no need for another tmpfilemanager impl

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

@@ -23,7 +23,7 @@ trait TempFileManager extends AutoCloseable {
   def newTmpPath(tmpdir: String, prefix: String, extension: String = null): String
 }
 
-class OwningTempFileManager(fs: FS) extends TempFileManager {
+class OwningTempFileManager(val fs: FS) extends TempFileManager {
   private[this] val tmpPaths = mutable.ArrayBuffer[String]()
 
   override def newTmpPath(tmpdir: String, prefix: String, extension: String): String = {

hail/src/main/scala/is/hail/backend/api/Py4JBackendApi.scala

@@ -39,7 +39,6 @@ import com.sun.net.httpserver.{HttpExchange, HttpServer}
 import org.apache.hadoop
 import org.apache.hadoop.conf.Configuration
 import org.apache.spark.sql.DataFrame
-import org.json4s
 import org.json4s._
 import org.json4s.jackson.{JsonMethods, Serialization}
 import sourcecode.Enclosing
@@ -52,6 +51,7 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
 
   private[this] val flags: HailFeatureFlags = HailFeatureFlags.fromEnv()
   private[this] val hcl = new HailClassLoader(getClass.getClassLoader)
+
   private[this] val references = mutable.Map(ReferenceGenome.builtinReferences().toSeq: _*)
   private[this] val bmCache = new BlockMatrixCache()
   private[this] val codeCache = new Cache[CodeCacheKey, CompiledFunction[_]](50)
@@ -61,29 +61,12 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
   private[this] var irID: Int = 0
   private[this] var tmpdir: String = _
   private[this] var localTmpdir: String = _
-
-  private[this] object tmpFileManager extends TempFileManager {
-    private[this] var fs = newFs(CloudStorageFSConfig.fromFlagsAndEnv(None, flags))
-    private[this] var manager = new OwningTempFileManager(fs)
-
-    def setFs(fs: FS): Unit = {
-      close()
-      this.fs = fs
-      manager = new OwningTempFileManager(fs)
-    }
-
-    def getFs: FS =
-      fs
-
-    override def newTmpPath(tmpdir: String, prefix: String, extension: String): String =
-      manager.newTmpPath(tmpdir, prefix, extension)
-
-    override def close(): Unit =
-      manager.close()
-  }
+  private[this] var tmpFileManager = new OwningTempFileManager(
+    newFs(CloudStorageFSConfig.fromFlagsAndEnv(None, flags))
+  )
 
   def pyFs: FS =
-    using(weak.acquire())(_ => tmpFileManager.getFs)
+    using(weak.acquire())(_ => tmpFileManager.fs)
 
   def pyGetFlag(name: String): String =
     using(weak.acquire())(_ => flags.get(name))
@@ -102,6 +85,8 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
 
   def pySetGcsRequesterPaysConfig(project: String, buckets: util.List[String]): Unit =
     using(weak.acquire()) { _ =>
+      tmpFileManager.close()
+
       val cloudfsConf = CloudStorageFSConfig.fromFlagsAndEnv(None, flags)
 
       val rpConfig: Option[RequesterPaysConfig] =
@@ -126,15 +111,15 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
         )
       )
 
-      tmpFileManager.setFs(fs)
+      tmpFileManager = new OwningTempFileManager(fs)
     }
 
   def pyRemoveJavaIR(id: Int): Unit =
     using(weak.acquire())(_ => persistedIr.remove(id))
 
   def pyAddSequence(name: String, fastaFile: String, indexFile: String): Unit =
     using(weak.acquire()) { _ =>
-      val seq = IndexedFastaSequenceFile(tmpFileManager.getFs, fastaFile, indexFile)
+      val seq = IndexedFastaSequenceFile(tmpFileManager.fs, fastaFile, indexFile)
       references(name).addSequence(seq)
     }
 
@@ -240,28 +225,26 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
 
   def pyReadMultipleMatrixTables(jsonQuery: String): util.List[MatrixIR] =
     withExecuteContext() { ctx =>
+      implicit val fmts: Formats = DefaultFormats
       log.info("pyReadMultipleMatrixTables: got query")
-      val kvs = JsonMethods.parse(jsonQuery) match {
-        case json4s.JObject(values) => values.toMap
-      }
 
-      val paths = kvs("paths").asInstanceOf[json4s.JArray].arr.toArray.map {
-        case json4s.JString(s) => s
-      }
-
-      val intervalPointType = parseType(kvs("intervalPointType").asInstanceOf[json4s.JString].s)
+      val kvs = JsonMethods.parse(jsonQuery).extract[Map[String, JValue]]
+      val paths = kvs("paths").extract[IndexedSeq[String]]
+      val intervalPointType = parseType(kvs("intervalPointType").extract[String])
       val intervalObjects =
         JSONAnnotationImpex.importAnnotation(kvs("intervals"), TArray(TInterval(intervalPointType)))
           .asInstanceOf[IndexedSeq[Interval]]
 
       val opts = NativeReaderOptions(intervalObjects, intervalPointType)
-      val matrixReaders: IndexedSeq[MatrixIR] = paths.map { p =>
-        log.info(s"creating MatrixRead node for $p")
-        val mnr = MatrixNativeReader(ctx.fs, p, Some(opts))
-        MatrixRead(mnr.fullMatrixTypeWithoutUIDs, false, false, mnr): MatrixIR
-      }
+      val matrixReaders: util.List[MatrixIR] =
+        paths.map { p =>
+          log.info(s"creating MatrixRead node for $p")
+          val mnr = MatrixNativeReader(ctx.fs, p, Some(opts))
+          MatrixRead(mnr.fullMatrixTypeWithoutUIDs, false, false, mnr): MatrixIR
+        }.asJava
+
       log.info("pyReadMultipleMatrixTables: returning N matrix tables")
-      matrixReaders.asJava
+      matrixReaders
     }._1
 
   def pyAddReference(jsonConfig: String): Unit =
@@ -274,7 +257,7 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
     using(weak.acquire()) { _ =>
       references(name).addLiftover(
         references(destRGName),
-        LiftOver(tmpFileManager.getFs, chainFile),
+        LiftOver(tmpFileManager.fs, chainFile),
       )
     }
 
@@ -316,7 +299,7 @@ final class Py4JBackendApi(backend: Backend) extends Closeable with ErrorHandlin
           tmpdir = tmpdir,
           localTmpdir = localTmpdir,
           backend = backend,
-          fs = tmpFileManager.getFs,
+          fs = tmpFileManager.fs,
           timer = timer,
           tempFileManager =
             if (selfContainedExecution) null