indicates the failure, including the condition (error) message on the last attempt. Warnings propagate to the user in the normal way.

getURL <- function(URL, FUN, ..., N.TRIES=1L) {
    N.TRIES <- as.integer(N.TRIES)
    stopifnot(length(N.TRIES) == 1L, !is.na(N.TRIES))

    while (N.TRIES > 0L) {
        result <- tryCatch(FUN(URL, ...), error=identity)
        if (!inherits(result, "error"))
            break
        N.TRIES <- N.TRIES - 1L
    }

    if (N.TRIES == 0L) {
        stop("'getURL()' failed:",
             "\n  URL: ", URL,
             "\n  error: ", conditionMessage(result))
    }

    result
}

Base R functions using url() connections respect getOption("timeout"); see ?url for details.

FUN might be implemented to retrieve the resource and test for status, e.g.,

FUN <- function(URL, ...) {
    response <- httr::GET(URL, timeout(getOption("timeout")), ...)
    stop_for_status(response)
    response
}