Try to improve resliancy to race conditions resulting in duplicate ca…

…che entries (#76)

R/caching.R

@@ -34,10 +34,25 @@
 #' BiocFileCache::BiocFileCache()
 #' @param hash unique hash representing a query.
 .addToCache <- function(bfc, result, hash) {
-    tf <- tempfile()
-    saveRDS(result, file = tf)
-    bfcadd(bfc, rname = hash, fpath = tf, action = "copy")
+
+  if(!dir.exists(.biomartCacheLocation()))
+    dir.create(.biomartCacheLocation())
+
+  ## write our file to the biomart cache location directly
+  tf <- tempfile(tmpdir = biomaRt:::.biomartCacheLocation())
+  saveRDS(result, file = tf)
+
+  ## check once more that there isn't an entry with this hash
+  ## if its free add our new file
+  ## if there's a clash don't add anything and tidy up
+  if(!.checkInCache(bfc, hash = hash)) {
+    bfcadd(bfc, rname = hash, fpath = tf, action = "asis")
+    res <- TRUE
+  } else {
     file.remove(tf)
+    res <- FALSE
+  }
+  return(invisible(res))
 }
 
 #' @param bfc Object of class BiocFileCache, created by a call to 

tests/testthat/test_z_cache.R

@@ -1,3 +1,5 @@
+library(biomaRt)
+
 cache <- file.path(tempdir(), "biomart_cache_test")
 Sys.setenv(BIOMART_CACHE = cache)
 
@@ -43,7 +45,8 @@ test_that("We find cache for previous query", {
     expect_identical(result, .readFromCache(bfc, hash = hash))
 })
 
-## add an invalid file
+## add an invalid file.  We are only expecting .rds files, and this is a 
+## text file
 tf <- tempfile()
 writeLines(LETTERS, con = tf)
 BiocFileCache::bfcadd(bfc, rname = "invalid-file", fpath = tf)
@@ -55,6 +58,13 @@ test_that("invalid cache entry detected", {
 })
 
 
+## check we can't write multiple entries with the same hash
+test_that("we can't create multiple entries with the same hash", {
+  expect_true(.addToCache(bfc = bfc, result = 1:100, hash = "testing"))
+  expect_false(.addToCache(bfc = bfc, result = 1:100, hash = "testing"))
+})
+
+
 
 test_that("Cache details are printed", {
     expect_message( biomartCacheInfo(),