Migrate texera database from mysql to postgres

core/amber/src/main/scala/edu/uci/ics/amber/engine/architecture/scheduling/CostEstimator.scala

@@ -1,18 +1,17 @@
 package edu.uci.ics.amber.engine.architecture.scheduling
 
-import edu.uci.ics.amber.core.storage.{DocumentFactory, StorageConfig}
+import edu.uci.ics.amber.core.storage.DocumentFactory
 import edu.uci.ics.amber.core.tuple.Tuple
+import edu.uci.ics.amber.core.virtualidentity.ActorVirtualIdentity
 import edu.uci.ics.amber.core.workflow.WorkflowContext
 import edu.uci.ics.amber.engine.architecture.scheduling.DefaultCostEstimator.DEFAULT_OPERATOR_COST
 import edu.uci.ics.amber.engine.common.AmberLogging
-import edu.uci.ics.amber.core.virtualidentity.ActorVirtualIdentity
 import edu.uci.ics.texera.dao.SqlServer
 import edu.uci.ics.texera.dao.SqlServer.withTransaction
 import edu.uci.ics.texera.dao.jooq.generated.Tables.{WORKFLOW_EXECUTIONS, WORKFLOW_VERSION}
-import org.jooq.types.UInteger
 
-import scala.util.{Failure, Success, Try}
 import java.net.URI
+import scala.util.{Failure, Success, Try}
 
 /**
   * A cost estimator should estimate a cost of running a region under the given resource constraints as units.
@@ -85,11 +84,7 @@ class DefaultCostEstimator(
 
     val uriString: String = withTransaction(
       SqlServer
-        .getInstance(
-          StorageConfig.jdbcUrl,
-          StorageConfig.jdbcUsername,
-          StorageConfig.jdbcPassword
-        )
+        .getInstance()
         .createDSLContext()
     ) { context =>
       context
@@ -99,7 +94,7 @@ class DefaultCostEstimator(
         .on(WORKFLOW_VERSION.VID.eq(WORKFLOW_EXECUTIONS.VID))
         .where(
           WORKFLOW_VERSION.WID
-            .eq(UInteger.valueOf(wid))
+            .eq(wid.toInt)
             .and(WORKFLOW_EXECUTIONS.STATUS.eq(3.toByte))
         )
         .orderBy(WORKFLOW_EXECUTIONS.STARTING_TIME.desc())

core/amber/src/main/scala/edu/uci/ics/texera/web/ComputingUnitMaster.scala

@@ -2,7 +2,7 @@ package edu.uci.ics.texera.web
 
 import com.fasterxml.jackson.module.scala.DefaultScalaModule
 import com.typesafe.scalalogging.LazyLogging
-import edu.uci.ics.amber.core.storage.DocumentFactory
+import edu.uci.ics.amber.core.storage.{DocumentFactory, StorageConfig}
 import edu.uci.ics.amber.core.storage.util.mongo.MongoDatabaseManager
 import edu.uci.ics.amber.core.workflow.{PhysicalPlan, WorkflowContext}
 import edu.uci.ics.amber.engine.architecture.controller.ControllerConfig
@@ -16,6 +16,7 @@ import edu.uci.ics.amber.engine.common.client.AmberClient
 import edu.uci.ics.amber.engine.common.storage.SequentialRecordStorage
 import edu.uci.ics.amber.engine.common.{AmberConfig, AmberRuntime, Utils}
 import edu.uci.ics.amber.core.virtualidentity.ExecutionIdentity
+import edu.uci.ics.texera.dao.SqlServer
 import edu.uci.ics.texera.web.auth.JwtAuth.setupJwtAuth
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.WorkflowExecutions
 import edu.uci.ics.texera.web.resource.WorkflowWebsocketResource
@@ -98,6 +99,12 @@ class ComputingUnitMaster extends io.dropwizard.Application[Configuration] with
 
   override def run(configuration: Configuration, environment: Environment): Unit = {
 
+    SqlServer.initConnection(
+      StorageConfig.jdbcUrl,
+      StorageConfig.jdbcUsername,
+      StorageConfig.jdbcPassword
+    )
+
     val webSocketUpgradeFilter =
       WebSocketUpgradeFilter.configureContext(environment.getApplicationContext)
     webSocketUpgradeFilter.getFactory.getPolicy.setIdleTimeout(Duration.ofHours(1).toMillis)
@@ -149,7 +156,7 @@ class ComputingUnitMaster extends io.dropwizard.Application[Configuration] with
     */
   private def cleanExecutions(
       executions: List[WorkflowExecutions],
-      statusChangeFunc: Byte => Byte
+      statusChangeFunc: Short => Short
   ): Unit = {
     // drop the collection and update the status to ABORTED
     executions.foreach(execEntry => {

