add protected and private modifiers to DAO hierarchy (#6698)

* add protected and private modifiers to DAO hierarchy

* format

app/WebKnossosModule.scala

@@ -21,7 +21,6 @@ class WebKnossosModule extends AbstractModule {
     bind(classOf[UserService]).asEagerSingleton()
     bind(classOf[TaskService]).asEagerSingleton()
     bind(classOf[UserDAO]).asEagerSingleton()
-    bind(classOf[UserTeamRolesDAO]).asEagerSingleton()
     bind(classOf[UserExperiencesDAO]).asEagerSingleton()
     bind(classOf[UserDataSetConfigurationDAO]).asEagerSingleton()
     bind(classOf[UserCache]).asEagerSingleton()

app/controllers/InitialDataController.scala

@@ -38,7 +38,6 @@ class InitialDataController @Inject()(initialDataService: InitialDataService, si
 class InitialDataService @Inject()(userService: UserService,
                                    userDAO: UserDAO,
                                    multiUserDAO: MultiUserDAO,
-                                   userTeamRolesDAO: UserTeamRolesDAO,
                                    userExperiencesDAO: UserExperiencesDAO,
                                    taskTypeDAO: TaskTypeDAO,
                                    dataStoreDAO: DataStoreDAO,
@@ -182,9 +181,8 @@ Samplecountry
             _ <- multiUserDAO.insertOne(multiUser)
             _ <- userDAO.insertOne(user)
             _ <- userExperiencesDAO.updateExperiencesForUser(user, Map("sampleExp" -> 10))
-            _ <- userTeamRolesDAO.insertTeamMembership(
-              user._id,
-              TeamMembership(organizationTeam._id, isTeamManager = isTeamManager))
+            _ <- userDAO.insertTeamMembership(user._id,
+                                              TeamMembership(organizationTeam._id, isTeamManager = isTeamManager))
             _ = logger.info("Inserted default user")
           } yield ()
       }

app/controllers/TeamController.scala

@@ -4,21 +4,19 @@ import com.mohiva.play.silhouette.api.Silhouette
 import com.scalableminds.util.tools.Fox
 import io.swagger.annotations._
 import models.team._
-import models.user.UserTeamRolesDAO
+import models.user.UserDAO
 import oxalis.security.WkEnv
 import play.api.i18n.Messages
 import play.api.libs.json._
-import utils.ObjectId
-import javax.inject.Inject
 import play.api.mvc.{Action, AnyContent}
+import utils.ObjectId
 
+import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 
 @Api
-class TeamController @Inject()(teamDAO: TeamDAO,
-                               userTeamRolesDAO: UserTeamRolesDAO,
-                               teamService: TeamService,
-                               sil: Silhouette[WkEnv])(implicit ec: ExecutionContext)
+class TeamController @Inject()(teamDAO: TeamDAO, userDAO: UserDAO, teamService: TeamService, sil: Silhouette[WkEnv])(
+    implicit ec: ExecutionContext)
     extends Controller {
 
   private def teamNameReads: Reads[String] =
@@ -46,7 +44,7 @@ class TeamController @Inject()(teamDAO: TeamDAO,
       _ <- bool2Fox(!team.isOrganizationTeam) ?~> "team.delete.organizationTeam" ~> FORBIDDEN
       _ <- teamService.assertNoReferences(teamIdValidated) ?~> "team.delete.inUse" ~> FORBIDDEN
       _ <- teamDAO.deleteOne(teamIdValidated)
-      _ <- userTeamRolesDAO.removeTeamFromAllUsers(teamIdValidated)
+      _ <- userDAO.removeTeamFromAllUsers(teamIdValidated)
       _ <- teamDAO.removeTeamFromAllDatasetsAndFolders(teamIdValidated)
     } yield JsonOk(Messages("team.deleted"))
   }

app/models/annotation/Annotation.scala

@@ -144,12 +144,12 @@ class AnnotationLayerDAO @Inject()(SQLClient: SQLClient)(implicit ec: ExecutionC
 class AnnotationDAO @Inject()(sqlClient: SQLClient, annotationLayerDAO: AnnotationLayerDAO)(
     implicit ec: ExecutionContext)
     extends SQLDAO[Annotation, AnnotationsRow, Annotations](sqlClient) {
-  val collection = Annotations
+  protected val collection = Annotations
 
-  def idColumn(x: Annotations): Rep[String] = x._Id
-  def isDeletedColumn(x: Annotations): Rep[Boolean] = x.isdeleted
+  protected def idColumn(x: Annotations): Rep[String] = x._Id
+  protected def isDeletedColumn(x: Annotations): Rep[Boolean] = x.isdeleted
 
