Tests/r (#275)

* Added install R

* Added devtools build

* devtools build and test

* Clean up rscript

* Added line breaks

* Added devtools('.')

* Added testthat package

* Added roxygen

* Replaced rscript

* Test live

* Added environment variables to test

* Fixed test

* Removed

* Fixed tests

* makeClusters to makeCluster

* Error handling to stop exit

* Added params to setup function

* Removed pool names

* Get / Get Cluster List

* Added utility R source

* Fixed tests

* Fixed remove error handling with combine test

* Forgot \ lines

tests/test_scripts/test.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
+
+gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
+gpg -a --export E084DAB9 | sudo apt-key add -
+
+sudo apt-get update
+sudo apt-get install -y r-base r-base-dev libcurl4-openssl-dev
+sudo apt-get install -y libssl-dev libxml2-dev libgdal-dev libproj-dev libgsl-dev
+
+sudo R \
+  -e "Sys.setenv(BATCH_ACCOUNT_NAME = '$BATCH_ACCOUNT_NAME')" \
+  -e "Sys.setenv(BATCH_ACCOUNT_KEY = '$BATCH_ACCOUNT_KEY')" \
+  -e "Sys.setenv(BATCH_ACCOUNT_URL = '$BATCH_ACCOUNT_URL')" \
+  -e "Sys.setenv(STORAGE_ACCOUNT_NAME = '$STORAGE_ACCOUNT_NAME')" \
+  -e "Sys.setenv(STORAGE_ACCOUNT_KEY = '$STORAGE_ACCOUNT_KEY')" \
+  -e "getwd();" \
+  -e "install.packages(c('devtools', 'remotes', 'testthat', 'roxygen2'));" \
+  -e "devtools::install();" \
+  -e "devtools::build();" \
+  -e "res <- devtools::test(reporter='summary');" \
+  -e "df <- as.data.frame(res);" \
+  -e "if(sum(df[['failed']]) > 0 || any(df[['error']])) { q(status=1) }"

tests/testthat/test-async-cluster.R

@@ -1,38 +1,27 @@
-# Run this test for users to make sure the async cluster creation features
+context("Cluster Management Test")
-# of doAzureParallel are still working
+test_that("Get Cluster List / Get Cluster test", {
-context("async cluster scenario test")
-test_that("Async cluster scenario test", {
-  testthat::skip("Live test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
 
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
+  settings <- getSettings()
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
 
   cluster <-
-    doAzureParallel::makeCluster(clusterSetting = clusterFileName, wait = FALSE)
+    doAzureParallel::makeCluster(settings$clusterConfig, wait = FALSE)
 
   cluster <- getCluster(cluster$poolId)
-  getClusterList()
+  clusterList <- getClusterList()
-  filter <- filter <- list()
+  filter <- list()
   filter$state <- c("active", "deleting")
-  getClusterList(filter)
-  doAzureParallel::registerDoAzureParallel(cluster)
 
-  '%dopar%' <- foreach::'%dopar%'
+  testthat::expect_true('test-pool' %in% clusterList$Id)
-  res <-
-    foreach::foreach(i = 1:4) %dopar% {
-      mean(1:3)
-    }
 
-  res
+  clusterList <- getClusterList(filter)
 
-  testthat::expect_equal(length(res), 4)
+  for (i in 1:length(clusterList$State)) {
-  testthat::expect_equal(res, list(2, 2, 2, 2))
+    testthat::expect_true(clusterList$State[i] == 'active' ||
-
+                          clusterList$State[i] == 'deleting')
-  stopCluster(cluster)
+  }
 })

tests/testthat/test-error-handling.R

@@ -1,16 +1,13 @@
 context("error handling test")
 test_that("Remove error handling with combine test", {
-  testthat::skip("Live test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
+  settings <- getSettings()
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
+
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   '%dopar%' <- foreach::'%dopar%'
@@ -23,28 +20,27 @@ test_that("Remove error handling with combine test", {
       sqrt(i)
     }
 
-  res
+  res <- unname(res)
 
-  testthat::expect_equal(length(res), 2)
+  testthat::expect_equal(length(res), 3)
+  testthat::expect_equal(res, c(sqrt(1), sqrt(2), sqrt(5)))
 })
 
 test_that("Remove error handling test", {
-  testthat::skip("Live test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
+  settings <- getSettings()
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
+
+  settings$clusterConfig$poolId <- "error-handling-test"
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   '%dopar%' <- foreach::'%dopar%'
   res <-
-    foreach::foreach(i = 1:4, .errorhandling = "remove") %dopar% {
+    foreach::foreach(i = 1:5, .errorhandling = "remove") %dopar% {
       if (i == 3 || i == 4) {
         randomObject
       }
@@ -52,23 +48,21 @@ test_that("Remove error handling test", {
       i
     }
 
