reformat

hail/src/main/scala/is/hail/backend/BackendServer.scala

@@ -4,16 +4,17 @@ import is.hail.expr.ir.{IRParser, IRParserEnvironment}
 import is.hail.utils._
 
 import scala.util.control.NonFatal
+
+import java.io.Closeable
 import java.net.InetSocketAddress
 import java.nio.charset.StandardCharsets
 import java.util.concurrent._
+
 import com.sun.net.httpserver.{HttpExchange, HttpHandler, HttpServer}
 import org.json4s._
 import org.json4s.jackson.JsonMethods
 import org.json4s.jackson.JsonMethods.compact
 
-import java.io.Closeable
-
 case class IRTypePayload(ir: String)
 case class LoadReferencesFromDatasetPayload(path: String)
 

hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala

@@ -5,14 +5,17 @@ import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend._
 import is.hail.expr.Validate
-import is.hail.expr.ir.{Compile, IR, IRParser, IRParserEnvironment, IRSize, LoweringAnalyses, MakeTuple, SortField, TableIR, TableReader, TypeCheck}
+import is.hail.expr.ir.{
+  Compile, IR, IRParser, IRParserEnvironment, IRSize, LoweringAnalyses, MakeTuple, SortField,
+  TableIR, TableReader, TypeCheck,
+}
 import is.hail.expr.ir.analyses.SemanticHash
 import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.expr.ir.lowering._
 import is.hail.io.fs._
 import is.hail.linalg.BlockMatrix
-import is.hail.services.JobGroupStates.Failure
 import is.hail.services.{BatchClient, _}
+import is.hail.services.JobGroupStates.Failure
 import is.hail.types._
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
@@ -22,17 +25,18 @@ import is.hail.variant.ReferenceGenome
 
 import scala.annotation.switch
 import scala.reflect.ClassTag
+
 import java.io._
 import java.nio.charset.StandardCharsets
+import java.nio.file.Path
 import java.util.concurrent._
+
 import org.apache.log4j.Logger
 import org.json4s.{DefaultFormats, Formats}
 import org.json4s.JsonAST._
 import org.json4s.jackson.JsonMethods
 import sourcecode.Enclosing
 
-import java.nio.file.Path
-
 class ServiceBackendContext(
   val billingProject: String,
   val remoteTmpDir: String,
@@ -181,7 +185,7 @@ class ServiceBackend(
     val uploadContexts = executor.submit[Unit](() =>
       retryTransientErrors {
         fs.writePDOS(s"$root/contexts") { os =>
-          var o = 12L * n  // 12L = sizeof(Long) + sizeof(Int)
+          var o = 12L * n // 12L = sizeof(Long) + sizeof(Int)
           collection.foreach { context =>
             val len = context.length
             os.writeLong(o)

hail/src/main/scala/is/hail/backend/service/Worker.scala

@@ -1,22 +1,24 @@
 package is.hail.backend.service
 
+import is.hail.{HAIL_REVISION, HailContext, HailFeatureFlags}
 import is.hail.asm4s._
 import is.hail.backend.HailTaskContext
 import is.hail.io.fs._
 import is.hail.services._
 import is.hail.utils._
-import is.hail.{HAIL_REVISION, HailContext, HailFeatureFlags}
-import org.apache.log4j.Logger
+
+import scala.collection.mutable
+import scala.concurrent.{Await, ExecutionContext, Future}
+import scala.concurrent.duration.Duration
+import scala.util.control.NonFatal
 
 import java.io._
 import java.nio.charset._
 import java.nio.file.Path
 import java.util
 import java.util.{concurrent => javaConcurrent}
-import scala.collection.mutable
-import scala.concurrent.duration.Duration
-import scala.concurrent.{Await, ExecutionContext, Future}
-import scala.util.control.NonFatal
+
+import org.apache.log4j.Logger
 
 class ServiceTaskContext(val partitionId: Int) extends HailTaskContext {
   override def stageId(): Int = 0

hail/src/main/scala/is/hail/io/fs/AzureStorageFS.scala

@@ -5,21 +5,21 @@ import is.hail.services.oauth2.AzureCloudCredentials
 import is.hail.services.retryTransientErrors
 import is.hail.shadedazure.com.azure.core.credential.AzureSasCredential
 import is.hail.shadedazure.com.azure.core.util.HttpClientOptions
+import is.hail.shadedazure.com.azure.storage.blob.{
+  BlobClient, BlobContainerClient, BlobServiceClient, BlobServiceClientBuilder,
+}
 import is.hail.shadedazure.com.azure.storage.blob.models.{
   BlobItem, BlobRange, BlobStorageException, ListBlobsOptions,
 }
 import is.hail.shadedazure.com.azure.storage.blob.specialized.BlockBlobClient
-import is.hail.shadedazure.com.azure.storage.blob.{
-  BlobClient, BlobContainerClient, BlobServiceClient, BlobServiceClientBuilder,
-}
 
