Adding timeout, adding tries to 3

QiStark · Mar 8, 2017 · 5b7de31 · 5b7de31
1 parent a127704
commit 5b7de31
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Showing 5 changed files with 9 additions and 7 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -128,6 +128,7 @@ importFrom(grDevices,rainbow)
 importFrom(grid,gpar)
 importFrom(grid,grid.rect)
 importFrom(gridExtra,rbind.gtable)
+importFrom(httr,timeout)
 importFrom(igraph,"V<-")
 importFrom(igraph,E)
 importFrom(igraph,V)

diff --git a/R/TCGAInternal.R b/R/TCGAInternal.R
@@ -658,7 +658,7 @@ getResults <- function(query, rows, cols){
 }
 
 
-getURL <- function(URL, FUN, ..., N.TRIES=1L) {
+getURL <- function(URL, FUN, ..., N.TRIES=3L) {
     N.TRIES <- as.integer(N.TRIES)
     stopifnot(length(N.TRIES) == 1L, !is.na(N.TRIES))
 

diff --git a/R/TCGAPrepare.R b/R/TCGAPrepare.R
@@ -817,9 +817,9 @@ getBarcodeInfo <- function(barcode) {
     #message(paste0(baseURL,paste(options.pretty,options.expand, option.size, options.filter, sep = "&")))
     url <- paste0(baseURL,paste(options.pretty,options.expand, option.size, options.filter, sep = "&"))
     json  <- tryCatch(
-        getURL(url,fromJSON,simplifyDataFrame = TRUE),
+        getURL(url,fromJSON,timeout(600),simplifyDataFrame = TRUE),
         error = function(e) {
-            fromJSON(content(getURL(url,GET), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
+            fromJSON(content(getURL(url,GET,timeout(600)), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
         }
     )
 

diff --git a/R/TCGAQuery.R b/R/TCGAQuery.R
@@ -77,6 +77,7 @@
 #' @return A data frame with the results and the parameters used
 #' @importFrom  jsonlite fromJSON
 #' @importFrom knitr kable
+#' @importFrom httr timeout
 GDCquery <- function(project,
                      data.category,
                      data.type,
@@ -149,9 +150,9 @@ GDCquery <- function(project,
                            legacy = legacy)
         message("ooo Project: ", proj)
         json  <- tryCatch(
-            getURL(url,fromJSON,simplifyDataFrame = TRUE),
+            getURL(url,fromJSON,timeout(600),simplifyDataFrame = TRUE),
             error = function(e) {
-                fromJSON(content(getURL(url,GET), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
+                fromJSON(content(getURL(url,GET,timeout(600)), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
             }
         )
         json$data$hits$acl <- NULL

diff --git a/R/TCGAquery_clinical.R b/R/TCGAquery_clinical.R
@@ -129,9 +129,9 @@ GDCquery_clinic <- function(project, type = "clinical", save.csv = FALSE){
                              URLencode('"]}}]}'))
     url <- paste0(baseURL,paste(options.pretty,options.expand, option.size, options.filter,"format=json", sep = "&"))
     json  <- tryCatch(
-        getURL(url,fromJSON,simplifyDataFrame = TRUE),
+        getURL(url,fromJSON,timeout(600),simplifyDataFrame = TRUE),
         error = function(e) {
-            fromJSON(content(getURL(url,GET), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
+            fromJSON(content(getURL(url,GET,timeout(600)), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE)
         }
     )