-  res
+  res <- unname(res)
 
-  testthat::expect_equal(length(res), 2)
+  testthat::expect_equal(res, list(1, 2, 5))
 })
 
 test_that("Pass error handling test", {
-  testthat::skip("Live test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
+  settings <- getSettings()
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
+
+  settings$clusterConfig$poolId <- "error-handling-test"
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   '%dopar%' <- foreach::'%dopar%'
@@ -88,17 +82,16 @@ test_that("Pass error handling test", {
 })
 
 test_that("Stop error handling test", {
-  testthat::skip("Live test")
+  testthat::skip("Manual Test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
+  settings <- getSettings()
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
+
+  settings$clusterConfig$poolId <- "error-handling-test"
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   '%dopar%' <- foreach::'%dopar%'

tests/testthat/test-foreach-options.R

@@ -0,0 +1,41 @@
+context("foreach options test")
+test_that("chunksize", {
+  testthat::skip_on_travis()
+  source("utility.R")
+  settings <- getSettings()
+
+  # set your credentials
+  doAzureParallel::setCredentials(settings$credentials)
+
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
+  doAzureParallel::registerDoAzureParallel(cluster)
+
+  '%dopar%' <- foreach::'%dopar%'
+  res <-
+    foreach::foreach(i = 1:10,
+                     .options.azure = list(chunkSize = 3)) %dopar% {
+                       i
+                     }
+
+  testthat::expect_equal(length(res),
+                         10)
+
+  for (index in 1:10) {
+    testthat::expect_equal(res[[index]],
+                           index)
+  }
+
+  res <-
+    foreach::foreach(i = 1:2,
+                     .options.azure = list(chunkSize = 2)) %dopar% {
+                       i
+                     }
+
+  testthat::expect_equal(length(res),
+                         2)
+
+  for (index in 1:2) {
+    testthat::expect_equal(res[[index]],
+                           index)
+  }
+})

tests/testthat/test-live.R

@@ -1,18 +1,16 @@
+context("Integration Test")
+
 # Run this test for users to make sure the core features
 # of doAzureParallel are still working
-context("live scenario test")
+test_that("simple foreach 1 to 4", {
-test_that("Basic scenario test", {
-  testthat::skip("Live test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  source("utility.R")
-  clusterFileName <- "cluster.json"
+  settings <- getSettings()
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
 
   # set your credentials
-  doAzureParallel::setCredentials(credentialsFileName)
+  doAzureParallel::setCredentials(settings$credentials)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
+
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   '%dopar%' <- foreach::'%dopar%'
@@ -21,37 +19,8 @@ test_that("Basic scenario test", {
       i
     }
 
-  res
+  res <- unname(res)
 
   testthat::expect_equal(length(res), 4)
-  testthat::expect_equal(res, list(2, 2, 2, 2))
+  testthat::expect_equal(res, list(1, 2, 3, 4))
-})
-
-test_that("Chunksize Test", {
-  testthat::skip("Live test")
-  testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
-  clusterFileName <- "cluster.json"
-
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
-  doAzureParallel::generateClusterConfig(clusterFileName)
-
-  doAzureParallel::setCredentials(credentialsFileName)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
-  doAzureParallel::registerDoAzureParallel(cluster)
-
-  '%dopar%' <- foreach::'%dopar%'
-  res <-
-    foreach::foreach(i = 1:10,
-                     .options.azure = list(chunkSize = 3)) %dopar% {
-      i
-    }
-
-  testthat::expect_equal(length(res),
-                         10)
-
-  for (i in 1:10) {
-    testthat::expect_equal(res[[i]],
-                           i)
-  }
 })

tests/testthat/test-local-merge.R

@@ -2,16 +2,16 @@
 # of doAzureParallel are still working
 context("merge job result locally test")
 test_that("merge job result locally test", {
-  testthat::skip("merge job result locally test")
   testthat::skip_on_travis()
-  credentialsFileName <- "credentials.json"
+  testthat::skip("Skipping merge job locally")
-  clusterFileName <- "cluster.json"
+  source("utility.R")
+  settings <- gettingSettings()
+  settings <- getSettings()
 
-  doAzureParallel::generateCredentialsConfig(credentialsFileName)
+  # set your credentials
-  doAzureParallel::generateClusterConfig(clusterFileName)
+  doAzureParallel::setCredentials(settings$credentials)
 
