Merge branch 'dev'

* dev:
  Rename addins
  Bug fix in progress bar
  Create RStudio addins #72
  Add function to retrieve status of all VMs #72
  Fix merge errors
  Update tests #70
  Export read.AzureSMR.config() and enable reading settings file in createAzureContext() #70
  Remove spurious reference to storageAccountK
  Add resourceGroup argument when polling for script actions #58
  Fix  example_azureCreateHDI.R - Remove DEBUG flag, set legal password
  test-6-ARM.R - Changed Deploy 2 to a quicker VNET build.

DESCRIPTION

@@ -23,7 +23,11 @@ Imports:
     jsonlite,
     XML,
     base64enc,
-    digest
+    digest,
+	shiny (>= 0.13),
+	miniUI (>= 0.1.1),
+	rstudioapi (>= 0.5),
+	DT
 Depends:
     R(>= 3.0.0)
 Suggests:

NAMESPACE

@@ -24,6 +24,7 @@ export(azureDeleteVM)
 export(azureDeletestorageAccount)
 export(azureDeployStatus)
 export(azureDeployTemplate)
+export(azureGetAllVMstatus)
 export(azureGetBlob)
 export(azureHDIConf)
 export(azureHiveSQL)
@@ -57,7 +58,10 @@ export(azureVMStatus)
 export(createAzureContext)
 export(dumpAzureContext)
 export(is.azureActiveContext)
+export(read.AzureSMR.config)
 export(setAzureContext)
+importFrom(DT,dataTableOutput)
+importFrom(DT,renderDataTable)
 importFrom(XML,htmlParse)
 importFrom(XML,xmlValue)
 importFrom(XML,xpathApply)
@@ -78,6 +82,12 @@ importFrom(httr,headers)
 importFrom(httr,http_status)
 importFrom(httr,status_code)
 importFrom(jsonlite,fromJSON)
+importFrom(miniUI,gadgetTitleBar)
+importFrom(miniUI,miniContentPanel)
+importFrom(miniUI,miniPage)
+importFrom(shiny,observeEvent)
+importFrom(shiny,paneViewer)
+importFrom(shiny,runGadget)
 importFrom(utils,URLencode)
 importFrom(utils,browseURL)
 importFrom(utils,ls.str)

R/AzureContextObject.R

@@ -7,19 +7,30 @@
 #' @inheritParams setAzureContext
 #' @family azureActiveContext functions
 #'
-#' @seealso [setAzureContext()], [azureAuthenticate()]
+#' @seealso [setAzureContext()], [azureAuthenticate()], [read.AzureSMR.config)]
 #' @return An `azureActiveContext` object
 #' @export
-createAzureContext <- function(tenantID, clientID, authKey){
+createAzureContext <- function(tenantID, clientID, authKey, configFile){
   azEnv <- new.env(parent = emptyenv())
   azEnv <- as.azureActiveContext(azEnv)
 
-  if (!missing(tenantID)) azEnv$tenantID <- tenantID else azEnv$tenantID <- "?"
-  if (!missing(clientID)) azEnv$clientID <- clientID else azEnv$tenantID <- "?"
-  if (!missing(authKey))  azEnv$authKey <- authKey   else azEnv$tenantID <- "?"
+  list2env(
+    list(tenantID = "", clientID = "", authKey = ""),
+    envir = azEnv
+  )
+  if (!missing(configFile)) {
+    config <- read.AzureSMR.config(configFile)
+    list2env(config, envir = azEnv)
+    azureAuthenticate(azEnv)
+  } else {
+    if (!missing(tenantID)) azEnv$tenantID <- tenantID
+    if (!missing(clientID)) azEnv$clientID <- clientID
+    if (!missing(authKey)) azEnv$authKey <- authKey
+    if (!missing(tenantID) && !missing(clientID) && !missing(authKey)) {
+      azureAuthenticate(azEnv)
+    }
+  }
 
-  if (!missing(tenantID) && !missing(clientID) && !missing(authKey) )
-      azureAuthenticate(azEnv,tenantID, clientID, authKey)
   return(azEnv)
 }
 

