Merge branch 'dev'

* dev: Bump version number to 0.2.3 Document deprecated functions. Remove references to deprecated functions. Remove azToken from all functions #50 Fix roxygen markdown links #57
microsoft · May 21, 2017 · b9753ca · b9753ca
2 parents 3890565 + 4c50cd1
commit b9753ca
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diff --git a/AzureSMR.Rproj b/AzureSMR.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,8 +5,8 @@ Description: Helps users to manage Azure Services and objects from within an
     Machines and HDInsight (Spark, Hive). Requires that an Active Directory
     application and service principal has been configured to access Azure resources.
 Type: Package
-Version: 0.2.2
-Date: 2016-12-22
+Version: 0.2.3
+Date: 2017-05-21
 Authors@R: c(
       person(family="Microsoft Corporation", role="cph"),
       person("Alan", "Weaver", role=c("aut", "cre"), email="[email protected]"),

diff --git a/R/AzureAuthenticate.R b/R/AzureAuthenticate.R
@@ -6,8 +6,8 @@
 #' @note See \url{https://azure.microsoft.com/en-us/documentation/articles/resource-group-create-service-principal-portal/} for instructions to set up an Active Directory application
 #' @references \url{https://azure.microsoft.com/en-us/documentation/articles/resource-group-create-service-principal-portal/}
 #'
-#' @return Retunrs Azure Tokem and sets AzureContext Token
-#' @family Resources
+#' @return Returns Azure token and sets AzureContext token
+#' @family Azure resource functions
 #' 
 #' @importFrom utils URLencode
 #' @export
@@ -65,11 +65,11 @@ azureAuthenticate <- function(azureActiveContext, tenantID, clientID, authKey, v
 
 
 
-#' Check the timestamp of a Token and Renew if needed.
+#' Check the timestamp of a token and renew if needed.
 #'
 #' @inheritParams setAzureContext
 #' @inheritParams azureAuthenticate
-#' @family Resources
+#' @family Azure resource functions
 #' @export
 azureCheckToken <- function(azureActiveContext) {
   if (missing(azureActiveContext) || is.null(azureActiveContext)) return(NA)

diff --git a/R/AzureBlob.R b/R/AzureBlob.R
@@ -5,13 +5,13 @@
 #' @inheritParams azureAuthenticate
 #' @inheritParams azureSAGetKey
 #'
-#' @param maxresults Optional. Specifies the maximum number of blobs to return, including all BlobPrefix elements. If the request does not specify maxresults or specifies a value greater than 5,000, the server will return up to 5,000 items.  Setting maxresults to a value less than or equal to zero results in error response code 400 (Bad Request).
+#' @param maxresults Optional. Specifies the maximum number of blobs to return, including all BlobPrefix elements. If the request does not specify maxresults or specifies a value greater than 5,000, the server will return up to 5,000 items.  Setting `maxresults` to a value less than or equal to zero results in error response code 400 (Bad Request).
 #' @param prefix Optional. Filters the results to return only blobs whose names begin with the specified prefix.
 #' @param delimiter Optional. When the request includes this parameter, the operation returns a BlobPrefix element in the response body that acts as a placeholder for all blobs whose names begin with the same substring up to the appearance of the delimiter character. The delimiter may be a single character or a string.
 #' @param marker Optional. A string value that identifies the portion of the list to be returned with the next list operation. The operation returns a marker value within the response body if the list returned was not complete. The marker value may then be used in a subsequent call to request the next set of list items.  The marker value is opaque to the client.
 #'
-#' @return Returns a data frame. This data frame has an attribute called "marker" that can be used with the "marker" argument to return the next set of values.
-#' @family blob store functions
+#' @return Returns a data frame. This data frame has an attribute called `marker` that can be used with the `marker` argument to return the next set of values.
+#' @family Blob store functions
 #' @export
 azureListStorageBlobs <- function(azureActiveContext, storageAccount, storageKey,
                              container, resourceGroup, maxresults, prefix, delimiter, marker, verbose = FALSE) {
@@ -117,7 +117,7 @@ azureListStorageBlobs <- function(azureActiveContext, storageAccount, storageKey
 #' @param directory Blob store directory to list for content
 #' @param recursive If TRUE, list blob store directories recursively
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 azureBlobLS <- function(azureActiveContext, directory, recursive = FALSE,
                         storageAccount, storageKey, container, resourceGroup, verbose = FALSE) {
@@ -275,9 +275,9 @@ azureBlobLS <- function(azureActiveContext, directory, recursive = FALSE,
 #' @inheritParams azureSAGetKey
 #' @inheritParams azureBlobLS
 
