chore: clean up sbt clean compile warnings

amber/src/main/scala/org/apache/texera/web/auth/JwtAuth.scala

@@ -25,8 +25,8 @@ import io.dropwizard.setup.Environment
 import org.apache.texera.auth.JwtAuth.jwtConsumer
 import org.apache.texera.auth.SessionUser
 
-// TODO: move this logic to Auth
-@Deprecated
+// TODO: move this logic to common/auth once it depends on Dropwizard, so amber
+// services can drop the toastshaman dropwizard-auth-jwt filter.
 object JwtAuth {
   def setupJwtAuth(environment: Environment): Unit = {
     // register JWT Auth layer

amber/src/main/scala/org/apache/texera/web/service/ExecutionResultService.scala

@@ -62,6 +62,7 @@ import java.lang.Byte.{SIZE => BitsPerByte}
 import java.util.UUID
 import scala.collection.mutable
 import scala.concurrent.duration.DurationInt
+import scala.language.existentials
 
 object ExecutionResultService {
 

common/pybuilder/src/main/scala/org/apache/texera/amber/pybuilder/BoundaryValidator.scala

@@ -21,6 +21,24 @@ package org.apache.texera.amber.pybuilder
 
 import scala.reflect.macros.blackbox
 
+object BoundaryValidator {
+
+  final case class CompileTimeContext[Pos](
+      leftPart: String,
+      rightPart: String,
+      prefixSource: String,
+      argIndex: Int,
+      errorPos: Pos
+  )
+
+  final case class RuntimeContext(
+      leftPart: String,
+      rightPart: String,
+      prefixSource: String,
+      argIndex: Int
+  )
+}
+
 /**
   * Macro-only helper: validates boundaries for Encodable insertions.
   *
@@ -30,6 +48,7 @@ import scala.reflect.macros.blackbox
 final class BoundaryValidator[C <: blackbox.Context](val c: C) {
   import PythonLexerUtils._
   import c.universe._
+  import BoundaryValidator.{CompileTimeContext, RuntimeContext}
 
   /**
     * Centralized, templatized error messages (Option A).
@@ -75,22 +94,7 @@ final class BoundaryValidator[C <: blackbox.Context](val c: C) {
         "Add whitespace or punctuation to separate tokens."
   }
 
-  final case class CompileTimeContext(
-      leftPart: String,
-      rightPart: String,
-      prefixSource: String,
-      argIndex: Int,
-      errorPos: Position
-  )
-
-  final case class RuntimeContext(
-      leftPart: String,
-      rightPart: String,
-      prefixSource: String,
-      argIndex: Int
-  )
-
-  def validateCompileTime(ctx: CompileTimeContext): Unit = {
+  def validateCompileTime(ctx: CompileTimeContext[Position]): Unit = {
     val prefixLine = lineTail(ctx.prefixSource)
     val argNum = ctx.argIndex + 1
 

common/pybuilder/src/main/scala/org/apache/texera/amber/pybuilder/PythonTemplateBuilder.scala

@@ -363,7 +363,13 @@ object PythonTemplateBuilder {
             if (argExpr.tree.pos != NoPosition) argExpr.tree.pos else macroCtx.enclosingPosition
 
           validator.validateCompileTime(
-            validator.CompileTimeContext(leftPart, rightPart, prefixSource, argIndex, errorPos)
+            BoundaryValidator.CompileTimeContext(
+              leftPart,
+              rightPart,
+              prefixSource,
+              argIndex,
+              errorPos
+            )
           )
 
         case _ => // no-op
@@ -414,7 +420,7 @@ object PythonTemplateBuilder {
 
             val argIdent = Ident(TermName(s"__pyb_arg$argIndex"))
             validator.runtimeChecksForNestedBuilder(
-              validator.RuntimeContext(leftPart, rightPart, prefixSource, argIndex),
+              BoundaryValidator.RuntimeContext(leftPart, rightPart, prefixSource, argIndex),
               argIdent
             )
 

common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/TestOperators.scala

@@ -31,7 +31,6 @@ import org.apache.texera.amber.operator.keywordSearch.KeywordSearchOpDesc
 import org.apache.texera.amber.operator.source.scan.csv.CSVScanSourceOpDesc
 import org.apache.texera.amber.operator.source.scan.json.JSONLScanSourceOpDesc
 import org.apache.texera.amber.operator.source.sql.asterixdb.AsterixDBSourceOpDesc
-import org.apache.texera.amber.operator.source.sql.mysql.MySQLSourceOpDesc
 import org.apache.texera.amber.operator.udf.python.PythonUDFOpDescV2
 import org.apache.texera.amber.operator.udf.python.source.PythonUDFSourceOpDescV2
 
@@ -140,25 +139,6 @@ object TestOperators {
     aggOp
   }
 
-  def inMemoryMySQLSourceOpDesc(
-      host: String,
-      port: String,
-      database: String,
-      table: String,
-      username: String,
-      password: String
-  ): MySQLSourceOpDesc = {
-    val inMemoryMySQLSourceOpDesc = new MySQLSourceOpDesc()
-    inMemoryMySQLSourceOpDesc.host = host
-    inMemoryMySQLSourceOpDesc.port = port
-    inMemoryMySQLSourceOpDesc.database = database
-    inMemoryMySQLSourceOpDesc.table = table
-    inMemoryMySQLSourceOpDesc.username = username
-    inMemoryMySQLSourceOpDesc.password = password
-    inMemoryMySQLSourceOpDesc.limit = Some(1000)
-    inMemoryMySQLSourceOpDesc
-  }
-
   // TODO: use mock data to perform the test, remove dependency on the real AsterixDB
   def asterixDBSourceOpDesc(): AsterixDBSourceOpDesc = {
     val asterixDBOp = new AsterixDBSourceOpDesc()

file-service/src/main/scala/org/apache/texera/service/type/serde/DatasetFileNodeSerializer.java