-  def parse(r: AnnotationsRow): Fox[Annotation] =
+  protected def parse(r: AnnotationsRow): Fox[Annotation] =
     for {
       state <- AnnotationState.fromString(r.state).toFox
       typ <- AnnotationType.fromString(r.typ).toFox
@@ -180,7 +180,8 @@ class AnnotationDAO @Inject()(sqlClient: SQLClient, annotationLayerDAO: Annotati
       )
     }
 
-  override def anonymousReadAccessQ(sharingToken: Option[String]) = s"visibility = '${AnnotationVisibility.Public}'"
+  override protected def anonymousReadAccessQ(sharingToken: Option[String]) =
+    s"visibility = '${AnnotationVisibility.Public}'"
 
   private def listAccessQ(requestingUserId: ObjectId): String =
     s"""
@@ -206,7 +207,7 @@ class AnnotationDAO @Inject()(sqlClient: SQLClient, annotationLayerDAO: Annotati
         )
        """
 
-  override def readAccessQ(requestingUserId: ObjectId): String =
+  override protected def readAccessQ(requestingUserId: ObjectId): String =
     s"""(
               visibility = '${AnnotationVisibility.Public}'
            or (visibility = '${AnnotationVisibility.Internal}'
@@ -218,12 +219,12 @@ class AnnotationDAO @Inject()(sqlClient: SQLClient, annotationLayerDAO: Annotati
              in (select _organization from webknossos.users_ where _id = '$requestingUserId' and isAdmin)
          )"""
 
-  override def deleteAccessQ(requestingUserId: ObjectId) =
+  override protected def deleteAccessQ(requestingUserId: ObjectId) =
     s"""(_team in (select _team from webknossos.user_team_roles where isTeamManager and _user = '$requestingUserId') or _user = '$requestingUserId'
        or (select _organization from webknossos.teams where webknossos.teams._id = _team)
         in (select _organization from webknossos.users_ where _id = '$requestingUserId' and isAdmin))"""
 
-  override def updateAccessQ(requestingUserId: ObjectId): String =
+  override protected def updateAccessQ(requestingUserId: ObjectId): String =
     deleteAccessQ(requestingUserId)
 
   // read operations
@@ -543,20 +544,16 @@ class AnnotationDAO @Inject()(sqlClient: SQLClient, annotationLayerDAO: Annotati
       _ <- run(
         sqlu"insert into webknossos.annotation_contributors (_annotation, _user) values($id, $userId) on conflict do nothing")
     } yield ()
-}
-
-class SharedAnnotationsDAO @Inject()(annotationDAO: AnnotationDAO, sqlClient: SQLClient)(implicit ec: ExecutionContext)
-    extends SimpleSQLDAO(sqlClient) {
 
   // Does not use access query (because they dont support prefixes). Use only after separate access check!
   def findAllSharedForTeams(teams: List[ObjectId]): Fox[List[Annotation]] =
     for {
       result <- run(
-        sql"""select distinct #${annotationDAO.columnsWithPrefix("a.")} from webknossos.annotations_ a
+        sql"""select distinct #${columnsWithPrefix("a.")} from webknossos.annotations_ a
                             join webknossos.annotation_sharedTeams l on a._id = l._annotation
                             where l._team in #${writeStructTupleWithQuotes(teams.map(t => sanitize(t.toString)))}"""
           .as[AnnotationsRow])
-      parsed <- Fox.combined(result.toList.map(annotationDAO.parse))
+      parsed <- Fox.combined(result.toList.map(parse))
     } yield parsed
 
   def updateTeamsForSharedAnnotation(annotationId: ObjectId, teams: List[ObjectId])(
@@ -568,11 +565,10 @@ class SharedAnnotationsDAO @Inject()(annotationDAO: AnnotationDAO, sqlClient: SQ
 
     val composedQuery = DBIO.sequence(List(clearQuery) ++ insertQueries)
     for {
-      _ <- annotationDAO.assertUpdateAccess(annotationId)
+      _ <- assertUpdateAccess(annotationId)
       _ <- run(composedQuery.transactionally.withTransactionIsolation(Serializable),
                retryCount = 50,
                retryIfErrorContains = List(transactionSerializationError))
     } yield ()
   }
-
 }

app/models/annotation/AnnotationPrivateLink.scala

@@ -45,13 +45,13 @@ class AnnotationPrivateLinkService @Inject()()(implicit ec: ExecutionContext) {
 
 class AnnotationPrivateLinkDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[AnnotationPrivateLink, AnnotationPrivatelinksRow, AnnotationPrivatelinks](sqlClient) {
-  val collection = AnnotationPrivatelinks
+  protected val collection = AnnotationPrivatelinks
 