R/AzureHDI.R

@@ -457,8 +457,11 @@ azureRunScriptAction <- function(azureActiveContext, scriptname, scriptURL,
   stopWithAzureError(r)
 
   azureActiveContext$clustername <- clustername
+  azureActiveContext$resourceGroup <- resourceGroup
+
+
   message("Accepted")
-  if (wait) pollStatusScriptAction(azureActiveContext, scriptname = scriptname)
+  if (wait) pollStatusScriptAction(azureActiveContext, scriptname = scriptname, resourceGroup = resourceGroup)
   return(TRUE)
 }
 
@@ -497,7 +500,7 @@ azureScriptActionHistory <- function(azureActiveContext, resourceGroup,
   r <- GET(URL, azureApiHeaders(azToken), verbosity)
   stopWithAzureError(r)
 
-  rc <- content(r)$value
+  rc <- content(r, bigint_as_char = TRUE)$value
   if (length(rc) == 0) {
     message("No script action history found")
   }

R/AzureStorageAccount.R

@@ -64,7 +64,6 @@ azureSAGetKey <- function(azureActiveContext, storageAccount,
   rl <- content(r, "text", encoding = "UTF-8")
   df <- fromJSON(rl)
   azureActiveContext$storageAccount  <- storageAccount
-  azureActiveContext$storageAccountK <- storageAccount
   azureActiveContext$resourceGroup   <- resourceGroup
   azureActiveContext$storageKey <- df$keys$value[1]
 

R/AzureVM.R

@@ -50,6 +50,41 @@ azureListVM <- function(azureActiveContext, resourceGroup, location, subscriptio
   return(dfn)
 }
 
+#' List the status of every virtual machine in the azure active context.
+#'
+#' First queries the azure active context for all visible resources, then sequentially queries the status of all virtuam machines.
+#'
+#' @inheritParams setAzureContext
+#' @inheritParams azureListAllResources
+#'
+#' @family Virtual machine functions
+#' @export
+azureGetAllVMstatus <- function(azureActiveContext) {
+  res <- azureListAllResources(azureActiveContext)
+  vms <- res[res$type == "Microsoft.Compute/virtualMachines",]
+  n <- nrow(vms)
+  pb <- txtProgressBar(min = 0, max = n, style = 3)
+  on.exit(close(pb))
+  z <- lapply(seq_len(n), function(i) {
+    setTxtProgressBar(pb, i)
+    z <- tryCatch(azureVMStatus(azureActiveContext,
+                  resourceGroup = vms$resourceGroup[i],
+                  vmName = vms$name[i],
+                  subscriptionID = vms$subscriptionID[i]
+                  ), error = function(e) e)
+    z <- if (inherits(z, "error")) NA_character_ else z
+    data.frame(
+      name = vms$name[i],
+      resourceGroup = vms$resourceGroup[i],
+      subscriptionID = vms$subscriptionID[i],
+      provisioning = gsub("Provisioning (.*?), .*$", "\\1", z),
+      status = gsub(".*?, VM (.*)$", "\\1", z)
+    )
+  })
+  do.call(rbind, z)
+}
+
+
 
 #' Start a Virtual Machine.
 #'

R/addins.R

@@ -0,0 +1,45 @@
+# this is a template to view a DT object
+# @param data.frame
+# @param title Text to display in pane title
+
+#' @importFrom miniUI miniPage gadgetTitleBar miniContentPanel
+#' @importFrom DT dataTableOutput renderDataTable
+#' @importFrom shiny observeEvent paneViewer runGadget
+dataTableViewer <- function(x, title = "") {
+
+  ui <- miniPage(
+    gadgetTitleBar(title),
+    miniContentPanel(
+      DT::dataTableOutput("dt", height = "100%")
+    )
+  )
+
+  server <- function(input, output, session) {
+    output$dt <- DT::renderDataTable(x)
+
+    observeEvent(input$done, stopApp())
+  }
+
+  viewer <- paneViewer()
+  runGadget(ui, server, viewer = viewer)
+
+}
+
+
+addinListAllResources <- function() {
+  settingsfile <- getOption("AzureSMR.config")
+  assert_that(file.exists(settingsfile))
+  az <- createAzureContext(configFile = settingsfile)
+  z <- azureListAllResources(az)
+  z$id <- NULL
+  dataTableViewer(z, title = "All resources")
+}
+
+addinGetAllVMstatus <- function() {
+  settingsfile <- getOption("AzureSMR.config")
+  assert_that(file.exists(settingsfile))
+  az <- createAzureContext(configFile = settingsfile)
+  z <- azureGetAllVMstatus(az)
+  z$id <- NULL
+  dataTableViewer(z, title = "All virtual machines")
+}

