Improve R console UI experience (#193)

* Improve UI experience

* Added verbose mode to deleteJob and deleteStorageContainer

* Refactor print method

Author: brnleehng

R/doAzureParallel.R

@@ -489,9 +489,20 @@ setHttpTraffic <- function(value = FALSE) {
     }
   }
 
-  cat("Job Summary: ", fill = TRUE)
+
   job <- rAzureBatch::getJob(id)
-  cat(sprintf("Id: %s", job$id), fill = TRUE)
+
+  printJobInformation(
+    jobId = job$id,
+    chunkSize = chunkSize,
+    enableCloudCombine = enableCloudCombine,
+    errorHandling = obj$errorHandling,
+    wait = wait,
+    autoDeleteJob = autoDeleteJob,
+    cranPackages = obj$packages,
+    githubPackages = githubPackages,
+    bioconductorPackages = bioconductorPackages
+  )
 
   if (!is.null(job$id)) {
     saveMetadataBlob(job$id, metadata)
@@ -531,12 +542,16 @@ setHttpTraffic <- function(value = FALSE) {
       containerImage = data$containerImage
     )
 
+    cat("\r", sprintf("Submitting tasks (%s/%s)", i, length(endIndices)), sep = "")
+    flush.console()
+
     return(taskId)
   })
 
   rAzureBatch::updateJob(id)
 
   if (enableCloudCombine) {
+    cat("\nSubmitting merge task")
     mergeTaskId <- paste0(id, "-merge")
     .addTask(
       jobId = id,
@@ -554,6 +569,7 @@ setHttpTraffic <- function(value = FALSE) {
       outputFiles = obj$options$azure$outputFiles,
       containerImage = data$containerImage
     )
+    cat(". . .")
   }
 
   if (wait) {
@@ -603,12 +619,10 @@ setHttpTraffic <- function(value = FALSE) {
           errorValue <- foreach::getErrorValue(it)
           errorIndex <- foreach::getErrorIndex(it)
 
-          cat(sprintf("Number of errors: %i", numberOfFailedTasks),
-              fill = TRUE)
-
           # delete job from batch service and job result from storage blob
           if (autoDeleteJob) {
-            deleteJob(id)
+            # Default behavior is to delete the job data
+            deleteJob(id, verbose = !autoDeleteJob)
           }
 
           if (identical(obj$errorHandling, "stop") &&

R/jobUtilities.R

@@ -258,18 +258,28 @@ getJobResult <- function(jobId) {
 #' deleteJob("job-001")
 #' }
 #' @export
-deleteJob <- function(jobId) {
-  deleteStorageContainer(jobId)
+deleteJob <- function(jobId, verbose = TRUE) {
+  deleteStorageContainer(jobId, verbose)
 
   response <- rAzureBatch::deleteJob(jobId, content = "response")
 
-  if (response$status_code == 202) {
-    cat(sprintf("Your job '%s' has been deleted.", jobId),
-        fill = TRUE)
-  } else if (response$status_code == 404) {
-    cat(sprintf("Job '%s' does not exist.", jobId),
-        fill = TRUE)
-  }
+  tryCatch({
+      httr::stop_for_status(response)
+
+      if (verbose) {
+        cat(sprintf("Your job '%s' has been deleted.", jobId),
+            fill = TRUE)
+      }
+    },
+    error = function(e) {
+      if (verbose) {
+        response <- httr::content(response, encoding = "UTF-8")
+        cat("Call: deleteJob", fill = TRUE)
+        cat(sprintf("Exception: %s", response$message$value),
+            fill = TRUE)
+      }
+    }
+  )
 }
 
 #' Terminate a job
@@ -301,7 +311,7 @@ terminateJob <- function(jobId) {
 #' @export
 waitForTasksToComplete <-
   function(jobId, timeout, errorHandling = "stop") {
-    cat("Waiting for tasks to complete. . .", fill = TRUE)
+    cat("\nWaiting for tasks to complete. . .", fill = TRUE)
 
     totalTasks <- 0
     currentTasks <- rAzureBatch::listTask(jobId)

R/storage_management.R

@@ -34,19 +34,29 @@ listStorageContainers <- function(prefix = "") {
 #' @param container The name of the container
 #'
 #' @export
-deleteStorageContainer <- function(container) {
+deleteStorageContainer <- function(container, verbose = TRUE) {
   response <-
     rAzureBatch::deleteContainer(container, content = "response")
 
-  if (response$status_code == 202) {
-    cat(sprintf("Your storage container '%s' has been deleted.", container),
-        fill = TRUE)
-  } else if (response$status_code == 404) {
-    cat(sprintf("storage container '%s' does not exist.", container),
-        fill = TRUE)
-  }
-
-  response
+  tryCatch({
+      httr::stop_for_status(response)
+
+      if (verbose) {
+        cat(sprintf("Your storage container '%s' has been deleted.", jobId),
+            fill = TRUE)
+      }
+    },
+    error = function(e) {
+      # Checking for status code instead of using xml2 package
+      # Storage helper functions require xml2 package which requires special installations
+      if (verbose && response$status_code == 404) {
+        cat(sprintf("Call: deleteStorageContainer"),
+            fill = TRUE)
+        cat(sprintf("Exception: %s", "The specified storage container does not exist"),
+            fill = TRUE)
+      }
+    }
+  )
 }
 
 #' List storage files from Azure storage.

R/stringUtilities.R

@@ -14,3 +14,39 @@ getTaskFailedErrorString <- function(...) {
 
   return(errorMessage)
 }
+
+getJobPackageSummary <- function(packages) {
+  if (length(packages) > 0) {
+    cat(sprintf("%s: ", deparse(substitute(packages))), fill = TRUE)
+    cat("\t")
+    for (i in 1:length(packages)) {
+      cat(packages[i], "; ", sep = "")
+    }
+    cat("\n")
+  }
+}
+
+printJobInformation <- function(jobId,
+                                chunkSize,
+                                enableCloudCombine,
+                                errorHandling,
+                                wait,
+                                autoDeleteJob,
+                                cranPackages,
+                                githubPackages,
+                                bioconductorPackages) {
+  cat(strrep('=', options("width")), fill = TRUE)
+  cat(sprintf("Id: %s", jobId), fill = TRUE)
+  cat(sprintf("chunkSize: %s", as.character(chunkSize)), fill = TRUE)
+  cat(sprintf("enableCloudCombine: %s", as.character(enableCloudCombine)), fill = TRUE)
+
+  packages <- cranPackages
+  getJobPackageSummary(packages)
+  getJobPackageSummary(githubPackages)
+  getJobPackageSummary(bioconductorPackages)
+
+  cat(sprintf("errorHandling: %s", as.character(errorHandling)), fill = TRUE)
+  cat(sprintf("wait: %s", as.character(wait)), fill = TRUE)
+  cat(sprintf("autoDeleteJob: %s", as.character(autoDeleteJob)), fill = TRUE)
+  cat(strrep('=', options("width")), fill = TRUE)
+}