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Feature/nationalcloud (#239)
* support national cloud * fix hardcoded domain name in createOutputFile * update rAzureBatch version etc * auto discovery of storage account endpoint suffix * styling fix * fix test failure * add back endpointSuffix for storage account * add storage account endpoint suffix to downloadBlob call * update docs
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‎DESCRIPTION‎

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@@ -17,7 +17,7 @@ Depends:
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foreach (>= 1.4.3),
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iterators (>= 1.0.8)
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Imports:
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rAzureBatch (>= 0.5.3),
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rAzureBatch (>= 0.5.7),
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jsonlite,
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rjson,
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xml2,
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caret,
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plyr,
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lintr
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Remotes: Azure/rAzureBatch@v0.5.6
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Remotes: Azure/rAzureBatch@v0.5.7
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RoxygenNote: 6.0.1

‎R/credentials.R‎

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@@ -22,7 +22,10 @@
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#' generateCredentialsConfig("test_config.json")
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#' generateCredentialsConfig("test_config.json", batchAccount = "testbatchaccount",
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#' batchKey = "test_batch_account_key", batchUrl = "http://testbatchaccount.azure.com",
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#' storageAccount = "teststorageaccount", storageKey = "test_storage_account_key")
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#' storageAccount = "teststorageaccount", storageKey = "test_storage_account_key",
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#' storageEndpointSuffix = "core.windows.net")
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#' supported storage account endpoint suffix: core.windows.net (default),
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#' core.chinacloudapi.cn, core.cloudapi.de, core.usgovcloudapi.net, etc.
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#' }
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#' @export
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generateCredentialsConfig <- function(fileName, ...) {
@@ -46,6 +49,11 @@ generateCredentialsConfig <- function(fileName, ...) {
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"storage_account_key",
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args$storageKey)
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storageSuffix <-
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ifelse(is.null(args$storageEndpointSuffix),
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"core.windows.net",
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args$storageEndpointSuffix)
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githubAuthenticationToken <-
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ifelse(is.null(args$githubAuthenticationToken),
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"",
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key = batchKey,
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url = batchUrl),
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storageAccount = list(name = storageName,
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key = storageKey),
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key = storageKey,
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endpointSuffix = storageEndpointSuffix),
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githubAuthenticationToken = githubAuthenticationToken,
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dockerAuthentication = list(username = dockerUsername,
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password = dockerPassword,

‎R/doAzureParallel.R‎

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@@ -272,7 +272,8 @@ setHttpTraffic <- function(value = FALSE) {
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assign(
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"inputs",
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list(name = storageCredentials$name,
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sasToken = sasToken),
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sasToken = sasToken,
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endpointSuffix = storageCredentials$endpointSuffix),
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.doAzureBatchGlobals
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)
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}
@@ -417,20 +418,33 @@ setHttpTraffic <- function(value = FALSE) {
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# Creating read-only SAS token blob resource file urls
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sasToken <- rAzureBatch::createSasToken("r", "c", id)
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workerScriptUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "worker.R", sasToken)
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "worker.R", sasToken, storageCredentials$endpointSuffix)
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mergerScriptUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "merger.R", sasToken)
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "merger.R", sasToken, storageCredentials$endpointSuffix)
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installGithubScriptUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name,
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id,
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"install_github.R",
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sasToken)
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sasToken,
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storageCredentials$endpointSuffix)
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installCranScriptUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "install_cran.R", sasToken)
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rAzureBatch::createBlobUrl(storageCredentials$name,
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id,
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"install_cran.R",
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sasToken,
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storageCredentials$endpointSuffix)
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installBioConductorScriptUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, id, "install_bioconductor.R", sasToken)
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rAzureBatch::createBlobUrl(storageCredentials$name,
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id,
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"install_bioconductor.R",
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sasToken,
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storageCredentials$endpointSuffix)
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jobCommonFileUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, id, jobFileName, sasToken)
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rAzureBatch::createBlobUrl(storageCredentials$name,
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id,
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jobFileName,
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sasToken,
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storageCredentials$endpointSuffix)
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requiredJobResourceFiles <- list(
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rAzureBatch::createResourceFile(url = workerScriptUrl, fileName = "worker.R"),
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paste0("result/", "merge-result.rds"),
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sasToken = sasToken,
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accountName = storageCredentials$name,
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endpointSuffix = storageCredentials$endpointSuffix,
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downloadPath = tempFile,
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overwrite = TRUE
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)
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azureStorageUrl <-
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paste0("http://",
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storageCredentials$name,
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".blob.core.windows.net/",
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sprintf(".blob.%s/", storageCredentials$endpointSuffix),
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id)
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staticHtml <- "<h1>Errors:</h1>"