-  doAzureParallel::setCredentials(credentialsFileName)
+  cluster <- doAzureParallel::makeCluster(settings$clusterConfig)
-  cluster <- doAzureParallel::makeCluster(clusterFileName)
   doAzureParallel::registerDoAzureParallel(cluster)
 
   setChunkSize(2)
@@ -37,6 +37,4 @@ test_that("merge job result locally test", {
     testthat::expect_equal(res[[i]],
                            i)
   }
-
-  stopCluster(cluster)
 })

tests/testthat/test-long-running-job.R

@@ -43,7 +43,6 @@ test_that("Long Running Job Test", {
 
   # get job result
   jobResult <- doAzureParallel::getJobResult(jobId)
-  doAzureParallel::stopCluster(cluster)
 
   # verify the job result is correct
   testthat::expect_equal(length(jobResult),

tests/testthat/test-package-installation-bioc.R

@@ -113,6 +113,4 @@ test_that("pool multiple bioconductor package install Test", {
                          list(
                            c(TRUE, TRUE, TRUE),
                            c(TRUE, TRUE, TRUE)))
-
-  doAzureParallel::stopCluster(cluster)
 })

tests/testthat/test-package-installation-github.R

@@ -116,6 +116,4 @@ test_that("pool multiple github package install Test", {
                          list(c(TRUE, TRUE, TRUE),
                               c(TRUE, TRUE, TRUE),
                               c(TRUE, TRUE, TRUE)))
-
-  doAzureParallel::stopCluster(cluster)
 })

tests/testthat/test-package-installation.R

@@ -1,4 +1,4 @@
-context("package installation")
+context("Package Command Line Tests")
 test_that("successfully create cran job package command line", {
   jobInstallation <-
     getJobPackageInstallationCommand("cran", c("hts", "lubridate", "tidyr", "dplyr"))

tests/testthat/unit-tests.R

@@ -1,7 +1,6 @@
+context("Unit Tests")
 if (requireNamespace("nycflights13", quietly = TRUE)) {
-  context("hasDataSet function")
+  test_that("hasDataSet Test - Contains Data", {
-
-  test_that("Arguments contains data set", {
     byCarrierList <- split(nycflights13::flights, nycflights13::flights$carrier)
     it <- iterators::iter(byCarrierList)
     argsList <- as.list(it)
@@ -11,7 +10,7 @@ if (requireNamespace("nycflights13", quietly = TRUE)) {
     expect_equal(hasDataSet, TRUE)
   })
 
-  test_that("Arguments does not contain data set", {
+  test_that("hasDataSet Test - Contains no Data Set", {
     args <- seq(1:10)
     it <- iterators::iter(args)
     argsList <- as.list(it)
@@ -20,5 +19,4 @@ if (requireNamespace("nycflights13", quietly = TRUE)) {
 
     expect_equal(hasDataSet, FALSE)
   })
-
 }

tests/testthat/utility.R

@@ -0,0 +1,49 @@
+getSettings <- function(dedicatedMin = 2,
+                        dedicatedMax = 2,
+                        lowPriorityMin = 2,
+                        lowPriorityMax = 2,
+                        poolName = "test-pool"){
+  list(
+    credentials = list(
+      "sharedKey" = list(
+        "batchAccount" = list(
+          "name" = Sys.getenv("BATCH_ACCOUNT_NAME"),
+          "key" = Sys.getenv("BATCH_ACCOUNT_KEY"),
+          "url" = Sys.getenv("BATCH_ACCOUNT_URL")
+        ),
+        "storageAccount" = list(
+          "name" = Sys.getenv("STORAGE_ACCOUNT_NAME"),
+          "key" = Sys.getenv("STORAGE_ACCOUNT_KEY"),
+          "endpointSuffix" = "core.windows.net"
+        )
+      ),
+      "githubAuthenticationToken" = "",
+      "dockerAuthentication" = list("username" = "",
+                                    "password" = "",
+                                    "registry" = "")
+    ),
+    clusterConfig = list(
+      "name" = poolName,
+      "vmSize" = "Standard_D2_v2",
+      "maxTasksPerNode" = 1,
+      "poolSize" = list(
+        "dedicatedNodes" = list(
+          "min" = dedicatedMin,
+          "max" = dedicatedMax
+        ),
+        "lowPriorityNodes" = list(
+          "min" = lowPriorityMin,
+          "max" = lowPriorityMax
+        ),
+        "autoscaleFormula" = "QUEUE"
+      ),
+      "containerImage" = "rocker/tidyverse:latest",
+      "rPackages" = list(
+        "cran" = list(),
+        "github" = list(),
+        "bioconductor" = list()
+      ),
+      "commandLine" = list()
+    )
+  )
+}