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ehighamehigham
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reformat
1 parent c29c0ff commit 7a5cb52

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13 files changed

+73
-52
lines changed

13 files changed

+73
-52
lines changed

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,16 +4,17 @@ import is.hail.expr.ir.{IRParser, IRParserEnvironment}
44
import is.hail.utils._
55

66
import scala.util.control.NonFatal
7+
8+
import java.io.Closeable
79
import java.net.InetSocketAddress
810
import java.nio.charset.StandardCharsets
911
import java.util.concurrent._
12+
1013
import com.sun.net.httpserver.{HttpExchange, HttpHandler, HttpServer}
1114
import org.json4s._
1215
import org.json4s.jackson.JsonMethods
1316
import org.json4s.jackson.JsonMethods.compact
1417

15-
import java.io.Closeable
16-
1718
case class IRTypePayload(ir: String)
1819
case class LoadReferencesFromDatasetPayload(path: String)
1920

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

Lines changed: 9 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,14 +5,17 @@ import is.hail.annotations._
55
import is.hail.asm4s._
66
import is.hail.backend._
77
import is.hail.expr.Validate
8-
import is.hail.expr.ir.{Compile, IR, IRParser, IRParserEnvironment, IRSize, LoweringAnalyses, MakeTuple, SortField, TableIR, TableReader, TypeCheck}
8+
import is.hail.expr.ir.{
9+
Compile, IR, IRParser, IRParserEnvironment, IRSize, LoweringAnalyses, MakeTuple, SortField,
10+
TableIR, TableReader, TypeCheck,
11+
}
912
import is.hail.expr.ir.analyses.SemanticHash
1013
import is.hail.expr.ir.functions.IRFunctionRegistry
1114
import is.hail.expr.ir.lowering._
1215
import is.hail.io.fs._
1316
import is.hail.linalg.BlockMatrix
14-
import is.hail.services.JobGroupStates.Failure
1517
import is.hail.services.{BatchClient, _}
18+
import is.hail.services.JobGroupStates.Failure
1619
import is.hail.types._
1720
import is.hail.types.physical._
1821
import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
@@ -22,17 +25,18 @@ import is.hail.variant.ReferenceGenome
2225

2326
import scala.annotation.switch
2427
import scala.reflect.ClassTag
28+
2529
import java.io._
2630
import java.nio.charset.StandardCharsets
31+
import java.nio.file.Path
2732
import java.util.concurrent._
33+
2834
import org.apache.log4j.Logger
2935
import org.json4s.{DefaultFormats, Formats}
3036
import org.json4s.JsonAST._
3137
import org.json4s.jackson.JsonMethods
3238
import sourcecode.Enclosing
3339

34-
import java.nio.file.Path
35-
3640
class ServiceBackendContext(
3741
val billingProject: String,
3842
val remoteTmpDir: String,
@@ -181,7 +185,7 @@ class ServiceBackend(
181185
val uploadContexts = executor.submit[Unit](() =>
182186
retryTransientErrors {
183187
fs.writePDOS(s"$root/contexts") { os =>
184-
var o = 12L * n // 12L = sizeof(Long) + sizeof(Int)
188+
var o = 12L * n // 12L = sizeof(Long) + sizeof(Int)
185189
collection.foreach { context =>
186190
val len = context.length
187191
os.writeLong(o)

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

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,24 @@
11
package is.hail.backend.service
22

3+
import is.hail.{HAIL_REVISION, HailContext, HailFeatureFlags}
34
import is.hail.asm4s._
45
import is.hail.backend.HailTaskContext
56
import is.hail.io.fs._
67
import is.hail.services._
78
import is.hail.utils._
8-
import is.hail.{HAIL_REVISION, HailContext, HailFeatureFlags}
9-
import org.apache.log4j.Logger
9+
10+
import scala.collection.mutable
11+
import scala.concurrent.{Await, ExecutionContext, Future}
12+
import scala.concurrent.duration.Duration
13+
import scala.util.control.NonFatal
1014

