R/ecitmatch.R

In reutils: Talk to the NCBI EUtils

#' @include eutil.R
NULL

#' @export
.ecitmatch <- setRefClass(
  Class    = "ecitmatch",
  contains = "eutil",
  methods  = list(
    initialize = function(method, ...) {
      callSuper()
      perform_query(method = method, ...)
      if (errors$all_empty() && retmode() != "xml") {
        ## Switch off error checking even if retmode is set to "xml"
        ## because weirdly enough with ecitmatch retmode must be set to 'xml'
        ## but at least currently it doesn't return XML results but
        ## bar separated citation strings with the PMID as last entry.
        errors$check_errors(.self)
      }
    },
    show = function() {
      cat("Object of class", sQuote(eutil()), "\n")
      if (no_errors()) {
        cat(get_content("text"))
      } else {
        methods::show(get_error())
      }
    }
  )
)

parse_ecitmatch <- function(object) {
  if (object$no_errors()) {
    vapply(strsplit(object$get_content("text"), '\n')[[1]], function(x) {
      strsplit(x, '|', fixed = TRUE)[[1]][7]
    }, "", USE.NAMES = FALSE)
  } else NA_character_
}

#' @describeIn content Return PubMed IDs if \code{as = "parsed"}.
setMethod("content", "ecitmatch", function(x, as = "text") {
  as <- match.arg(as, c("text", "parsed"))
  callNextMethod(x = x, as = as)
})

#' \code{ecitmatch} serves as an API to the PubMed
#' \href{https://www.ncbi.nlm.nih.gov/pubmed/batchcitmatch}{batch citation matcher}.
#' It retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings.
#' 
#' @title ecitmatch - searching PubMed with citation data
#' @param bdata Citation strings. Each input citation must be represented
#' by a citation string in the following format:
#' \emph{journal_title|year|volume|first_page|author_name|your_key|}
#' @param db Database to search. The only supported value is \sQuote{pubmed}.
#' @param retmode Retrieval mode. The only supported value is \sQuote{xml}.
#' @return An \code{\linkS4class{ecitmatch}} object.
#' @export
#' @examples
#' citstrings <- c("proc natl acad sci u s a|1991|88|3248|mann bj|Art1|",
#'                 "science|1987|235|182|palmenber ac|Art2|")
#' x <- ecitmatch(citstrings)
#' x
#' if (x$no_errors()) {
#'   content(x, "parsed")
#' }
#' 
ecitmatch <- function(bdata, db = "pubmed", retmode = "xml") {
  if (missing(bdata)) {
    stop("No citation string provided", call. = FALSE)
  }
  if (length(bdata) > 1) {
    bdata <- paste0(bdata, collapse = '\r')
  }
  db <- match.arg(db, "pubmed")
  retmode <- match.arg(retmode, "xml")
  .ecitmatch('GET', db = db, retmode = retmode, bdata = bdata)
}