improve API query error handling

Author: mwmclean

NAMESPACE

@@ -58,6 +58,7 @@ importFrom(httr,content)
 importFrom(httr,http_error)
 importFrom(httr,modify_url)
 importFrom(httr,status_code)
+importFrom(httr,stop_for_status)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(lubridate,"%within%")

R/GetDOIs.R

@@ -37,10 +37,11 @@ GetDOIs <- function(bib){
     json.res <- httr::POST("http://search.crossref.org/links", body = json.bib,
                            config = list(add_headers = headers),
                            encode = "json")
-    if (http_error(json.res) ||
+    status <- status_code(json.res)
+    if (status != 200 ||
         !(json.res <- content(json.res, type = "application/json",
                               encoding = "UTF-8"))[[2L]])
-      message("Failed to retrieve any DOIs.")
+        message(gettextf("Failed to retrieve any DOIs [%s].", status))
     else{
       matches <- vapply(json.res[[1L]], "[[", FALSE, "match")
       if (!any(matches))

R/ReadCrossRef.R

@@ -212,6 +212,7 @@ ReadCrossRef <- function(query = "", filter = list(), limit = 5, offset = 0,
 }
 
 #' @keywords internal
+#' @importFrom httr GET status_code content http_error
 #' @noRd
 GetCrossRefBibTeX <- function(doi, tmp.file){
     ## temp <- try(getURLContent(url=doi,
@@ -233,9 +234,9 @@ GetCrossRefBibTeX <- function(doi, tmp.file){
         if (http_error(temp) ||
             !grepl("^[[:space:]]*@", parsed, useBytes = TRUE)){
             doi.text <- sub("^https?://(dx[.])?doi.org/", "", doi)
-            message(gettextf("Server error for doi %s, you may want to %s",
-                             dQuote(doi.text),
-                             "try again, or BibTeX unavailable for this doi"))
+            message(gettextf("Server error [%s] for doi %s, you may want to%s",
+                             status_code(temp), dQuote(doi.text),
+                             " try again, or BibTeX unavailable for this doi"))
             return(1L)
         }
     }

R/ReadPubMed.R

@@ -42,7 +42,7 @@
 #' are available.
 #' @references \url{https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch}
 #' @family pubmed
-#' @importFrom httr GET http_error
+#' @importFrom httr GET http_error stop_for_status
 #' @importFrom xml2 read_xml xml_find_all xml_text
 #' @examples
 #' if (interactive() && !httr::http_error("https://eutils.ncbi.nlm.nih.gov/"))
@@ -67,8 +67,7 @@ ReadPubMed <- function(query, database = "PubMed", ...){
   .parms$usehistory <- "y"
   ## results <- try(getForm(base.url, .params = .parms))
   results <- GET(base.url, query = .parms)
-  if (http_error(results))
-    stop("Unable to GET results")
+  stop_for_status(results)
 
   tdoc <- read_xml(results, encoding = "UTF-8")