-  def idColumn(x: AnnotationPrivatelinks): Rep[String] = x._Id
+  protected def idColumn(x: AnnotationPrivatelinks): Rep[String] = x._Id
 
-  def isDeletedColumn(x: AnnotationPrivatelinks): Rep[Boolean] = x.isdeleted
+  protected def isDeletedColumn(x: AnnotationPrivatelinks): Rep[Boolean] = x.isdeleted
 
-  def parse(r: AnnotationPrivatelinksRow): Fox[AnnotationPrivateLink] =
+  protected def parse(r: AnnotationPrivatelinksRow): Fox[AnnotationPrivateLink] =
     Fox.successful(
       AnnotationPrivateLink(
         ObjectId(r._Id),
@@ -62,7 +62,7 @@ class AnnotationPrivateLinkDAO @Inject()(sqlClient: SQLClient)(implicit ec: Exec
       )
     )
 
-  override def readAccessQ(requestingUserId: ObjectId): String =
+  override protected def readAccessQ(requestingUserId: ObjectId): String =
     s"""(_annotation in (select _id from webknossos.annotations_ where _user = '${requestingUserId.id}'))"""
 
   def insertOne(aPL: AnnotationPrivateLink): Fox[Unit] =

app/models/annotation/AnnotationService.scala

@@ -105,8 +105,7 @@ class AnnotationService @Inject()(
     nmlWriter: NmlWriter,
     temporaryFileCreator: TemporaryFileCreator,
     meshDAO: MeshDAO,
-    meshService: MeshService,
-    sharedAnnotationsDAO: SharedAnnotationsDAO
+    meshService: MeshService
 )(implicit ec: ExecutionContext, val materializer: Materializer)
     extends BoxImplicits
     with FoxImplicits
@@ -589,11 +588,11 @@ class AnnotationService @Inject()(
 
   // Does not use access query (because they dont support prefixes). Use only after separate access check!
   def sharedAnnotationsFor(userTeams: List[ObjectId]): Fox[List[Annotation]] =
-    sharedAnnotationsDAO.findAllSharedForTeams(userTeams)
+    annotationDAO.findAllSharedForTeams(userTeams)
 
   def updateTeamsForSharedAnnotation(annotationId: ObjectId, teams: List[ObjectId])(
       implicit ctx: DBAccessContext): Fox[Unit] =
-    sharedAnnotationsDAO.updateTeamsForSharedAnnotation(annotationId, teams)
+    annotationDAO.updateTeamsForSharedAnnotation(annotationId, teams)
 
   def zipAnnotations(annotations: List[Annotation], zipFileName: String, skipVolumeData: Boolean)(
       implicit

app/models/annotation/TracingStore.scala

@@ -59,12 +59,12 @@ class TracingStoreService @Inject()(tracingStoreDAO: TracingStoreDAO, rpc: RPC)(
 
 class TracingStoreDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[TracingStore, TracingstoresRow, Tracingstores](sqlClient) {
-  val collection = Tracingstores
+  protected val collection = Tracingstores
 
-  def idColumn(x: Tracingstores): Rep[String] = x.name
-  def isDeletedColumn(x: Tracingstores): Rep[Boolean] = x.isdeleted
+  protected def idColumn(x: Tracingstores): Rep[String] = x.name
+  protected def isDeletedColumn(x: Tracingstores): Rep[Boolean] = x.isdeleted
 
-  def parse(r: TracingstoresRow): Fox[TracingStore] =
+  protected def parse(r: TracingstoresRow): Fox[TracingStore] =
     Fox.successful(
       TracingStore(
         r.name,

app/models/binary/DataSet.scala

@@ -62,11 +62,11 @@ class DataSetDAO @Inject()(sqlClient: SQLClient,
                            dataSetDataLayerDAO: DataSetDataLayerDAO,
                            organizationDAO: OrganizationDAO)(implicit ec: ExecutionContext)
     extends SQLDAO[DataSet, DatasetsRow, Datasets](sqlClient) {
-  val collection = Datasets
+  protected val collection = Datasets
 
-  def idColumn(x: Datasets): Rep[String] = x._Id
+  protected def idColumn(x: Datasets): Rep[String] = x._Id
 