core/amber/src/main/scala/edu/uci/ics/texera/web/ComputingUnitWorker.scala

@@ -26,6 +26,7 @@ object ComputingUnitWorker {
 
   def main(args: Array[String]): Unit = {
     val argMap = parseArgs(args)
+
     // start actor system worker node
     AmberRuntime.startActorWorker(argMap.get(Symbol("serverAddr")).asInstanceOf[Option[String]])
   }

core/amber/src/main/scala/edu/uci/ics/texera/web/ServletAwareConfigurator.scala

@@ -4,7 +4,6 @@ import com.typesafe.scalalogging.LazyLogging
 import edu.uci.ics.texera.web.auth.JwtAuth.jwtConsumer
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
 import org.apache.http.client.utils.URLEncodedUtils
-import org.jooq.types.UInteger
 
 import java.net.URI
 import java.nio.charset.Charset
@@ -39,7 +38,7 @@ class ServletAwareConfigurator extends ServerEndpointConfig.Configurator with La
           config.getUserProperties.put(
             classOf[User].getName,
             new User(
-              UInteger.valueOf(claims.getClaimValue("userId").asInstanceOf[Long]),
+              claims.getClaimValue("userId").asInstanceOf[Long].toInt,
               claims.getSubject,
               String.valueOf(claims.getClaimValue("email").asInstanceOf[String]),
               null,

core/amber/src/main/scala/edu/uci/ics/texera/web/TexeraWebApplication.scala

@@ -4,9 +4,11 @@ import com.fasterxml.jackson.databind.module.SimpleModule
 import com.fasterxml.jackson.module.scala.DefaultScalaModule
 import com.github.dirkraft.dropwizard.fileassets.FileAssetsBundle
 import com.typesafe.scalalogging.LazyLogging
+import edu.uci.ics.amber.core.storage.StorageConfig
 import edu.uci.ics.amber.core.storage.util.dataset.GitVersionControlLocalFileStorage
 import edu.uci.ics.amber.engine.common.Utils
 import edu.uci.ics.amber.util.PathUtils
+import edu.uci.ics.texera.dao.SqlServer
 import edu.uci.ics.texera.web.auth.JwtAuth.setupJwtAuth
 import edu.uci.ics.texera.web.auth.SessionUser
 import edu.uci.ics.texera.web.resource._
@@ -98,6 +100,12 @@ class TexeraWebApplication
     // serve backend at /api
     environment.jersey.setUrlPattern("/api/*")
 
+    SqlServer.initConnection(
+      StorageConfig.jdbcUrl,
+      StorageConfig.jdbcUsername,
+      StorageConfig.jdbcPassword
+    )
+
     // redirect all 404 to index page, according to Angular routing requirements
     val eph = new ErrorPageErrorHandler
     eph.addErrorPage(404, "/")
@@ -148,5 +156,6 @@ class TexeraWebApplication
     environment.jersey.register(classOf[AdminExecutionResource])
     environment.jersey.register(classOf[UserQuotaResource])
     environment.jersey.register(classOf[AIAssistantResource])
+
   }
 }

core/amber/src/main/scala/edu/uci/ics/texera/web/WebsocketInput.scala

@@ -3,17 +3,16 @@ package edu.uci.ics.texera.web
 import edu.uci.ics.texera.web.model.websocket.request.TexeraWebSocketRequest
 import io.reactivex.rxjava3.disposables.Disposable
 import io.reactivex.rxjava3.subjects.PublishSubject
-import org.jooq.types.UInteger
 
 import scala.reflect.{ClassTag, classTag}
 
 class WebsocketInput(errorHandler: Throwable => Unit) {
-  private val wsInput = PublishSubject.create[(TexeraWebSocketRequest, Option[UInteger])]()
+  private val wsInput = PublishSubject.create[(TexeraWebSocketRequest, Option[Integer])]()
 
   def subscribe[T <: TexeraWebSocketRequest: ClassTag](
-      callback: (T, Option[UInteger]) => Unit
+      callback: (T, Option[Integer]) => Unit
   ): Disposable = {
-    wsInput.subscribe((evt: (TexeraWebSocketRequest, Option[UInteger])) => {
+    wsInput.subscribe((evt: (TexeraWebSocketRequest, Option[Integer])) => {
       evt._1 match {
         case req: T if classTag[T].runtimeClass.isInstance(req) =>
           try {
@@ -28,7 +27,7 @@ class WebsocketInput(errorHandler: Throwable => Unit) {
     })
   }
 
