Fix all Auto-Application Errors

- using scalafix
- used `scalafixAll dependency:fix.scala213.ExplicitNonNullaryApply@org.scala-lang:scala-rewrites:0.1.5`
- fixed some false positives

DAFFODIL-2152

Author: olabusayoT

daffodil-cli/src/main/scala/org/apache/daffodil/cli/InfosetTypes.scala

@@ -369,7 +369,7 @@ class JDOMInfosetParseResult(parseResult: ParseResult, output: JDOMInfosetOutput
   extends InfosetParseResult(parseResult) {
 
   override def write(os: OutputStream): Unit = {
-    new org.jdom2.output.XMLOutputter().output(output.getResult, os)
+    new org.jdom2.output.XMLOutputter().output(output.getResult(), os)
   }
 }
 
@@ -410,7 +410,7 @@ class ScalaXMLInfosetParseResult(parseResult: ParseResult, output: ScalaXMLInfos
 
   override def write(os: OutputStream): Unit = {
     val writer = new java.io.OutputStreamWriter(os, StandardCharsets.UTF_8)
-    scala.xml.XML.write(writer, output.getResult, "UTF-8", true, null)
+    scala.xml.XML.write(writer, output.getResult(), "UTF-8", true, null)
     writer.flush()
   }
 }
@@ -461,7 +461,7 @@ class W3CDOMInfosetParseResult(parseResult: ParseResult, output: W3CDOMInfosetOu
     val tf = TransformerFactory.newInstance()
     val transformer = tf.newTransformer()
     val result = new StreamResult(os)
-    val source = new DOMSource(output.getResult)
+    val source = new DOMSource(output.getResult())
     transformer.transform(source, result)
   }
 }

daffodil-cli/src/main/scala/org/apache/daffodil/cli/Main.scala

@@ -1288,7 +1288,7 @@ class Main(
                           if (loc.bitLimit0b.isDefined) {
                             (loc.bitLimit0b.get - loc.bitPos0b).toString
                           } else {
-                            "at least " + (inStream.inputSource.knownBytesAvailable * 8)
+                            "at least " + (inStream.inputSource.knownBytesAvailable() * 8)
                           }
                         Logger.log.error(
                           s"Left over data after consuming 0 bits while streaming. Stopped after consuming ${loc.bitPos0b} bit(s) with ${remainingBits} bit(s) remaining."
@@ -1309,7 +1309,7 @@ class Main(
                       val bitsAlreadyConsumed = (loc.bitPos0b % 8).toInt
                       val firstByteString = if (bitsAlreadyConsumed != 0) {
                         val bitsToDisplay = 8 - bitsAlreadyConsumed
-                        val pbp = inStream.inputSource.position + 1
+                        val pbp = inStream.inputSource.position() + 1
                         val firstByteBitArray = inStream.getByteArray(bitsToDisplay, finfo)
                         val fbs = firstByteBitArray(0).toBinaryString
                           .takeRight(8)
@@ -1325,8 +1325,8 @@ class Main(
                           f"\nLeft over data starts with partial byte. Left over data (Binary) at byte $pbp is: (0b$bits)"
                         dumpString
                       } else ""
-                      val curBytePosition1b = inStream.inputSource.position + 1
-                      val bytesAvailable = inStream.inputSource.knownBytesAvailable
+                      val curBytePosition1b = inStream.inputSource.position() + 1
+                      val bytesAvailable = inStream.inputSource.knownBytesAvailable()
                       val bytesLimit = math.min(8, bytesAvailable).toInt
                       val destArray = new Array[Byte](bytesLimit)
                       val destArrayFilled = inStream.inputSource.get(destArray, 0, bytesLimit)
@@ -1684,23 +1684,23 @@ class Main(
               .flatMap(testName => {
                 if (testOpts.regex()) {
                   val regex = testName.r
-                  val matches = tdmlRunner.testCases.filter(testCase =>
-                    regex.pattern.matcher(testCase.tcName).matches
-                  )
+                  val matches = tdmlRunner
+                    .testCases()
+                    .filter(testCase => regex.pattern.matcher(testCase.tcName).matches)
                   matches match {
                     case m if !m.isEmpty => m.map(testCase => (testCase.tcName, Some(testCase)))
                     case _ => Seq((testName, None))
                   }
                 } else {
-                  List((testName, tdmlRunner.testCases.find(_.tcName == testName)))
+                  List((testName, tdmlRunner.testCases().find(_.tcName == testName)))
                 }
               })
           } else {
-            tdmlRunner.testCases.map(test => (test.tcName, Some(test)))
+            tdmlRunner.testCases().map(test => (test.tcName, Some(test)))
           }
         }.distinct.sortBy(_._1)
 
