test code for R

bigdatagenomics · Jan 25, 2018 · cc93505 · cc93505
1 parent 7cf9628
commit cc93505
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Showing 2 changed files with 24 additions and 4 deletions.
diff --git a/adam-r/bdgenomics.adam/R/rdd.R b/adam-r/bdgenomics.adam/R/rdd.R
@@ -254,19 +254,19 @@ setMethod("cache",
               replaceRdd(ardd, sparkR.callJMethod(ardd@jrdd, "cache"))
           })
 
-
 #' Persists the existing ardd
 #'
 #' @param ardd The RDD to apply this to.
 #' @param sl the StorageLevel to persist in.
 #'
-#' @importFrom SparkR sparkR.callJMethod
+#' @importFrom SparkR sparkR.callJMethod sparkR.callJStatic
 #'
 #' @export
 setMethod("persist",
           signature(ardd = "GenomicRDD",
-                    sl = "StorageLevel"),
-          function(ardd) {
+                    sl = "character"),
+          function(ardd, sl) {
+              storageLevel <- sparkR.callJStatic("org.apache.spark.storage.StorageLevel", "fromString", sl)
               replaceRdd(ardd, sparkR.callJMethod(ardd@jrdd, "persist", sl))
           })
 

diff --git a/adam-r/bdgenomics.adam/tests/testthat/test_alignmentRecordRdd.R b/adam-r/bdgenomics.adam/tests/testthat/test_alignmentRecordRdd.R
@@ -105,3 +105,23 @@ test_that("transmute to coverage", {
     expect_true(is(readsAsCoverage, "CoverageRDD"))
     expect_equal(count(toDF(readsAsCoverage)), 5)
 })
+
+test_that("reads can cache", {
+
+    readsPath <- resourceFile("unsorted.sam")
+    reads <- loadAlignments(ac, readsPath)
+
+    cache(reads)
+    unpersist(reads)
+})
+
+test_that("reads can persist with storage level", {
+
+    readsPath <- resourceFile("unsorted.sam")
+    reads <- loadAlignments(ac, readsPath)
+    storageLevel <- "MEMORY_AND_DISK"
+
+    persist(reads, storageLevel)
+    unpersist(reads)
+})
+