R/githubUtils.R

In seandavi/BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

#' Extract GitHub user and repo name from GitHub URL
#'
#' @param urls `character()` A vector of URLs
#'
#' @return A `data.frame` with four columns:
#'   * url: The original GitHub URL
#'   * user_repo: The GitHub "username/repo", combined
#'   * user:  The GitHub username
#'   * repo: The GitHub repo name
#'
#' @importFrom stringr str_match
#'
#' @examples
#' # find GitHub URL details for
#' # Bioconductor packages
#' bpkgl = biocPkgList()
#' urldetails = githubURLParts(bpkgl$URL)
#' urldetails = urldetails[!is.na(urldetails$url),]
#' head(urldetails)
#'
#' @export
githubURLParts <- function(urls) {
    tmp = str_match(urls,'.*http[s]?://github.com/(([^/]+)/([^/]+)).*')
    tmp = data.frame(tmp, stringsAsFactors = FALSE)
    colnames(tmp) = c('url', 'user_repo', 'user', 'repo')
    ## remove ".git" from tail of GitHub repo
    tmp$user_repo = sub('\\.git$','', tmp$user_repo)
    tmp$repo = sub('\\.git$','', tmp$repo)
    tmp
}


.gh_pkg_info <- function(user_repo) {
    f = tryCatch(gh(sprintf('/repos/%s', user_repo)),
                 error=function(e) {
                     warning(sprintf("package %s not found", user_repo))
                     NA
                 })
    f[is.null(f)]=""
    f
}


#' Get package details from GitHub
#'
#' For packages that live on GitHub, we can mine
#' further details. This function returns the
#' GitHub details for the listed packages.
#'
#' @details
#' The \code{\link[gh]{gh}} function is used to
#' do the fetching. If the number of packages supplied
#' to this function is large (>40 or so), it is possible
#' to run into problems with API rate limits. The \code{gh}
#' package uses the environment variable "GITHUB_PAT"
#' (for personal access token) to authenticate and then
#' provide higher rate limits. If you run into problems
#' with rate limits, set sleep to some small positive
#' number to slow queries. Alternatively, create a Personal
#' Access Token on GitHub and register it. See the \code{gh}
#' package for details.
#'
#' @importFrom gh gh
#'
#' @param pkgs a character() vector of username/repo
#' for one or more GitHub repos, such as `seandavi/GEOquery`.
#'
#' @param sleep numeric() denoting the number of seconds to
#' sleep between GitHub API calls. Since GitHub rate limits
#' its APIs, it might be necessary to either use small
#' chunks of packages iteratively or to supply a non-zero
#' argument here. See the `details` section for a better
#' solution using GitHub tokens.
#'
#' @examples
#' pkglist = biocPkgList()
#'
#' # example of "pkgs" format.
#' head(pkglist$URL)
#'
#' gh_list = githubURLParts(pkglist$URL)
#' gh_list = gh_list[!is.null(gh_list$user_repo),]
#'
#' head(gh_list$user_repo)
#'
#' ghd = githubDetails(gh_list$user_repo[1:5])
#' lapply(ghd, '[[', "stargazers")
#'
#' @export
githubDetails <- function(pkgs, sleep=0) {
    vals = lapply(pkgs, function(pkg) {
        Sys.sleep(sleep)
        .gh_pkg_info(pkg)
    })
    names(vals) = pkgs
    vals = vals[!is.na(vals)]
    vals
}