-  def isDeletedColumn(x: Datasets): Rep[Boolean] = x.isdeleted
+  protected def isDeletedColumn(x: Datasets): Rep[Boolean] = x.isdeleted
 
   private def parseScaleOpt(literalOpt: Option[String]): Fox[Option[Vec3Double]] = literalOpt match {
     case Some(literal) =>
@@ -79,7 +79,7 @@ class DataSetDAO @Inject()(sqlClient: SQLClient,
   private def writeScaleLiteral(scale: Vec3Double): String =
     writeStructTuple(List(scale.x, scale.y, scale.z).map(_.toString))
 
-  def parse(r: DatasetsRow): Fox[DataSet] =
+  protected def parse(r: DatasetsRow): Fox[DataSet] =
     for {
       scale <- parseScaleOpt(r.scale)
       defaultViewConfigurationOpt <- Fox.runOptional(r.defaultviewconfiguration)(
@@ -405,7 +405,7 @@ class DataSetDAO @Inject()(sqlClient: SQLClient,
 
 class DataSetResolutionsDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SimpleSQLDAO(sqlClient) {
-  def parseRow(row: DatasetResolutionsRow): Fox[Vec3Int] =
+  private def parseRow(row: DatasetResolutionsRow): Fox[Vec3Int] =
     for {
       resolution <- Vec3Int.fromList(parseArrayTuple(row.resolution).map(_.toInt)) ?~> "could not parse resolution"
     } yield resolution
@@ -447,7 +447,7 @@ class DataSetDataLayerDAO @Inject()(sqlClient: SQLClient, dataSetResolutionsDAO:
     implicit ec: ExecutionContext)
     extends SimpleSQLDAO(sqlClient) {
 
-  def parseRow(row: DatasetLayersRow, dataSetId: ObjectId, skipResolutions: Boolean = false): Fox[DataLayer] = {
+  private def parseRow(row: DatasetLayersRow, dataSetId: ObjectId, skipResolutions: Boolean): Fox[DataLayer] = {
     val result: Fox[Fox[DataLayer]] = for {
       category <- Category.fromString(row.category).toFox ?~> "Could not parse Layer Category"
       boundingBox <- BoundingBox

app/models/binary/DataStore.scala

@@ -82,15 +82,15 @@ class DataStoreService @Inject()(dataStoreDAO: DataStoreDAO)(implicit ec: Execut
 
 class DataStoreDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[DataStore, DatastoresRow, Datastores](sqlClient) {
-  val collection = Datastores
+  protected val collection = Datastores
 
-  def idColumn(x: Datastores): Rep[String] = x.name
-  def isDeletedColumn(x: Datastores): Rep[Boolean] = x.isdeleted
+  protected def idColumn(x: Datastores): Rep[String] = x.name
+  protected def isDeletedColumn(x: Datastores): Rep[Boolean] = x.isdeleted
 
-  override def readAccessQ(requestingUserId: ObjectId): String =
+  override protected def readAccessQ(requestingUserId: ObjectId): String =
     s"(onlyAllowedOrganization is null) OR (onlyAllowedOrganization in (select _organization from webknossos.users_ where _id = '$requestingUserId'))"
 
-  def parse(r: DatastoresRow): Fox[DataStore] =
+  protected def parse(r: DatastoresRow): Fox[DataStore] =
     Fox.successful(
       DataStore(
         r.name,

app/models/binary/Publication.scala

@@ -54,13 +54,13 @@ class PublicationService @Inject()(dataSetService: DataSetService,
 
 class PublicationDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[Publication, PublicationsRow, Publications](sqlClient) {
-  val collection = Publications
+  protected val collection = Publications
 
-  def idColumn(x: Publications): Rep[String] = x._Id
+  protected def idColumn(x: Publications): Rep[String] = x._Id
 
-  def isDeletedColumn(x: Publications): Rep[Boolean] = x.isdeleted
+  protected def isDeletedColumn(x: Publications): Rep[Boolean] = x.isdeleted
 
-  def parse(r: PublicationsRow): Fox[Publication] =
+  protected def parse(r: PublicationsRow): Fox[Publication] =
     Fox.successful(
       Publication(
         ObjectId(r._Id),

app/models/folder/Folder.scala

@@ -75,22 +75,22 @@ class FolderService @Inject()(teamDAO: TeamDAO,
 class FolderDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[Folder, FoldersRow, Folders](sqlClient) {
 
-  val collection = Folders
-  def idColumn(x: Folders): Rep[String] = x._Id
-  def isDeletedColumn(x: Folders): Rep[Boolean] = x.isdeleted
+  protected val collection = Folders
+  protected def idColumn(x: Folders): Rep[String] = x._Id
+  protected def isDeletedColumn(x: Folders): Rep[Boolean] = x.isdeleted
 
-  def parse(r: FoldersRow): Fox[Folder] =
+  protected def parse(r: FoldersRow): Fox[Folder] =
     Fox.successful(Folder(ObjectId(r._Id), r.name))
 