-#' @param type String, either "text" or "raw". Passed to `httr::content`
+#' @param type String, either "text" or "raw". Passed to [httr::content()]
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 
 azureGetBlob <- function(azureActiveContext, blob, directory, type = "text",
@@ -379,7 +379,7 @@ azureGetBlob <- function(azureActiveContext, blob, directory, type = "text",
 #' @param contents - Object or value to store
 #' @param file - Local filename to store in Azure blob
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 azurePutBlob <- function(azureActiveContext, blob, contents = "", file = "",
                          directory, storageAccount, storageKey,
@@ -487,7 +487,7 @@ azurePutBlob <- function(azureActiveContext, blob, contents = "", file = "",
 #' @inheritParams azureSAGetKey
 #' @inheritParams azurePutBlob
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 azureBlobFind <- function(azureActiveContext, file, storageAccount, storageKey,
                           container, resourceGroup, verbose = FALSE) {
@@ -551,7 +551,7 @@ azureBlobFind <- function(azureActiveContext, file, storageAccount, storageKey,
 #' @inheritParams azureBlobLS
 #' @inheritParams azurePutBlob
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 azureBlobCD <- function(azureActiveContext, directory, container, file,
                         storageAccount, storageKey, resourceGroup, verbose = FALSE) {
@@ -640,7 +640,7 @@ azureBlobCD <- function(azureActiveContext, directory, container, file,
 #' @inheritParams azureSAGetKey
 #' @inheritParams azureBlobLS
 #'
-#' @family blob store functions
+#' @family Blob store functions
 #' @export
 
 azureDeleteBlob <- function(azureActiveContext, blob, directory,

diff --git a/R/AzureContainer.R b/R/AzureContainer.R
@@ -4,29 +4,26 @@
 #' @inheritParams azureAuthenticate
 #' @inheritParams azureSAGetKey
 
-#' @family container functions
+#' @family Container functions
 #'
 #' @export
 azureListStorageContainers <- function(azureActiveContext, storageAccount, storageKey,
-                                  resourceGroup, azToken, subscriptionID, verbose = FALSE) {
+                                  resourceGroup, subscriptionID, verbose = FALSE) {
   azureCheckToken(azureActiveContext)
 
   if (missing(subscriptionID)) {
-    SUBIDI <- azureActiveContext$subscriptionID
-  } else (SUBIDI <- subscriptionID)
-  if (missing(azToken)) {
-    ATI <- azureActiveContext$Token
-  } else (ATI <- azToken)
+    subscriptionID <- azureActiveContext$subscriptionID
+  } else (subscriptionID <- subscriptionID)
   if (missing(resourceGroup)) {
-    RGI <- azureActiveContext$resourceGroup
-  } else (RGI <- resourceGroup)
+    resourceGroup <- azureActiveContext$resourceGroup
+  } else (resourceGroup <- resourceGroup)
   if (missing(storageAccount)) {
     SAI <- azureActiveContext$storageAccount
   } else (SAI <- storageAccount)
   verbosity <- if (verbose)
     httr::verbose(TRUE) else NULL
 
-  if (length(RGI) < 1) {
+  if (length(resourceGroup) < 1) {
     stop("Error: No resourceGroup provided: Use resourceGroup argument or set in AzureContext")
   }
   if (length(SAI) < 1) {
@@ -36,7 +33,7 @@ azureListStorageContainers <- function(azureActiveContext, storageAccount, stora
   STK <- if (length(azureActiveContext$storageAccountK) < 1 ||
       SAI != azureActiveContext$storageAccountK ||
       length(azureActiveContext$storageKey) < 1) {
-    azureSAGetKey(azureActiveContext, resourceGroup = RGI, storageAccount = SAI)
+    azureSAGetKey(azureActiveContext, resourceGroup = resourceGroup, storageAccount = SAI)
   } else {
     azureActiveContext$storageKey
   }
@@ -87,7 +84,7 @@ azureListStorageContainers <- function(azureActiveContext, storageAccount, stora
   }
 
   azureActiveContext$storageAccount <- SAI
-  azureActiveContext$resourceGroup  <- RGI
+  azureActiveContext$resourceGroup  <- resourceGroup
   azureActiveContext$storageKey     <- STK
 
   data.frame(
@@ -109,22 +106,19 @@ azureListStorageContainers <- function(azureActiveContext, storageAccount, stora
 #' @inheritParams azureAuthenticate
 #' @inheritParams azureSAGetKey
 