-        tdmlRunner.reset
+        tdmlRunner.reset()
 
         if (testOpts.list()) {
           if (testOpts.info() > 0) {

daffodil-cli/src/main/scala/org/apache/daffodil/cli/debugger/CLIDebuggerRunner.scala

@@ -44,7 +44,7 @@ class CLIDebuggerRunner(cmdsIter: Iterator[String], in: InputStream, out: PrintS
   }
 
   def this(file: File, in: InputStream, out: PrintStream) = {
-    this(Source.fromFile(file).getLines, in, out)
+    this(Source.fromFile(file).getLines(), in, out)
   }
 
   def this(seq: Seq[String], in: InputStream, out: PrintStream) = {
@@ -80,7 +80,7 @@ class CLIDebuggerRunner(cmdsIter: Iterator[String], in: InputStream, out: PrintS
 
   def getCommand: String = {
     val cmd = if (cmdsIter.hasNext) {
-      val line = cmdsIter.next
+      val line = cmdsIter.next()
       if (line.length > 0) {
         reader.get.getHistory.add(line)
       }

daffodil-core/src/main/scala/org/apache/daffodil/core/dsom/DFDLDefineVariable.scala

@@ -101,7 +101,7 @@ class DFDLDefineVariable private (node: Node, doc: SchemaDocument)
       this.SDE("Variables must have primitive type. Type was '%s'.", typeQName.toPrettyString)
     )
 
-  final def createVariableInstance = variableRuntimeData.createVariableInstance
+  final def createVariableInstance = variableRuntimeData.createVariableInstance()
 }
 
 sealed abstract class VariableReference(node: Node, decl: AnnotatedSchemaComponent)

daffodil-core/src/main/scala/org/apache/daffodil/core/dsom/GlobalElementDecl.scala

@@ -38,7 +38,7 @@ final class GlobalElementDecl private (xmlArg: Node, schemaDocument: SchemaDocum
 
   lazy val asRoot = Root(xml, schemaDocument, namedQName, this)
 
-  requiredEvaluationsIfActivated(validateChoiceBranchKey)
+  requiredEvaluationsIfActivated(validateChoiceBranchKey())
 
   private def validateChoiceBranchKey(): Unit = {
     // Ensure that the global element decl does not have choiceBranchKey set.

daffodil-core/src/main/scala/org/apache/daffodil/core/util/TestUtils.scala

@@ -203,7 +203,7 @@ object TestUtils {
     val input = InputSourceDataInputStream(is)
     val actual = p.parse(input, outputter)
     if (actual.isProcessingError) throwDiagnostics(actual.getDiagnostics)
-    (actual, outputter.getResult)
+    (actual, outputter.getResult())
   }
 
   private val defaultIncludeImports =
@@ -425,7 +425,7 @@ class StreamParser private (val schema: Node) {
     val procErr = res.isProcessingError
     val validationErr = res.isValidationError
     val diags = res.getDiagnostics
-    val doc = if (!procErr) outputter.getResult else null
+    val doc = if (!procErr) outputter.getResult() else null
     val bitPos1b = res.resultState.currentLocation.bitPos1b
     val r = new StreamParser.Result(doc, diags, procErr, validationErr, bitPos1b)
     outputter.reset()

daffodil-core/src/test/scala/org/apache/daffodil/core/dsom/TestExternalVariables.scala

@@ -365,13 +365,13 @@ class TestExternalVariables {
     )
 
     val res1 = dp1.parse(input, outputter)
-    assertTrue(outputter.getResult.toString.contains("default1"))
+    assertTrue(outputter.getResult().toString.contains("default1"))
 
     val res2 = dp2.parse(input, outputter)
-    assertTrue(outputter.getResult.toString.contains("value1"))
+    assertTrue(outputter.getResult().toString.contains("value1"))
 
     val res3 = dp1.parse(input, outputter)
-    assertTrue(outputter.getResult.toString.contains("default1"))
+    assertTrue(outputter.getResult().toString.contains("default1"))
 
     checkResult(dp1.variableMap, "{http://example.com}var1", "default1")
     checkResult(dp2.variableMap, "{http://example.com}var1", "value1")