R/config.R

@@ -1,14 +1,17 @@
-# Reads settings from configuration file in JSON format.
+#' Reads settings from configuration file in JSON format.
+#'
+#' @param config location of file that contains configuration in JSON format
+#' @export
 #
-# @param config location of file that contains configuration in JSON format
-#
-read.AzureSMR.config <- function(config = getOption("AzureSMR.config")){
-  z <- tryCatch(fromJSON(file(config)),
+read.AzureSMR.config <- function(configFile = getOption("AzureSMR.config")) {
+  assert_that(is.character(configFile))
+  assert_that(file.exists(configFile))
+  z <- tryCatch(fromJSON(file(configFile)),
                 error = function(e)e
   )
   # Error check the settings file for invalid JSON
   if(inherits(z, "error")) {
-    msg <- sprintf("Your config file contains invalid json", config)
+    msg <- sprintf("Your config file contains invalid json", configFile)
     msg <- paste(msg, z$message, sep = "\n\n")
     stop(msg, call. = FALSE)
   }

R/internal.R

@@ -161,9 +161,8 @@ extractStorageAccount    <- function(x) gsub(".*?/storageAccounts/(.*?)(/.*)*$",
 
 
 refreshStorageKey <- function(azureActiveContext, storageAccount, resourceGroup){
-  if (length(azureActiveContext$storageAccountK) < 1 ||
-      storageAccount != azureActiveContext$storageAccountK ||
-      length(azureActiveContext$storageKey) <1
+  if (storageAccount != azureActiveContext$storageAccount ||
+      length(azureActiveContext$storageKey) == 0
   ) {
     message("Fetching Storage Key..")
     azureSAGetKey(azureActiveContext, resourceGroup = resourceGroup, storageAccount = storageAccount)

R/pollStatus.R

@@ -126,15 +126,16 @@ pollStatusHDI <- function(azureActiveContext, clustername) {
 }
 
 
-pollStatusScriptAction <- function(azureActiveContext, scriptname) {
+pollStatusScriptAction <- function(azureActiveContext, scriptname, resourceGroup) {
 
   message("Script action request submitted: ", Sys.time())
   message("Key: A - accepted, (.) - in progress, S - succeeded, E - error, F - failed")
   iteration <- 0
   waiting <- TRUE
   while (iteration < 500 && waiting) {
 
-    status <- azureScriptActionHistory(azureActiveContext)
+    status <- azureScriptActionHistory(azureActiveContext, 
+      resourceGroup = resourceGroup)
     idx <- which(sapply(status, "[[", "name") == scriptname)[1]
     summary <- status[[idx]]$status
     rc <- switch(tolower(summary),

R/zzz.R

@@ -1,5 +1,6 @@
-AzureSMR.config.default <- "~/.azureml/settings.json"
+AzureSMR.config.default <- "~/.azuresmr/config.json"
 
-.onAttach <- function(libname, pkgname){
+.onAttach <- function(libname, pkgname) {
+  if (is.null(getOption("AzureSMR.config")))
   options(AzureSMR.config = AzureSMR.config.default)
 }

inst/examples/example_azureCreateHDI.R

@@ -1,16 +1,12 @@
 \dontrun{
-library(AzureSMR)
-
-  azureCreateHDI(context, 
-                 resourceGroup = RG, 
+azureCreateHDI(context,
+                 resourceGroup = RG,
                  clustername = "smrhdi", # only low case letters, digit, and dash.
                  storageAccount = "smrhdisa",
-                 adminUser = "hdiadmin", 
+                 adminUser = "hdiadmin",
                  adminPassword = "AzureSMR_password123",
-                 sshUser = "hdisshuser", 
+                 sshUser = "hdisshuser",
                  sshPassword = "AzureSMR_password123", # need at least digits.
-                 kind = "rserver", 
-                 debug = FALSE
+                 kind = "rserver"
   )
-
-}
+}

inst/rstudio/addins.dcf

@@ -0,0 +1,9 @@
+Name: Azure-resources
+Description: List all Azure resources.
+Binding: addinListAllResources
+Interactive: true
+
+Name: Azure-VM status
+Description: List the status of all virtual machines.
+Binding: addinGetAllVMstatus
+Interactive: true