1115
import java.io._
1216
import java.nio.charset._
1317
import java.nio.file.Path
1418
import java.util
1519
import java.util.{concurrent => javaConcurrent}
16-
import scala.collection.mutable
17-
import scala.concurrent.duration.Duration
18-
import scala.concurrent.{Await, ExecutionContext, Future}
19-
import scala.util.control.NonFatal
20+
21+
import org.apache.log4j.Logger
2022

2123
class ServiceTaskContext(val partitionId: Int) extends HailTaskContext {
2224
override def stageId(): Int = 0

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

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -5,21 +5,21 @@ import is.hail.services.oauth2.AzureCloudCredentials
55
import is.hail.services.retryTransientErrors
66
import is.hail.shadedazure.com.azure.core.credential.AzureSasCredential
77
import is.hail.shadedazure.com.azure.core.util.HttpClientOptions
8+
import is.hail.shadedazure.com.azure.storage.blob.{
9+
BlobClient, BlobContainerClient, BlobServiceClient, BlobServiceClientBuilder,
10+
}
811
import is.hail.shadedazure.com.azure.storage.blob.models.{
912
BlobItem, BlobRange, BlobStorageException, ListBlobsOptions,
1013
}
1114
import is.hail.shadedazure.com.azure.storage.blob.specialized.BlockBlobClient
12-
import is.hail.shadedazure.com.azure.storage.blob.{
13-
BlobClient, BlobContainerClient, BlobServiceClient, BlobServiceClientBuilder,
14-
}
1515

16-
import java.io.{ByteArrayOutputStream, FileNotFoundException, OutputStream}
17-
import java.nio.file.Paths
18-
import java.time.Duration
1916
import scala.collection.JavaConverters._
2017
import scala.collection.mutable
2118
import scala.collection.mutable.ArrayBuffer
22-
import java.nio.file.Path
19+
20+
import java.io.{ByteArrayOutputStream, FileNotFoundException, OutputStream}
21+
import java.nio.file.{Path, Paths}
22+
import java.time.Duration
2323

2424
class AzureStorageFSURL(
2525
val account: String,

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
11
package is.hail.io.fs
22

3-
43
import is.hail.HailContext
54
import is.hail.backend.BroadcastValue
65
import is.hail.io.compress.{BGzipInputStream, BGzipOutputStream}
@@ -10,10 +9,12 @@ import is.hail.utils._
109

1110
import scala.collection.mutable
1211
import scala.io.Source
12+
1313
import java.io._
1414
import java.nio.ByteBuffer
1515
import java.nio.file.FileSystems
1616
import java.util.zip.GZIPOutputStream
17+
1718
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
1819
import org.apache.commons.io.IOUtils
1920
import org.apache.hadoop

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

Lines changed: 13 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,25 @@
11
package is.hail.io.fs
22

3-
import com.google.api.client.googleapis.json.GoogleJsonResponseException
4-
import com.google.cloud.http.HttpTransportOptions
5-
import com.google.cloud.storage.Storage.{BlobGetOption, BlobListOption, BlobSourceOption, BlobWriteOption}
6-
import com.google.cloud.storage.{Option => _, _}
7-
import com.google.cloud.{ReadChannel, WriteChannel}
83
import is.hail.HailFeatureFlags
94
import is.hail.io.fs.FSUtil.dropTrailingSlash
105
import is.hail.io.fs.GoogleStorageFS.RequesterPaysFailure
11-
import is.hail.services.oauth2.GoogleCloudCredentials
126
import is.hail.services.{isTransientError, retryTransientErrors}
7+
import is.hail.services.oauth2.GoogleCloudCredentials
138
import is.hail.utils._
149

10+
import scala.jdk.CollectionConverters._
11+
1512
import java.io.{FileNotFoundException, IOException}
1613
import java.nio.ByteBuffer
1714
import java.nio.file.{Path, Paths}
18-
import scala.jdk.CollectionConverters._
15+
16+
import com.google.api.client.googleapis.json.GoogleJsonResponseException
17+
import com.google.cloud.{ReadChannel, WriteChannel}
18+
import com.google.cloud.http.HttpTransportOptions
19+
import com.google.cloud.storage.{Option => _, _}
20+
import com.google.cloud.storage.Storage.{
21+
BlobGetOption, BlobListOption, BlobSourceOption, BlobWriteOption,
22+
}
1923