@@ -23,8 +23,8 @@
 import com.fasterxml.jackson.databind.SerializerProvider;
 import com.fasterxml.jackson.databind.ser.std.StdSerializer;
 import org.apache.texera.service.type.DatasetFileNode;
-import scala.collection.JavaConverters;
 import scala.collection.immutable.List;
+import scala.jdk.javaapi.CollectionConverters;
 
 import java.io.IOException;
 
@@ -53,7 +53,7 @@ public void serialize(DatasetFileNode value, JsonGenerator gen, SerializerProvid
             gen.writeFieldName("children");
             gen.writeStartArray();
             List<DatasetFileNode> children = value.getChildren();
-            for (DatasetFileNode child : JavaConverters.seqAsJavaList(children)) {
+            for (DatasetFileNode child : CollectionConverters.asJava(children)) {
                 serialize(child, gen, provider); // Recursively serialize children
             }
             gen.writeEndArray();

file-service/src/test/scala/org/apache/texera/service/type/serde/DatasetFileNodeSerializerSpec.scala

@@ -0,0 +1,100 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.apache.texera.service.`type`.serde
+
+import com.fasterxml.jackson.databind.module.SimpleModule
+import com.fasterxml.jackson.databind.{JsonNode, ObjectMapper}
+import com.fasterxml.jackson.module.scala.DefaultScalaModule
+import org.apache.texera.service.`type`.DatasetFileNode
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class DatasetFileNodeSerializerSpec extends AnyFlatSpec with Matchers {
+
+  private val mapper: ObjectMapper = {
+    val m = new ObjectMapper()
+    // DefaultScalaModule lets Jackson unwrap scala.Option for the "size" field.
+    m.registerModule(DefaultScalaModule)
+    val module = new SimpleModule()
+    module.addSerializer(classOf[DatasetFileNode], new DatasetFileNodeSerializer())
+    m.registerModule(module)
+    m
+  }
+
+  private def asJson(node: DatasetFileNode): JsonNode =
+    mapper.readTree(mapper.writeValueAsString(node))
+
+  // The serializer dereferences value.getParent().getFilePath(), so every node it
+  // sees needs a non-null parent. Tests build a tree rooted at "/" and serialize
+  // its descendants.
+  private def rootDir: DatasetFileNode =
+    new DatasetFileNode("/", "directory", null, "")
+
+  "DatasetFileNodeSerializer" should "serialize a file node with size and no children field" in {
+    val root = rootDir
+    val owner = new DatasetFileNode("alice@example.com", "directory", root, "alice@example.com")
+    val file = new DatasetFileNode("data.csv", "file", owner, "alice@example.com", Some(100L))
+
+    val json = asJson(file)
+
+    json.get("name").asText() shouldBe "data.csv"
+    json.get("type").asText() shouldBe "file"
+    json.get("parentDir").asText() shouldBe "/alice@example.com"
+    json.get("ownerEmail").asText() shouldBe "alice@example.com"
+    json.get("size").asLong() shouldBe 100L
+    json.has("children") shouldBe false
+  }
+
+  it should "recursively serialize a directory and its children" in {
+    val root = rootDir
+    val owner = new DatasetFileNode("alice@example.com", "directory", root, "alice@example.com")
+    val file = new DatasetFileNode("data.csv", "file", owner, "alice@example.com", Some(100L))
+    val subdir = new DatasetFileNode("subdir", "directory", owner, "alice@example.com")
+    val nested = new DatasetFileNode("nested.txt", "file", subdir, "alice@example.com", Some(200L))
+    subdir.children = Some(List(nested))
+    owner.children = Some(List(file, subdir))
+
+    val json = asJson(owner)
+
+    json.get("name").asText() shouldBe "alice@example.com"
+    json.get("type").asText() shouldBe "directory"
+    json.get("parentDir").asText() shouldBe "/"
+    val children = json.get("children")
+    children.isArray shouldBe true
+    children.size() shouldBe 2
+    children.get(0).get("name").asText() shouldBe "data.csv"
+    children.get(0).get("size").asLong() shouldBe 100L
+    children.get(1).get("name").asText() shouldBe "subdir"
+    children.get(1).get("children").get(0).get("name").asText() shouldBe "nested.txt"
+    children.get(1).get("children").get(0).get("size").asLong() shouldBe 200L
+  }
+
+  it should "emit an empty children array for a directory with no children" in {
+    val root = rootDir
+    val empty = new DatasetFileNode("empty", "directory", root, "alice@example.com")
+
+    val json = asJson(empty)
+
+    json.get("type").asText() shouldBe "directory"
+    val children = json.get("children")
+    children.isArray shouldBe true
+    children.size() shouldBe 0
+  }
+}