‎R/helpers.R‎

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@@ -26,7 +26,7 @@
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readToken <- rAzureBatch::createSasToken("r", "c", jobId)
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envFileUrl <-
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rAzureBatch::createBlobUrl(storageCredentials$name, jobId, envFile, readToken)
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rAzureBatch::createBlobUrl(storageCredentials$name, jobId, envFile, readToken, storageCredentials$endpointSuffix)
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resourceFiles <-
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list(rAzureBatch::createResourceFile(url = envFileUrl, fileName = envFile))
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}
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if (!is.null(cloudCombine)) {
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assign("cloudCombine", cloudCombine, .doAzureBatchGlobals)
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copyCommand <- sprintf(
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"%s %s %s --download --saskey $BLOBXFER_SASKEY --remoteresource . --include result/*.rds",
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"%s %s %s --endpoint %s --download --saskey $BLOBXFER_SASKEY --remoteresource . --include result/*.rds",
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accountName,
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jobId,
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"$AZ_BATCH_TASK_WORKING_DIR"
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"$AZ_BATCH_TASK_WORKING_DIR",
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storageCredentials$endpointSuffix
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)
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downloadCommand <-
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rAzureBatch::createBlobUrl(
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storageAccount = storageCredentials$name,
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containerName = jobId,
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sasToken = rAzureBatch::createSasToken("w", "c", jobId)
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sasToken = rAzureBatch::createSasToken("w", "c", jobId),
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storageEndpointSuffix = storageCredentials$endpointSuffix
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)
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outputFiles <- list(

‎R/utility.R‎

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@@ -170,13 +170,17 @@ createOutputFile <- function(filePattern, url) {
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)
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# Parsing url to obtain container's virtual directory path
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azureDomain <- "blob.core.windows.net"
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parsedValue <- strsplit(url, azureDomain)[[1]]
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# sample url: "https://accountname.blob.core.windows.net/outputs?se=2017-07-31&sr=c&st=2017-07-12"
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# after split by "/"
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# parsedValue[1] is "https"
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# parsedValue[2] is ""
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# parsedValue[3] is "accountname.blob.core.windows.net"
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# parsedValue[4] is "outputs?se=2017-07-31&sr=c&st=2017-07-12"
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accountName <- parsedValue[1]
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urlPath <- parsedValue[2]
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parsedValue <- strsplit(url, "/")[[1]]
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baseUrl <- paste0(accountName, azureDomain)
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baseUrl <- paste0(parsedValue[1], "//", parsedValue[3])
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urlPath <- sub(baseUrl, "", url)
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parsedUrlPath <- strsplit(urlPath, "?", fixed = TRUE)[[1]]
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storageContainerPath <- parsedUrlPath[1]

‎docs/33-programmatically-generate-config.md‎

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@@ -15,7 +15,8 @@ You can generate credentials by creating a R object as shown below:
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),
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"storageAccount" = list(
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"name" = "storageaccountname",
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"key" = "storageaccountkey"
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"key" = "storageaccountkey",
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"endpointSuffix" = "core.windows.net"
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),
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"githubAuthenticationToken" = "",
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"dockerAuthentication" = list("username" = "",

‎docs/34-national-clouds.md‎

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# Configuration for national clouds
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doAzureParallel is configured to run in public Azure cloud by default. To run workloads in national clouds, configure endpoint suffix for storage account in the cluster config which tells doAzureParallel which national cloud environment the storage account resides.
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EndpointSuffix is the last part of the connection string shown in the Storage Account Access keys blade from Azure portal. The possible values usually are:
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Azure public cloud: core.windows.net
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Azure China cloud: core.chinacloudapi.cn
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Azure US government cloud: core.usgovcloudapi.net
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Azure German cloud: core.cloudapi.de
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The value may be different if a DNS redirect is used, so it is better to double check its value on Storage Account Access keys blade.
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Below is a sample of credential config with endpoint suffix specified:
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```R
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{
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"batchAccount": {
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"name": <Azure Batch Account Name>,
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"key": <Azure Batch Account Key>,
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"url": <Azure Batch Account URL>
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},
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"storageAccount": {
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"name": <Azure Storage Account Name>,
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"key": <Azure Storage Account Key>,
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"endpointSuffix": <Azure Storage Account Endpoint Suffix>
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},
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"githubAuthenticationToken": {}
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}
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```

‎docs/README.md‎

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@@ -45,6 +45,10 @@ This section will provide information about how Azure works, how best to take ad
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Generate credentials and cluster config at runtime programmatically
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11. **National Cloud configuration" [(link)](/.34-national-clouds.md)
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How to run workload in Azure national clouds
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## Additional Documentation
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Take a look at our [**Troubleshooting Guide**](./40-troubleshooting.md) for information on how to diagnose common issues.
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