-#' @family container functions
+#' @family Container functions
 #'
 #' @export
 azureCreateStorageContainer <- function(azureActiveContext, container, storageAccount,
-                                   storageKey, resourceGroup, azToken, subscriptionID, verbose = FALSE) {
+                                   storageKey, resourceGroup, subscriptionID, verbose = FALSE) {
   # azureCheckToken(azureActiveContext)
 
   if (missing(subscriptionID)) {
-    SUBIDI <- azureActiveContext$subscriptionID
-  } else (SUBIDI <- subscriptionID)
-  if (missing(azToken)) {
-    ATI <- azureActiveContext$Token
-  } else (ATI <- azToken)
+    subscriptionID <- azureActiveContext$subscriptionID
+  } else (subscriptionID <- subscriptionID)
   if (missing(resourceGroup)) {
-    RGI <- azureActiveContext$resourceGroup
-  } else (RGI <- resourceGroup)
+    resourceGroup <- azureActiveContext$resourceGroup
+  } else (resourceGroup <- resourceGroup)
   if (missing(storageAccount)) {
     SAI <- azureActiveContext$storageAccount
   } else (SAI <- storageAccount)
@@ -137,14 +131,14 @@ azureCreateStorageContainer <- function(azureActiveContext, container, storageAc
   verbosity <- if (verbose)
     httr::verbose(TRUE) else NULL
 
-  if (length(RGI) < 1) {
+  if (length(resourceGroup) < 1) {
     stop("Error: No resourceGroup provided: Use resourceGroup argument or set in AzureContext")
   }
   if (length(SAI) < 1) {
     stop("Error: No storageAccount provided: Use storageAccount argument or set in AzureContext")
   }
 
-  STK <- refreshStorageKey(azureActiveContext, SAI, RGI)
+  STK <- refreshStorageKey(azureActiveContext, SAI, resourceGroup)
 
   if (length(STK) < 1) {
     stop("Error: No storageKey provided: Use storageKey argument or set in AzureContext")
@@ -165,7 +159,7 @@ azureCreateStorageContainer <- function(azureActiveContext, container, storageAc
 
   azureActiveContext$container <- container
   azureActiveContext$storageAccount <- SAI
-  azureActiveContext$resourceGroup <- RGI
+  azureActiveContext$resourceGroup <- resourceGroup
 
   URL <- paste("http://", SAI, ".blob.core.windows.net/", container,
                "?restype=container", sep = "")
@@ -203,22 +197,19 @@ azureCreateStorageContainer <- function(azureActiveContext, container, storageAc
 #' @inheritParams azureAuthenticate
 #' @inheritParams azureSAGetKey
 
-#' @family container functions
+#' @family Container functions
 #'
 #' @export
 azureDeleteStorageContainer <- function(azureActiveContext, container, storageAccount,
-                                   storageKey, resourceGroup, azToken, subscriptionID, verbose = FALSE) {
+                                   storageKey, resourceGroup, subscriptionID, verbose = FALSE) {
   azureCheckToken(azureActiveContext)
 
   if (missing(subscriptionID)) {
-    SUBIDI <- azureActiveContext$subscriptionID
-  } else (SUBIDI <- subscriptionID)
-  if (missing(azToken)) {
-    ATI <- azureActiveContext$Token
-  } else (ATI <- azToken)
+    subscriptionID <- azureActiveContext$subscriptionID
+  } else (subscriptionID <- subscriptionID)
   if (missing(resourceGroup)) {
-    RGI <- azureActiveContext$resourceGroup
-  } else (RGI <- resourceGroup)
+    resourceGroup <- azureActiveContext$resourceGroup
+  } else (resourceGroup <- resourceGroup)
   if (missing(storageAccount)) {
     SAI <- azureActiveContext$storageAccount
   } else (SAI <- storageAccount)
@@ -233,14 +224,14 @@ azureDeleteStorageContainer <- function(azureActiveContext, container, storageAc
 
   CNTR <- container
 
-  if (length(RGI) < 1) {
+  if (length(resourceGroup) < 1) {
     stop("Error: No resourceGroup provided: Use resourceGroup argument or set in AzureContext")
   }
   if (length(SAI) < 1) {
     stop("Error: No storageAccount provided: Use storageAccount argument or set in AzureContext")
   }
 
