[query] remove non-primitives from scala fs

Author: ehigham

hail/hail/src/is/hail/expr/ir/GenericLines.scala

@@ -2,7 +2,7 @@ package is.hail.expr.ir
 
 import is.hail.backend.spark.SparkBackend
 import is.hail.io.compress.BGzipInputStream
-import is.hail.io.fs.{BGZipCompressionCodec, FS, FileStatus, Positioned, PositionedInputStream}
+import is.hail.io.fs.{getCodecFromPath, BGZipCompressionCodec, FS, FileStatus, Positioned, PositionedInputStream}
 import is.hail.io.tabix.{TabixLineIterator, TabixReader}
 import is.hail.types.virtual.{TBoolean, TInt32, TInt64, TString, TStruct, Type}
 import is.hail.utils._
@@ -43,31 +43,36 @@ object GenericLines extends Logging {
         private var splitCompressed = false
         private val is: PositionedInputStream = {
           val rawIS = fs.openNoCompression(file)
-          val codec = fs.getCodecFromPath(file, gzAsBGZ)
-          if (codec == null) {
-            assert(split || filePerPartition)
-            rawIS.seek(start)
-            rawIS
-          } else if (codec == BGZipCompressionCodec) {
-            assert(split || filePerPartition)
-            splitCompressed = true
-            val bgzIS =
-              new BGzipInputStream(rawIS, start, end, SplittableCompressionCodec.READ_MODE.BYBLOCK)
-            new ProxyInputStream(bgzIS) with Positioned {
-              def getPosition: Long = bgzIS.getVirtualOffset
-            }
-          } else {
-            assert(!split || filePerPartition)
+          getCodecFromPath(file, gzAsBGZ) match {
+            case None =>
+              assert(split || filePerPartition)
+              rawIS.seek(start)
+              rawIS
+            case Some(BGZipCompressionCodec) =>
+              assert(split || filePerPartition)
+              splitCompressed = true
+              val bgzIS =
+                new BGzipInputStream(
+                  rawIS,
+                  start,
+                  end,
+                  SplittableCompressionCodec.READ_MODE.BYBLOCK,
+                )
+              new ProxyInputStream(bgzIS) with Positioned {
+                def getPosition: Long = bgzIS.getVirtualOffset
+              }
+            case Some(codec) =>
+              assert(!split || filePerPartition)
 
             val delegate =
               BoundedInputStream
                 .builder()
                 .setInputStream(codec.makeInputStream(rawIS))
                 .get()
 
-            new ProxyInputStream(delegate) with Positioned {
-              override def getPosition: Long = delegate.getCount
-            }
+              new ProxyInputStream(delegate) with Positioned {
+                override def getPosition: Long = delegate.getCount
+              }
           }
         }
 
@@ -291,9 +296,9 @@ object GenericLines extends Logging {
 
     val contexts = fileStatuses.flatMap { case (fileListEntry, fileNum) =>
       val size = fileListEntry.getLen
-      val codec = fs.getCodecFromPath(fileListEntry.getPath, gzAsBGZ)
+      val codec = getCodecFromPath(fileListEntry.getPath, gzAsBGZ)
 
-      val splittable = codec == null || codec == BGZipCompressionCodec
+      val splittable = codec.isEmpty || codec.contains(BGZipCompressionCodec)
       if (splittable && !filePerPartition) {
         var fileNParts = ((totalPartitions.toDouble * size) / totalSize + 0.5).toInt
         if (fileNParts == 0)
@@ -305,7 +310,7 @@ object GenericLines extends Logging {
           .map { i =>
             val start = partScan(i)
             var end = partScan(i + 1)
-            if (codec != null)
+            if (codec.isDefined)
               end = makeVirtualOffset(end, 0)
             Row(i, fileNum, fileListEntry.getPath, start, end, true)
           }

hail/hail/src/is/hail/expr/ir/MatrixWriter.scala

@@ -9,7 +9,7 @@ import is.hail.expr.ir.lowering.TableStage
 import is.hail.expr.ir.streams.StreamProducer
 import is.hail.io._
 import is.hail.io.bgen.BgenSettings
-import is.hail.io.fs.FS
+import is.hail.io.fs.{getCodecExtension, FS}
 import is.hail.io.gen.{BgenWriter, ExportGen}
 import is.hail.io.index.StagedIndexWriter
 import is.hail.io.plink.{BitPacker, ExportPlink}
@@ -755,7 +755,7 @@ case class MatrixVCFWriter(
 
     ExportVCF.checkFormatSignature(tm.entryType)
 
-    val ext = ctx.fs.getCodecExtension(path)
+    val ext = getCodecExtension(path)
 
     val folder = if (exportType == ExportType.CONCATENATED)
       ctx.createTmpPath("write-vcf-concatenated")
@@ -1271,7 +1271,7 @@ case class VCFExportFinalizer(
   def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
     : Unit = {
     val ctx: ExecuteContext = cb.emb.ctx
-    val ext = ctx.fs.getCodecExtension(outputPath)
+    val ext = getCodecExtension(outputPath)
 
     val annotations = writeAnnotations.getOrAssert(cb).asBaseStruct
 

hail/hail/src/is/hail/expr/ir/TableWriter.scala

@@ -10,7 +10,7 @@ import is.hail.expr.ir.functions.StringFunctions
 import is.hail.expr.ir.lowering.{LowererUnsupportedOperation, TableStage}
 import is.hail.expr.ir.streams.StreamProducer
 import is.hail.io.{AbstractTypedCodecSpec, BufferSpec, OutputBuffer, TypedCodecSpec}
-import is.hail.io.fs.FS
+import is.hail.io.fs.{getCodecExtension, FS}
 import is.hail.io.index.StagedIndexWriter
 import is.hail.rvd.{AbstractRVDSpec, IndexSpec, RVDPartitioner, RVDSpecMaker}
 import is.hail.types._
@@ -689,7 +689,7 @@ case class TableTextWriter(
   override def lower(ctx: ExecuteContext, ts: TableStage, r: RTable): IR = {
     require(exportType != ExportType.PARALLEL_COMPOSABLE)
 
-    val ext = ctx.fs.getCodecExtension(path)
+    val ext = getCodecExtension(path)
 
     val folder = if (exportType == ExportType.CONCATENATED)
       ctx.createTmpPath("write-table-concatenated")
@@ -813,7 +813,7 @@ case class TableTextFinalizer(
   def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
     : Unit = {
     val ctx: ExecuteContext = cb.emb.ctx
-    val ext = ctx.fs.getCodecExtension(outputPath)
+    val ext = getCodecExtension(outputPath)
     val partPaths = writeAnnotations.getOrFatal(cb, "write annotations cannot be missing!")
     val files = partPaths.castTo(cb, region, SJavaArrayString(true), false).asInstanceOf[
       SJavaArrayStringValue