R/ReadZotero.R

In mwmclean/RefManageR: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management

# Mathew McLean
# October 26, 2013
# function for reading from Zotero library

# https://www.zotero.org/support/kb/ssl_certificate_error
# names(getCurlOptionsConstants())
# https://www.zotero.org/support/dev/server_api/v2/write_requests
#
# http://www.omegahat.net/RCurl/philosophy.html
# .opts explained: https://curl.haxx.se/libcurl/c/curl_easy_setopt.html

#' Get Bibliography Information From a Zotero Library.
#'
#' @param user Zotero userID for use in calls to the Zotero API.  This is not
#' the same as your Zotero username.  The userID for accessing user-owned
#' libraries can be found at \verb{https://www.zotero.org/settings/keys}
#' after logging in.
#' @param group Zotero groupID for use in calls to the Zotero API.  Only one
#' of \code{user} and \code{group} should be specified; \code{group} will be
#' ignored if both are specified.
#' @param .params A \emph{named} list of parameters to use in requests to the
#' Zotero API with possible values
#'  \itemize{
#'    \item q - Search string to use to search the library
#'    \item qmode - Search mode. Default is "titleCreatorYear".  Use "everything"
#'          to include full-text content in search.
#'    \item key - API key.  This must be specified to access non-public libraries.
#'    \item collection - name of a specific collection within the library to search
#'    \item itemType - type of entry to search for; e.g., "book" or "journalArticle"
#'    \item tag - name of tag to search for in library
#'    \item limit - maximum number of entries to return
#'    \item start - index of first entry to return
#'  }
#' @param temp.file character; file name where the BibTeX data returned by
#' Zotero will be temporarily written.
#' @param delete.file boolean; should \code{temp.file} be removed on exit?
#' @return An object of class BibEntry
#' @export
#' @seealso \code{\link{BibEntry}}
#' @references \verb{https://www.zotero.org/support/dev/server_api/v2/read_requests}
#' @importFrom httr GET content
#' @examples
#' \dontrun{
#' ## first two entries in library with bayesian in title
#' ReadZotero(user = "1648676", .params = list(q = "bayesian",
#'   key = "7lhgvcwVq60CDi7E68FyE3br", limit=2))
#'
#' ## Search specific collection
#' ## collection key can be found by reading uri when collection is selected in Zotero
#' ReadZotero(user = "1648676", .params=list(q = "yu", key = "7lhgvcwVq60CDi7E68FyE3br",
#'   collection = "3STEQRNU"))
#'
#' ## Search by tag
#' ## Notice the issue with how Zotero uses a TechReport entry for arXiv manuscripts
#' ## This is one instance where the added fields of BibLaTeX are useful
#' ReadZotero(user = "1648676", .params=list(key = "7lhgvcwVq60CDi7E68FyE3br",
#'   tag = "Statistics - Machine Learning"))
#'
#' ## To read these in you must set check.entries to FALSE or "warn"
#' old.opts <- BibOptions(check.entries = FALSE)
#' length(ReadZotero(user = "1648676", .params = list(key = "7lhgvcwVq60CDi7E68FyE3br",
#'   tag = "Statistics - Machine Learning")))
#'
#' ## Example using groups
#' ReadZotero(group = "13495", .params = list(q = "Schmidhuber",
#'   collection = "QU23T27Q"))
#' BibOptions(old.opts)
#' }
#' @keywords database
ReadZotero <- function(user, group, .params,
                       temp.file = tempfile(fileext = ".bib"),
                       delete.file = TRUE){
  if (!requireNamespace("bibtex")){
    message("Sorry this feature currently cannot be used without the ",
            dQuote("bibtex"), " package installed.\nPlease install from ",
            "GitHub using the ", dQuote("remotes"),
            " (or ", dQuote("devtools"), ") package:\n\n",
            "remotes::install_github(\"ROpenSci/bibtex\")")
    return(invisible())
  }

  if (delete.file)
    on.exit(unlink(temp.file, force = TRUE))

  bad.ind <- which(!names(.params) %in% c("q", "itemType", "tag", "collection",
                                          "key", "limit", "start", "qmode"))
  .parms <- .params
  if (length(bad.ind)){
    warning("Invalid .params specified and will be ignored")
    .parms <- .parms[-bad.ind]
  }
  .parms$format <- "bibtex"
  if (is.null(.parms$limit))
    .parms$limit <- 99L

  coll <- if (is.null(.parms$collection))
            NULL
          else
            paste0("/collections/", .parms$collection)
  .parms$uri <- paste0("https://api.zotero.org/", if (!missing(user))
                        paste0("users/", user) else paste0("groups/", group),
                       coll, "/items")

  ## cert <- try(system.file("CurlSSL/cacert.pem", package = "RCurl"))
  uri <- paste0("https://api.zotero.org/", if (!missing(user))
                        paste0("users/", user) else paste0("groups/", group),
                       coll, "/items")
  res <- GET(uri, query = .parms)  #, config = list(ssl.verifypeer=TRUE,
                                   #     httpheader="Zotero-API-Version: 2",
                                   # forbid.reuse=TRUE, cainfo=cert))
  res <- content(res, as = "text", encoding = "UTF-8")

  if (.is_not_nonempty_text(res)){
    print("No results.")
    return()
  }
  write(res, file=temp.file, append = TRUE)

  bib.res <- try(ReadBib(file=temp.file, .Encoding="UTF-8"), TRUE)
  if (inherits(bib.res, "try-error")){
    stop(gettextf("Could not parse the returned BibTeX results.  If %s %s%s",
                  sQuote("delete.file"),
                  "is FALSE, you can try viewing and editing the file: ",
                  temp.file))
  }
  bib.res
}