-import java.io.{ByteArrayOutputStream, FileNotFoundException, OutputStream}
-import java.nio.file.Paths
-import java.time.Duration
 import scala.collection.JavaConverters._
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer
-import java.nio.file.Path
+
+import java.io.{ByteArrayOutputStream, FileNotFoundException, OutputStream}
+import java.nio.file.{Path, Paths}
+import java.time.Duration
 
 class AzureStorageFSURL(
   val account: String,

hail/src/main/scala/is/hail/io/fs/FS.scala

@@ -1,6 +1,5 @@
 package is.hail.io.fs
 
-
 import is.hail.HailContext
 import is.hail.backend.BroadcastValue
 import is.hail.io.compress.{BGzipInputStream, BGzipOutputStream}
@@ -10,10 +9,12 @@ import is.hail.utils._
 
 import scala.collection.mutable
 import scala.io.Source
+
 import java.io._
 import java.nio.ByteBuffer
 import java.nio.file.FileSystems
 import java.util.zip.GZIPOutputStream
+
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop

hail/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala

@@ -1,21 +1,25 @@
 package is.hail.io.fs
 
-import com.google.api.client.googleapis.json.GoogleJsonResponseException
-import com.google.cloud.http.HttpTransportOptions
-import com.google.cloud.storage.Storage.{BlobGetOption, BlobListOption, BlobSourceOption, BlobWriteOption}
-import com.google.cloud.storage.{Option => _, _}
-import com.google.cloud.{ReadChannel, WriteChannel}
 import is.hail.HailFeatureFlags
 import is.hail.io.fs.FSUtil.dropTrailingSlash
 import is.hail.io.fs.GoogleStorageFS.RequesterPaysFailure
-import is.hail.services.oauth2.GoogleCloudCredentials
 import is.hail.services.{isTransientError, retryTransientErrors}
+import is.hail.services.oauth2.GoogleCloudCredentials
 import is.hail.utils._
 
+import scala.jdk.CollectionConverters._
+
 import java.io.{FileNotFoundException, IOException}
 import java.nio.ByteBuffer
 import java.nio.file.{Path, Paths}
-import scala.jdk.CollectionConverters._
+
+import com.google.api.client.googleapis.json.GoogleJsonResponseException
+import com.google.cloud.{ReadChannel, WriteChannel}
+import com.google.cloud.http.HttpTransportOptions
+import com.google.cloud.storage.{Option => _, _}
+import com.google.cloud.storage.Storage.{
+  BlobGetOption, BlobListOption, BlobSourceOption, BlobWriteOption,
+}
 
 case class GoogleStorageFSURL(bucket: String, path: String) extends FSURL {
   def addPathComponent(c: String): GoogleStorageFSURL =
@@ -70,13 +74,13 @@ object GoogleStorageFS {
         case exc: StorageException =>
           Option(exc.getMessage).exists { message =>
             message == "userProjectMissing" ||
-              (exc.getCode == 400 && message.contains("requester pays"))
+            (exc.getCode == 400 && message.contains("requester pays"))
           }
 
         case exc: GoogleJsonResponseException =>
           Option(exc.getMessage).exists { message =>
             message == "userProjectMissing" ||
-              (exc.getStatusCode == 400 && message.contains("requester pays"))
+            (exc.getStatusCode == 400 && message.contains("requester pays"))
           }
 
         case _ =>

hail/src/main/scala/is/hail/io/fs/RouterFS.scala

@@ -3,11 +3,12 @@ package is.hail.io.fs
 import is.hail.HailFeatureFlags
 import is.hail.services.oauth2.{AzureCloudCredentials, GoogleCloudCredentials}
 import is.hail.utils.{FastSeq, SerializableHadoopConfiguration}
-import org.apache.hadoop.conf.Configuration
 
 import java.io.Serializable
 import java.nio.file.Path
 
+import org.apache.hadoop.conf.Configuration
+
 object RouterFSURL {
   def apply(fs: FS)(_url: fs.URL): RouterFSURL = RouterFSURL(_url, fs)
 }

hail/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala

@@ -3,14 +3,15 @@ package is.hail.io.fs
 import is.hail.services.oauth2.AzureCloudCredentials
 import is.hail.shadedazure.com.azure.storage.blob.BlobServiceClient
 import is.hail.utils._
+
+import scala.collection.mutable
+
 import org.apache.http.client.methods.HttpPost
 import org.apache.http.client.utils.URIBuilder
 import org.apache.http.impl.client.HttpClients
 import org.apache.http.util.EntityUtils
-import org.json4s.jackson.JsonMethods
 import org.json4s.{DefaultFormats, Formats}
-
-import scala.collection.mutable
+import org.json4s.jackson.JsonMethods
 
