Add JooqCodeGenerator to dao and remove core/util (#3160)

This PR removes the obsolete `core/util` package which is used to
generate jooq code. The generation logics has been moved to `dao` as
class `JooqCodeGenerator`

core/dao/build.sbt

@@ -88,4 +88,5 @@ libraryDependencies ++= Seq(
 
 libraryDependencies ++= Seq(
   "mysql" % "mysql-connector-java" % "8.0.33",          // MySQL connector
+  "org.yaml" % "snakeyaml" % "1.30",                    // for reading storage config yaml file
 )

core/dao/src/main/resources/jooq-conf.xml

@@ -0,0 +1,46 @@
+<configuration>
+    <generator>
+        <!-- The generator for dao -->
+        <generate>
+            <generatedAnnotation>false</generatedAnnotation>
+
+            <daos>true</daos>
+            <interfaces>true</interfaces>
+        </generate>
+        <!-- The default code generator. You can override this one, to generate your own code style.
+             Supported generators:
+             - org.jooq.codegen.JavaGenerator
+             - org.jooq.codegen.ScalaGenerator
+             Defaults to org.jooq.codegen.JavaGenerator -->
+        <name>org.jooq.codegen.JavaGenerator</name>
+
+        <database>
+            <!-- The database type. The format here is:
+                 org.jooq.meta.[database].[database]Database -->
+            <name>org.jooq.meta.mysql.MySQLDatabase</name>
+
+            <!-- The database schema (or in the absence of schema support, in your RDBMS this
+                 can be the owner, user, database name) to be generated -->
+            <inputSchema>texera_db</inputSchema>
+
+            <!-- All elements that are generated from your schema
+                 (A Java regular expression. Use the pipe to separate several expressions)
+                 Watch out for case-sensitivity. Depending on your database, this might be important! -->
+            <includes>.*</includes>
+
+            <!-- All elements that are excluded from your schema
+                 (A Java regular expression. Use the pipe to separate several expressions).
+                 Excludes match before includes, i.e. excludes have a higher priority -->
+            <excludes>(test_.*)|(ignore_.*)</excludes>
+
+        </database>
+
+        <target>
+            <!-- The destination package of your generated classes (within the destination directory) -->
+            <packageName>edu.uci.ics.texera.dao.jooq.generated</packageName>
+
+            <!-- The destination directory of your generated classes. Using Maven directory layout here -->
+            <directory>dao/src/main/scala</directory>
+        </target>
+    </generator>
+</configuration>

core/dao/src/main/scala/edu/uci/ics/texera/dao/JooqCodeGenerator.scala

@@ -0,0 +1,54 @@
+package edu.uci.ics.texera.dao
+
+import org.jooq.codegen.GenerationTool
+import org.jooq.meta.jaxb.{Configuration, Jdbc}
+import org.yaml.snakeyaml.Yaml
+
+import java.io.InputStream
+import java.nio.file.{Files, Path}
+import java.util.{Map => JMap}
+import scala.jdk.CollectionConverters._
+
+object JooqCodeGenerator {
+  @throws[Exception]
+  def main(args: Array[String]): Unit = {
+    // Load jOOQ configuration XML
+    val jooqXmlPath: Path =
+      Path.of("dao").resolve("src").resolve("main").resolve("resources").resolve("jooq-conf.xml")
+    val jooqConfig: Configuration = GenerationTool.load(Files.newInputStream(jooqXmlPath))
+
+    // Load YAML configuration
+    val yamlConfPath: Path = Path
+      .of("workflow-core")
+      .resolve("src")
+      .resolve("main")
+      .resolve("resources")
+      .resolve("storage-config.yaml")
+    val yaml = new Yaml
+    val inputStream: InputStream = Files.newInputStream(yamlConfPath)
+
+    val conf: Map[String, Any] =
+      yaml.load(inputStream).asInstanceOf[JMap[String, Any]].asScala.toMap
+
+    val jdbcConfig = conf("storage")
+      .asInstanceOf[JMap[String, Any]]
+      .asScala("jdbc")
+      .asInstanceOf[JMap[String, Any]]
+      .asScala
+
+    // Set JDBC configuration for jOOQ
+    val jooqJdbcConfig = new Jdbc
+    jooqJdbcConfig.setDriver("com.mysql.cj.jdbc.Driver")
+    jooqJdbcConfig.setUrl(jdbcConfig("url").toString)
+    jooqJdbcConfig.setUsername(jdbcConfig("username").toString)
+    jooqJdbcConfig.setPassword(jdbcConfig("password").toString)
+
+    jooqConfig.setJdbc(jooqJdbcConfig)
+
+    // Generate the code
+    GenerationTool.generate(jooqConfig)
+
+    // Close input stream
+    inputStream.close()
+  }
+}