Reverted changes (#227)

Azure · Feb 22, 2018 · 5b8431f · 5b8431f
1 parent 9bba37f
commit 5b8431f
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Showing 2 changed files with 29 additions and 18 deletions.
diff --git a/R/doAzureParallel.R b/R/doAzureParallel.R
@@ -358,6 +358,7 @@ setHttpTraffic <- function(value = FALSE) {
 
   retryCounter <- 0
   maxRetryCount <- 5
+  startupFolderName <- "startup"
 
   repeat {
     if (retryCounter > maxRetryCount) {
@@ -395,17 +396,17 @@ setHttpTraffic <- function(value = FALSE) {
       stop(paste0("Error creating job: ", containerContent$message$value))
     }
 
-    nodeScriptsDir <- system.file("startup", package = "doAzureParallel")
-    nodeScriptsFiles <- list.files(nodeScriptsDir, full.names = TRUE)
-
-    nodeScriptsZip <- "node_scripts.zip"
-    # Zip Flags: Keeping console output clean and removing junk paths
-    utils::zip(nodeScriptsZip, files = nodeScriptsFiles, extras = "-j -q")
-
     # Uploading common job files for the worker node
     rAzureBatch::uploadBlob(id,
-                            nodeScriptsZip)
-    file.remove(nodeScriptsZip)
+                            system.file(startupFolderName, "worker.R", package = "doAzureParallel"))
+    rAzureBatch::uploadBlob(id,
+                            system.file(startupFolderName, "merger.R", package = "doAzureParallel"))
+    rAzureBatch::uploadBlob(id,
+                            system.file(startupFolderName, "install_github.R", package = "doAzureParallel"))
+    rAzureBatch::uploadBlob(id,
+                            system.file(startupFolderName, "install_cran.R", package = "doAzureParallel"))
+    rAzureBatch::uploadBlob(id,
+                            system.file(startupFolderName, "install_bioconductor.R", package = "doAzureParallel"))
 
     # Creating common job environment for all tasks
     jobFileName <- paste0(id, ".rds")
@@ -415,13 +416,28 @@ setHttpTraffic <- function(value = FALSE) {
 
     # Creating read-only SAS token blob resource file urls
     sasToken <- rAzureBatch::createSasToken("r", "c", id)
-    nodeScriptsZipUrl <-
-      rAzureBatch::createBlobUrl(storageCredentials$name, id, nodeScriptsZip, sasToken)
+    workerScriptUrl <-
+      rAzureBatch::createBlobUrl(storageCredentials$name, id, "worker.R", sasToken)
+    mergerScriptUrl <-
+      rAzureBatch::createBlobUrl(storageCredentials$name, id, "merger.R", sasToken)
+    installGithubScriptUrl <-
+      rAzureBatch::createBlobUrl(storageCredentials$name,
+                                 id,
+                                 "install_github.R",
+                                 sasToken)
+    installCranScriptUrl <-
+      rAzureBatch::createBlobUrl(storageCredentials$name, id, "install_cran.R", sasToken)
+    installBioConductorScriptUrl <-
+      rAzureBatch::createBlobUrl(storageCredentials$name, id, "install_bioconductor.R", sasToken)
     jobCommonFileUrl <-
       rAzureBatch::createBlobUrl(storageCredentials$name, id, jobFileName, sasToken)
 
     requiredJobResourceFiles <- list(
-      rAzureBatch::createResourceFile(url = nodeScriptsZipUrl, fileName = nodeScriptsZip),
+      rAzureBatch::createResourceFile(url = workerScriptUrl, fileName = "worker.R"),
+      rAzureBatch::createResourceFile(url = mergerScriptUrl, fileName = "merger.R"),
+      rAzureBatch::createResourceFile(url = installGithubScriptUrl, fileName = "install_github.R"),
+      rAzureBatch::createResourceFile(url = installCranScriptUrl, fileName = "install_cran.R"),
+      rAzureBatch::createResourceFile(url = installBioConductorScriptUrl, fileName = "install_bioconductor.R"),
       rAzureBatch::createResourceFile(url = jobCommonFileUrl, fileName = jobFileName)
     )
 

diff --git a/R/helpers.R b/R/helpers.R
@@ -148,12 +148,7 @@
   poolInfo <- list("poolId" = poolId)
 
   # Default command for job preparation task
-  # Supports backwards compatibility if zip packages are missing, it will be installed
-  # Eventually, apt-get install command will be deprecated
-  commands <- c(
-    "apt-get -y install zip unzip",
-    "unzip -j $AZ_BATCH_JOB_PREP_WORKING_DIR/node_scripts.zip"
-  )
+  commands <- c("ls")
 
   if (!is.null(packages)) {
     jobPackages <-