 object TerraAzureStorageFS {
   private val TEN_MINUTES_IN_MS = 10 * 60 * 1000

hail/src/main/scala/is/hail/services/BatchClient.scala

@@ -3,15 +3,17 @@ package is.hail.services
 import is.hail.expr.ir.ByteArrayBuilder
 import is.hail.services.requests.{BatchServiceRequester, Requester}
 import is.hail.utils._
+
+import scala.util.Random
+
+import java.nio.charset.StandardCharsets
+import java.nio.file.Path
+
 import org.apache.http.entity.ByteArrayEntity
 import org.apache.http.entity.ContentType.APPLICATION_JSON
+import org.json4s.{CustomSerializer, DefaultFormats, Extraction, Formats, JInt, JObject, JString}
 import org.json4s.JsonAST.{JArray, JBool}
 import org.json4s.jackson.JsonMethods
-import org.json4s.{CustomSerializer, DefaultFormats, Extraction, Formats, JInt, JObject, JString}
-
-import java.nio.charset.StandardCharsets
-import java.nio.file.Path
-import scala.util.Random
 
 case class BatchRequest(
   billing_project: String,
@@ -87,7 +89,7 @@ object JobGroupStates {
 
 object BatchClient {
   def apply(deployConfig: DeployConfig, credentialsFile: Path, env: Map[String, String] = sys.env)
-  : BatchClient =
+    : BatchClient =
     new BatchClient(BatchServiceRequester(deployConfig, credentialsFile, env))
 }
 

hail/src/main/scala/is/hail/services/BatchConfig.scala

@@ -1,11 +1,12 @@
 package is.hail.services
 
 import is.hail.utils._
-import org.json4s._
-import org.json4s.jackson.JsonMethods
 
 import java.nio.file.{Files, Path}
 
+import org.json4s._
+import org.json4s.jackson.JsonMethods
+
 object BatchConfig {
   def fromConfigFile(file: Path): Option[BatchConfig] =
     if (!file.toFile.exists()) None

hail/src/main/scala/is/hail/services/oauth2.scala

@@ -1,19 +1,21 @@
 package is.hail.services
 
-import com.google.auth.oauth2.{GoogleCredentials, ServiceAccountCredentials}
 import is.hail.services.oauth2.AzureCloudCredentials.EnvVars.AzureApplicationCredentials
 import is.hail.services.oauth2.GoogleCloudCredentials.EnvVars.GoogleApplicationCredentials
 import is.hail.shadedazure.com.azure.core.credential.{TokenCredential, TokenRequestContext}
 import is.hail.shadedazure.com.azure.identity.{
   ClientSecretCredentialBuilder, DefaultAzureCredentialBuilder,
 }
 import is.hail.utils.{defaultJSONFormats, using}
-import org.json4s.Formats
-import org.json4s.jackson.JsonMethods
+
+import scala.collection.JavaConverters._
 
 import java.io.Serializable
 import java.nio.file.{Files, Path}
-import scala.collection.JavaConverters._
+
+import com.google.auth.oauth2.{GoogleCredentials, ServiceAccountCredentials}
+import org.json4s.Formats
+import org.json4s.jackson.JsonMethods
 
 object oauth2 {
 

hail/src/main/scala/is/hail/services/package.scala

@@ -1,16 +1,17 @@
 package is.hail
 
+import is.hail.services.requests.ClientResponseException
 import is.hail.shadedazure.com.azure.storage.common.implementation.Constants
 import is.hail.utils._
 
 import scala.util.Random
+
 import java.io._
 import java.net._
+
 import com.google.api.client.googleapis.json.GoogleJsonResponseException
 import com.google.api.client.http.HttpResponseException
 import com.google.cloud.storage.StorageException
-import is.hail.services.requests.ClientResponseException
-
 import javax.net.ssl.SSLException
 import org.apache.http.{ConnectionClosedException, NoHttpResponseException}
 import org.apache.http.conn.HttpHostConnectException

hail/src/main/scala/is/hail/services/requests.scala

@@ -2,20 +2,21 @@ package is.hail.services
 
 import is.hail.services.oauth2.{CloudCredentials, CloudScopes}
 import is.hail.utils.{log, _}
+
+import java.net.URL
+import java.nio.file.Path
+
+import org.apache.http.{HttpEntity, HttpEntityEnclosingRequest}
 import org.apache.http.client.config.RequestConfig
 import org.apache.http.client.methods.{HttpGet, HttpPatch, HttpPost, HttpUriRequest}
 import org.apache.http.entity.ContentType.APPLICATION_JSON
 import org.apache.http.entity.StringEntity
 import org.apache.http.impl.client.{CloseableHttpClient, HttpClients}
 import org.apache.http.util.EntityUtils
-import org.apache.http.{HttpEntity, HttpEntityEnclosingRequest}
 import org.json4s.JValue
 import org.json4s.JsonAST.JNothing
 import org.json4s.jackson.JsonMethods
 
-import java.net.URL
-import java.nio.file.Path
-
 object requests {
 
   class ClientResponseException(val status: Int, message: String) extends Exception(message)