better_fetch.R

better_fetch_pubmed_data = function (pubmed_id_list, retstart = 0, retmax = 500, format = "xml", 
                                     encoding = "UTF8") 
{
  myIDlist <- pubmed_id_list
  if ((!is.list(myIDlist)) | is.na(myIDlist$WebEnv) | is.na(myIDlist$QueryKey) | 
      is.na(myIDlist$Count) | !is.integer(as.integer(retstart)) | 
      !is.integer(as.integer(retmax))) {
    message("There is an issue with the PubMed ID list you supplied. Please, call the function again and supply the result of a <get_pubmed_ids()> call as argument. Thank you.")
    return(NULL)
  }
  
  myWebEnv <- myIDlist$WebEnv
  myKey <- myIDlist$QueryKey
  myCount <- as.numeric(as.character(myIDlist$Count))
  myRetstart = as.integer(retstart)
  if (myRetstart < 0) {
    myRetstart = 0
  }
  myRetmax <- as.integer(retmax)
  if (myRetmax > 5000) {
    myRetmax = 5000
  }
  if (myRetmax < 1) {
    myRetmax = 1
  }
  if (format[1] %in% c("medline", "uilist", "abstract", 
                       "asn.1", "xml")) {
    myFormat <- format[1]
  }
  else {
    myFormat <- "xml"
  }
  typeMode <- switch(myFormat, asn.1 = c("null", "asn.1"), 
                     xml = c("null", "xml"), medline = c("medline", "text"), 
                     uilist = c("uilist", "text"), abstract = c("abstract", 
                                                                "text"))
  efetch_url = paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?", 
                     "db=pubmed&WebEnv=", myWebEnv, "&query_key=", myKey, 
                     "&retstart=", myRetstart, "&retmax=", myRetmax, "&rettype=", 
                     typeMode[1], "&retmode=", typeMode[2], sep = "")
  api_key <- pubmed_id_list$APIkey
  if (!is.null(api_key)) {
    efetch_url <- paste(efetch_url, "&api_key=", api_key, 
                        sep = "")
  }
  
  tfile = tempfile(fileext = ".xml"); 
  xx = curl::curl_download(efetch_url,
                           destfile = tfile, quiet = FALSE)
  return(tfile)
}