2024
case class GoogleStorageFSURL(bucket: String, path: String) extends FSURL {
2125
def addPathComponent(c: String): GoogleStorageFSURL =
@@ -70,13 +74,13 @@ object GoogleStorageFS {
7074
case exc: StorageException =>
7175
Option(exc.getMessage).exists { message =>
7276
message == "userProjectMissing" ||
73-
(exc.getCode == 400 && message.contains("requester pays"))
77+
(exc.getCode == 400 && message.contains("requester pays"))
7478
}
7579

7680
case exc: GoogleJsonResponseException =>
7781
Option(exc.getMessage).exists { message =>
7882
message == "userProjectMissing" ||
79-
(exc.getStatusCode == 400 && message.contains("requester pays"))
83+
(exc.getStatusCode == 400 && message.contains("requester pays"))
8084
}
8185

8286
case _ =>

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,12 @@ package is.hail.io.fs
33
import is.hail.HailFeatureFlags
44
import is.hail.services.oauth2.{AzureCloudCredentials, GoogleCloudCredentials}
55
import is.hail.utils.{FastSeq, SerializableHadoopConfiguration}
6-
import org.apache.hadoop.conf.Configuration
76

87
import java.io.Serializable
98
import java.nio.file.Path
109

10+
import org.apache.hadoop.conf.Configuration
11+
1112
object RouterFSURL {
1213
def apply(fs: FS)(_url: fs.URL): RouterFSURL = RouterFSURL(_url, fs)
1314
}

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

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,15 @@ package is.hail.io.fs
33
import is.hail.services.oauth2.AzureCloudCredentials
44
import is.hail.shadedazure.com.azure.storage.blob.BlobServiceClient
55
import is.hail.utils._
6+
7+
import scala.collection.mutable
8+
69
import org.apache.http.client.methods.HttpPost
710
import org.apache.http.client.utils.URIBuilder
811
import org.apache.http.impl.client.HttpClients
912
import org.apache.http.util.EntityUtils
10-
import org.json4s.jackson.JsonMethods
1113
import org.json4s.{DefaultFormats, Formats}
12-
13-
import scala.collection.mutable
14+
import org.json4s.jackson.JsonMethods
1415

1516
object TerraAzureStorageFS {
1617
private val TEN_MINUTES_IN_MS = 10 * 60 * 1000

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

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3,15 +3,17 @@ package is.hail.services
33
import is.hail.expr.ir.ByteArrayBuilder
44
import is.hail.services.requests.{BatchServiceRequester, Requester}
55
import is.hail.utils._
6+
7+
import scala.util.Random
8+
9+
import java.nio.charset.StandardCharsets
10+
import java.nio.file.Path
11+
612
import org.apache.http.entity.ByteArrayEntity
713
import org.apache.http.entity.ContentType.APPLICATION_JSON
14+
import org.json4s.{CustomSerializer, DefaultFormats, Extraction, Formats, JInt, JObject, JString}
815
import org.json4s.JsonAST.{JArray, JBool}
916
import org.json4s.jackson.JsonMethods
10-
import org.json4s.{CustomSerializer, DefaultFormats, Extraction, Formats, JInt, JObject, JString}
11-
12-
import java.nio.charset.StandardCharsets
13-
import java.nio.file.Path
14-
import scala.util.Random
1517

1618
case class BatchRequest(
1719
billing_project: String,
@@ -87,7 +89,7 @@ object JobGroupStates {
8789

8890
object BatchClient {
8991
def apply(deployConfig: DeployConfig, credentialsFile: Path, env: Map[String, String] = sys.env)
90-
: BatchClient =
92+
: BatchClient =
9193
new BatchClient(BatchServiceRequester(deployConfig, credentialsFile, env))
9294
}
9395

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,12 @@
11
package is.hail.services
22

33
import is.hail.utils._
4-
import org.json4s._
5-
import org.json4s.jackson.JsonMethods
64

75
import java.nio.file.{Files, Path}
86

7+
import org.json4s._
8+
import org.json4s.jackson.JsonMethods
9+
910
object BatchConfig {
1011
def fromConfigFile(file: Path): Option[BatchConfig] =
1112
if (!file.toFile.exists()) None

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