-  STK <- refreshStorageKey(azureActiveContext, SAI, RGI)
+  STK <- refreshStorageKey(azureActiveContext, SAI, resourceGroup)
   if (length(STK) < 1) {
     stop("Error: No storageKey provided: Use storageKey argument or set in AzureContext")
   }
@@ -258,7 +249,7 @@ azureDeleteStorageContainer <- function(azureActiveContext, container, storageAc
 
   azureActiveContext$container <- CNTR
   azureActiveContext$storageAccount <- SAI
-  azureActiveContext$resourceGroup <- RGI
+  azureActiveContext$resourceGroup <- resourceGroup
   SIG <- getSig(azureActiveContext, url = URL, verb = "DELETE", key = STK,
                 storageAccount = SAI,
                 CMD = paste0(CNTR, "\nrestype:container"), dateSig = D1)

diff --git a/R/AzureContextObject.R b/R/AzureContextObject.R
@@ -1,66 +1,57 @@
 #' Create an AzureContext.
 #'
-#' Create a container (azureContextObject) for holding variables used by the AzureSMR package.  If the Tenant ID, Client ID and Authenication Key are provided the function will attempt to authenticate the session.
+#' Create a container (azureContextObject) for holding variables used by the `AzureSMR` package.  If the Tenant ID, Client ID and Authenication Key are provided the function will attempt to authenticate the session.
 #'
 #' See the Azure documentation (\url{https://azure.microsoft.com/en-us/documentation/articles/resource-group-create-service-principal-portal/}) for information to configure an Active Directory application.
 #'
 #' @inheritParams setAzureContext
 #' @family azureActiveContext functions
 #'
-#' @seealso `setAzureContext`
+#' @seealso [setAzureContext()]
 #' @export
 createAzureContext <- function(tenantID, clientID, authKey){
   azEnv <- new.env(parent = globalenv())
   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 <- "?"
+  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 <- "?"
 
   if (!missing(tenantID) && !missing(clientID) && !missing(authKey) )
       azureAuthenticate(azEnv,tenantID, clientID, authKey)
   return(azEnv)
 }
 
-#' Dumps out the contents of the AzureContext.
-#'
-#' @inheritParams setAzureContext
-#' @export
-dumpAzureContext <- function(azureActiveContext){
-  .Deprecated("str")
-  str(azureActiveContext)
-}
-
 #' Updates azureActiveContext object.
 #'
-#' Updates the value of an azureActiveContext object, created by `createAzureContext`
+#' Updates the value of an azureActiveContext object, created by [createAzureContext()]
 #'
 #' @param azureActiveContext A container used for caching variables used by AzureSMR
 #' @param tenantID The Tenant ID provided during creation of the Active Directory application / service principal
 #' @param clientID The Client ID provided during creation of the Active Directory application / service principal
 #' @param authKey The Authentication Key provided during creation of the Active Directory application / service principal
-#' @param subscriptionID Set the subscriptionID.  This is obtained automatically by `azureAuthenticate` when only a single subscriptionID is available via Active Directory
-#' @param azToken Azure authentication token, obtained by `azureAuthenticate`
+#' @param subscriptionID Set the subscriptionID.  This is obtained automatically by [azureAuthenticate()] when only a single subscriptionID is available via Active Directory
+#' @param azToken Azure authentication token, obtained by [azureAuthenticate()]
 #' @param resourceGroup Name of the resource group
 #' @param vmName Name of the virtual Machine
 #' @param storageAccount Name of the azure storage account
 #' @param storageKey Storage key associated with storage account
 #' @param blob Blob name
-#' @param clustername Cluster name, used for HDI and Spark clusters. See `azureCreateHDI`
-#' @param sessionID Spark sessionID. See `azureSparkCMD`
+#' @param clustername Cluster name, used for HDI and Spark clusters. See [azureCreateHDI()]
+#' @param sessionID Spark sessionID. See [azureSparkCMD()]
 #' @param hdiAdmin HDInsight admin username
 #' @param hdiPassword  HDInsight admin password
-#' @param container Storage container name. See `azureListStorageContainers`
+#' @param container Storage container name. See [azureListStorageContainers()]
 #' @param kind HDinsight kind: "hadoop","spark" or "pyspark"
 #'
 #' @family azureActiveContext functions
 #' @export
-setAzureContext <- function(azureActiveContext,tenantID, clientID, authKey,azToken,
-                            subscriptionID,resourceGroup,
-                            storageKey,storageAccount,
-                            container,blob,
+setAzureContext <- function(azureActiveContext, tenantID, clientID, authKey, azToken,
+                            subscriptionID, resourceGroup,
+                            storageKey, storageAccount,
+                            container, blob,
                             vmName,
-                            hdiAdmin,hdiPassword ,clustername,kind,sessionID)
+                            hdiAdmin, hdiPassword, clustername, kind, sessionID)
 {
   if (!missing(tenantID)) azureActiveContext$tenantID <- tenantID
   if (!missing(clientID)) azureActiveContext$clientID <- clientID