-  def parseWithParent(t: (String, String, Option[String])): Fox[FolderWithParent] =
+  private def parseWithParent(t: (String, String, Option[String])): Fox[FolderWithParent] =
     Fox.successful(FolderWithParent(ObjectId(t._1), t._2, t._3.map(ObjectId(_))))
 
-  override def readAccessQ(requestingUserId: ObjectId): String = readAccessQWithPrefix(requestingUserId, "")
+  override protected def readAccessQ(requestingUserId: ObjectId): String = readAccessQWithPrefix(requestingUserId, "")
 
-  def readAccessQWithPrefix(requestingUserId: ObjectId, prefix: String): String =
+  private def readAccessQWithPrefix(requestingUserId: ObjectId, prefix: String): String =
     rawAccessQ(write = false, requestingUserId, prefix)
 
-  override def updateAccessQ(requestingUserId: ObjectId): String =
+  override protected def updateAccessQ(requestingUserId: ObjectId): String =
     rawAccessQ(write = true, requestingUserId, prefix = "")
 
   private def rawAccessQ(write: Boolean, requestingUserId: ObjectId, prefix: String): String = {

app/models/job/Job.scala

@@ -92,12 +92,12 @@ case class Job(
 
 class JobDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[Job, JobsRow, Jobs](sqlClient) {
-  val collection = Jobs
+  protected val collection = Jobs
 
-  def idColumn(x: Jobs): Rep[String] = x._Id
-  def isDeletedColumn(x: Jobs): Rep[Boolean] = x.isdeleted
+  protected def idColumn(x: Jobs): Rep[String] = x._Id
+  protected def isDeletedColumn(x: Jobs): Rep[Boolean] = x.isdeleted
 
-  def parse(r: JobsRow): Fox[Job] =
+  protected def parse(r: JobsRow): Fox[Job] =
     for {
       manualStateOpt <- Fox.runOptional(r.manualstate)(JobState.fromString)
       state <- JobState.fromString(r.state)
@@ -120,7 +120,7 @@ class JobDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
       )
     }
 
-  override def readAccessQ(requestingUserId: ObjectId) =
+  override protected def readAccessQ(requestingUserId: ObjectId) =
     s"""_owner = '$requestingUserId'"""
 
   override def findAll(implicit ctx: DBAccessContext): Fox[List[Job]] =

app/models/job/Worker.scala

@@ -30,13 +30,13 @@ case class Worker(_id: ObjectId,
 
 class WorkerDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[Worker, WorkersRow, Workers](sqlClient) {
-  val collection = Workers
+  protected val collection = Workers
 
-  def idColumn(x: Workers): Rep[String] = x._Id
+  protected def idColumn(x: Workers): Rep[String] = x._Id
 
-  def isDeletedColumn(x: Workers): Rep[Boolean] = x.isdeleted
+  protected def isDeletedColumn(x: Workers): Rep[Boolean] = x.isdeleted
 
-  def parse(r: WorkersRow): Fox[Worker] =
+  protected def parse(r: WorkersRow): Fox[Worker] =
     Fox.successful(
       Worker(
         ObjectId(r._Id),

app/models/mesh/Mesh.scala

@@ -55,19 +55,19 @@ class MeshService @Inject()()(implicit ec: ExecutionContext) {
 
 class MeshDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContext)
     extends SQLDAO[MeshInfo, MeshesRow, Meshes](sqlClient) {
-  val collection = Meshes
+  protected val collection = Meshes
 
-  def idColumn(x: Meshes): Rep[String] = x._Id
+  protected def idColumn(x: Meshes): Rep[String] = x._Id
 
-  def isDeletedColumn(x: Meshes): Rep[Boolean] = x.isdeleted
+  protected def isDeletedColumn(x: Meshes): Rep[Boolean] = x.isdeleted
 
   private val infoColumns = (columnsList diff Seq("data")).mkString(", ")
   type InfoTuple = (ObjectId, ObjectId, String, String, Instant, Boolean)
 
-  override def parse(r: MeshesRow): Fox[MeshInfo] =
+  override protected def parse(r: MeshesRow): Fox[MeshInfo] =
     Fox.failure("not implemented, use parseInfo or get the data directly")
 
-  def parseInfo(r: InfoTuple): Fox[MeshInfo] =
+  private def parseInfo(r: InfoTuple): Fox[MeshInfo] =
     for {
       position <- Vec3Int.fromList(parseArrayTuple(r._4).map(_.toInt)) ?~> "could not parse mesh position"
     } yield {