-  def onNext(req: TexeraWebSocketRequest, uidOpt: Option[UInteger]): Unit = {
+  def onNext(req: TexeraWebSocketRequest, uidOpt: Option[Integer]): Unit = {
     wsInput.onNext((req, uidOpt))
   }
 

core/amber/src/main/scala/edu/uci/ics/texera/web/auth/GuestAuthFilter.scala

@@ -1,7 +1,7 @@
 package edu.uci.ics.texera.web.auth
 
 import edu.uci.ics.texera.web.auth.GuestAuthFilter.GUEST
-import edu.uci.ics.texera.dao.jooq.generated.enums.UserRole
+import edu.uci.ics.texera.dao.jooq.generated.enums.UserRoleEnum
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
 import io.dropwizard.auth.AuthFilter
 
@@ -18,7 +18,7 @@ import javax.ws.rs.core.SecurityContext
     override protected def newInstance = new GuestAuthFilter
   }
 
-  val GUEST: User = new User(null, "guest", null, null, null, UserRole.REGULAR, null)
+  val GUEST: User = new User(null, "guest", null, null, null, UserRoleEnum.REGULAR, null)
 }
 
 @PreMatching

core/amber/src/main/scala/edu/uci/ics/texera/web/auth/SessionUser.scala

@@ -1,8 +1,7 @@
 package edu.uci.ics.texera.web.auth
 
-import edu.uci.ics.texera.dao.jooq.generated.enums.UserRole
+import edu.uci.ics.texera.dao.jooq.generated.enums.UserRoleEnum
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
-import org.jooq.types.UInteger
 
 import java.security.Principal
 
@@ -11,11 +10,11 @@ class SessionUser(val user: User) extends Principal {
 
   override def getName: String = user.getName
 
-  def getUid: UInteger = user.getUid
+  def getUid: Integer = user.getUid
 
   def getEmail: String = user.getEmail
 
   def getGoogleId: String = user.getGoogleId
 
-  def isRoleOf(role: UserRole): Boolean = user.getRole == role
+  def isRoleOf(role: UserRoleEnum): Boolean = user.getRole == role
 }

core/amber/src/main/scala/edu/uci/ics/texera/web/auth/UserAuthenticator.scala

@@ -1,10 +1,10 @@
 package edu.uci.ics.texera.web.auth
 
 import com.typesafe.scalalogging.LazyLogging
-import edu.uci.ics.texera.dao.jooq.generated.enums.UserRole
+import edu.uci.ics.texera.dao.jooq.generated.enums.UserRoleEnum
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
 import io.dropwizard.auth.Authenticator
-import org.jooq.types.UInteger
+
 import org.jose4j.jwt.consumer.JwtContext
 
 import java.util.Optional
@@ -16,8 +16,9 @@ object UserAuthenticator extends Authenticator[JwtContext, SessionUser] with Laz
     try {
       val userName = context.getJwtClaims.getSubject
       val email = context.getJwtClaims.getClaimValue("email").asInstanceOf[String]
-      val userId = UInteger.valueOf(context.getJwtClaims.getClaimValue("userId").asInstanceOf[Long])
-      val role = UserRole.valueOf(context.getJwtClaims.getClaimValue("role").asInstanceOf[String])
+      val userId = context.getJwtClaims.getClaimValue("userId").asInstanceOf[Long].toInt
+      val role =
+        UserRoleEnum.valueOf(context.getJwtClaims.getClaimValue("role").asInstanceOf[String])
       val googleId = context.getJwtClaims.getClaimValue("googleId").asInstanceOf[String]
       val user = new User(userId, userName, email, null, googleId, role, null)
       Optional.of(new SessionUser(user))

core/amber/src/main/scala/edu/uci/ics/texera/web/auth/UserRoleAuthorizer.scala

@@ -1,10 +1,10 @@
 package edu.uci.ics.texera.web.auth
 
-import edu.uci.ics.texera.dao.jooq.generated.enums.UserRole
+import edu.uci.ics.texera.dao.jooq.generated.enums.UserRoleEnum
 import io.dropwizard.auth.Authorizer
 
 object UserRoleAuthorizer extends Authorizer[SessionUser] {
   override def authorize(user: SessionUser, role: String): Boolean = {
-    user.isRoleOf(UserRole.valueOf(role))
+    user.isRoleOf(UserRoleEnum.valueOf(role))
   }
 }

core/amber/src/main/scala/edu/uci/ics/texera/web/resource/CollaborationResource.scala

@@ -9,7 +9,6 @@ import edu.uci.ics.texera.web.model.collab.response.HeartBeatResponse
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
 import edu.uci.ics.texera.web.resource.CollaborationResource._
 import edu.uci.ics.texera.web.resource.dashboard.user.workflow.WorkflowAccessResource
-import org.jooq.types.UInteger
 
 import javax.websocket.server.ServerEndpoint
 import javax.websocket.{OnClose, OnMessage, OnOpen, Session}
@@ -25,7 +24,7 @@ object CollaborationResource {
   final val DUMMY_WID = -1
 
   private def checkIsReadOnly(wId: Int, uId: Int): Boolean = {
-    !WorkflowAccessResource.hasWriteAccess(UInteger.valueOf(wId), UInteger.valueOf(uId))
+    !WorkflowAccessResource.hasWriteAccess(Integer.valueOf(wId), Integer.valueOf(uId))
   }
 }
 

core/amber/src/main/scala/edu/uci/ics/texera/web/resource/UserConfigResource.scala

@@ -1,11 +1,10 @@
 package edu.uci.ics.texera.web.resource
 
-import edu.uci.ics.amber.core.storage.StorageConfig
 import edu.uci.ics.texera.dao.SqlServer
-import edu.uci.ics.texera.web.auth.SessionUser
 import edu.uci.ics.texera.dao.jooq.generated.Tables.USER_CONFIG
 import edu.uci.ics.texera.dao.jooq.generated.tables.daos.UserConfigDao
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.{User, UserConfig}
+import edu.uci.ics.texera.web.auth.SessionUser
 import io.dropwizard.auth.Auth
 
 import javax.annotation.security.RolesAllowed
@@ -25,7 +24,7 @@ import scala.jdk.CollectionConverters.CollectionHasAsScala
 class UserConfigResource {
   final private lazy val userDictionaryDao = new UserConfigDao(
     SqlServer
-      .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+      .getInstance()
       .createDSLContext()
       .configuration
   )
@@ -43,7 +42,7 @@ class UserConfigResource {
     */
   private def getDict(user: User): Map[String, String] = {
     SqlServer
-      .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+      .getInstance()
       .createDSLContext()
       .select()
       .from(USER_CONFIG)
@@ -79,7 +78,7 @@ class UserConfigResource {
     */
   private def getValueByKey(user: User, key: String): String = {
     SqlServer
-      .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+      .getInstance()
       .createDSLContext()
       .fetchOne(
         USER_CONFIG,
@@ -118,7 +117,7 @@ class UserConfigResource {
   private def dictEntryExists(user: User, key: String): Boolean = {
     userDictionaryDao.existsById(
       SqlServer
-        .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+        .getInstance()
         .createDSLContext()
         .newRecord(USER_CONFIG.UID, USER_CONFIG.KEY)
         .values(user.getUid, key)
@@ -154,7 +153,7 @@ class UserConfigResource {
   private def deleteDictEntry(user: User, key: String): Unit = {
     userDictionaryDao.deleteById(
       SqlServer
-        .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+        .getInstance()
         .createDSLContext()
         .newRecord(USER_CONFIG.UID, USER_CONFIG.KEY)
         .values(user.getUid, key)

core/amber/src/main/scala/edu/uci/ics/texera/web/resource/auth/AuthResource.scala

@@ -1,6 +1,5 @@
 package edu.uci.ics.texera.web.resource.auth
 
-import edu.uci.ics.amber.core.storage.StorageConfig
 import edu.uci.ics.amber.engine.common.AmberConfig
 import edu.uci.ics.texera.dao.SqlServer
 import edu.uci.ics.texera.web.auth.JwtAuth._
@@ -11,7 +10,7 @@ import edu.uci.ics.texera.web.model.http.request.auth.{
 }
 import edu.uci.ics.texera.web.model.http.response.TokenIssueResponse
 import edu.uci.ics.texera.dao.jooq.generated.Tables.USER
-import edu.uci.ics.texera.dao.jooq.generated.enums.UserRole
+import edu.uci.ics.texera.dao.jooq.generated.enums.UserRoleEnum
 import edu.uci.ics.texera.dao.jooq.generated.tables.daos.UserDao
 import edu.uci.ics.texera.dao.jooq.generated.tables.pojos.User
 import edu.uci.ics.texera.web.resource.auth.AuthResource._
@@ -24,7 +23,7 @@ object AuthResource {
 
   final private lazy val userDao = new UserDao(
     SqlServer
-      .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+      .getInstance()
       .createDSLContext()
       .configuration
   )
@@ -40,7 +39,7 @@ object AuthResource {
   def retrieveUserByUsernameAndPassword(name: String, password: String): Option[User] = {
     Option(
       SqlServer
-        .getInstance(StorageConfig.jdbcUrl, StorageConfig.jdbcUsername, StorageConfig.jdbcPassword)
+        .getInstance()
         .createDSLContext()
         .select()
         .from(USER)
@@ -88,7 +87,7 @@ class AuthResource {
         val user = new User
         user.setName(username)
         user.setEmail(username)
-        user.setRole(UserRole.ADMIN)
+        user.setRole(UserRoleEnum.ADMIN)
         // hash the plain text password
         user.setPassword(new StrongPasswordEncryptor().encryptPassword(request.password))
         userDao.insert(user)