Cleaning up findAll API

src/main/scala/org/mbari/vars/annotation/api/APIStack.scala

@@ -21,8 +21,6 @@ import java.time.format.DateTimeFormatter
 import java.time.{Duration, Instant}
 import java.util.UUID
 import java.util.concurrent.TimeUnit
-import java.util.function.{Consumer, Function}
-import java.util.stream.Stream
 
 import javax.servlet.http.HttpServletResponse
 import org.mbari.vars.annotation.Constants
@@ -33,7 +31,7 @@ import org.slf4j.LoggerFactory
 
 import scala.concurrent.duration.{Duration => SDuration}
 import scala.concurrent.{Await, Future}
-import scala.util.{Failure, Success, Try}
+import scala.util.Try
 
 /**
  * All Api classes should mixin this trait. It defines the common traits used by all implementations

src/main/scala/org/mbari/vars/annotation/api/v1/ImagedMomentV1Api.scala

@@ -43,8 +43,8 @@ class ImagedMomentV1Api(controller: ImagedMomentController)(implicit val executo
   }
 
   get("/") {
-    val limit = params.getAs[Int]("limit").getOrElse(1000)
-    val offset = params.getAs[Int]("offset").getOrElse(0)
+    val limit = params.getAs[Int]("limit").orElse(Some(100))
+    val offset = params.getAs[Int]("offset").orElse(Some(0))
     controller.findAll(limit, offset)
       .map(_.asJava)
       .map(toJson)

src/main/scala/org/mbari/vars/annotation/controllers/AnnotationController.scala

@@ -94,10 +94,14 @@ class AnnotationController(daoFactory: BasicDAOFactory) {
                                               endTimestamp: Instant,
                                 limit: Option[Int] = None,
                                  offset: Option[Int] = None): (Closeable, java.util.stream.Stream[Annotation]) = {
-    val dao = daoFactory.newImagedMomentDAO()
+//    val dao = daoFactory.newImagedMomentDAO()
+//    (() => dao.close(),
+//      dao.streamByVideoReferenceUUIDAndTimestamps(videoReferenceUuid, startTimestamp, endTimestamp, limit, offset)
+//        .flatMap(im => im.javaObservations.stream().map(obs => AnnotationImpl(obs))))
+    val dao = daoFactory.newObservationDAO()
     (() => dao.close(),
       dao.streamByVideoReferenceUUIDAndTimestamps(videoReferenceUuid, startTimestamp, endTimestamp, limit, offset)
-        .flatMap(im => im.javaObservations.stream().map(obs => AnnotationImpl(obs))))
+        .map(obs => AnnotationImpl(obs)))
   }
 
 

src/main/scala/org/mbari/vars/annotation/controllers/BaseController.scala

@@ -55,8 +55,8 @@ trait BaseController[A <: PersistentObject, B <: DAO[A]] {
     exec(fn)
   }
 
-  def findAll()(implicit ec: ExecutionContext): Future[Iterable[A]] =
-    exec(d => d.findAll())
+  def findAll(limit: Option[Int] = None, offset: Option[Int] = None)(implicit ec: ExecutionContext): Future[Iterable[A]] =
+    exec(d => d.findAll(limit, offset))
 
   def findByUUID(uuid: UUID)(implicit ec: ExecutionContext): Future[Option[A]] =
     exec(d => d.findByUUID(uuid))

src/main/scala/org/mbari/vars/annotation/controllers/ImagedMomentController.scala

@@ -40,7 +40,7 @@ class ImagedMomentController(val daoFactory: BasicDAOFactory)
 
   override def newDAO(): IMDAO = daoFactory.newImagedMomentDAO()
 
-  def findAll(limit: Int, offset: Int)(implicit ec: ExecutionContext): Future[Iterable[ImagedMoment]] =
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None)(implicit ec: ExecutionContext): Future[Iterable[ImagedMoment]] =
     exec(d => d.findAll(limit, offset))
 
   def findAllVideoReferenceUUIDs(limit: Option[Int] = None, offset: Option[Int] = None)(implicit ec: ExecutionContext): Future[Iterable[UUID]] =

src/main/scala/org/mbari/vars/annotation/dao/DAO.scala

@@ -37,8 +37,7 @@ trait DAO[A <: PersistentObject] {
   def delete(entity: A): Unit
   def deleteByUUID(primaryKey: UUID): Unit
   def findByUUID(primaryKey: UUID): Option[A]
-  def findAll(): Iterable[A]
-  def findAll(limit: Int, offset: Int): Iterable[A]
+  def findAll(limit: Option[Int] = None, offset:Option[Int] = None): Iterable[A]
   def runTransaction[R](fn: this.type => R)(implicit ec: ExecutionContext): Future[R]
   def close(): Unit
 

src/main/scala/org/mbari/vars/annotation/dao/jpa/AssociationDAOImpl.scala

@@ -90,11 +90,9 @@ class AssociationDAOImpl(entityManager: EntityManager)
     }
   }
 
-  override def findAll(): Iterable[AssociationImpl] =
-    findByNamedQuery("Association.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[AssociationImpl] =
-    findByNamedQuery("Association.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[AssociationImpl] =
+    findByNamedQuery("Association.findAll", limit = limit, offset = offset)
 
   override def countByToConcept(toConcept: String): Int = {
     //val query = entityManager.createNativeQuery("Association.countByToConcept")

src/main/scala/org/mbari/vars/annotation/dao/jpa/CachedAncillaryDatumDAOImpl.scala

@@ -76,11 +76,9 @@ class CachedAncillaryDatumDAOImpl(entityManager: EntityManager)
   override def asPersistentObject(datum: CachedAncillaryDatum): CachedAncillaryDatum =
     CachedAncillaryDatumImpl(datum)
 
-  override def findAll(): Iterable[CachedAncillaryDatumImpl] =
-    findByNamedQuery("AncillaryDatum.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[CachedAncillaryDatumImpl] =
-    findByNamedQuery("AncillaryDatum.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[CachedAncillaryDatumImpl] =
+    findByNamedQuery("AncillaryDatum.findAll", limit = limit, offset = offset)
 
   override def findByObservationUUID(observationUuid: UUID): Option[CachedAncillaryDatum] =
     findByNamedQuery(

src/main/scala/org/mbari/vars/annotation/dao/jpa/CachedVideoReferenceInfoDAOImpl.scala

@@ -46,11 +46,9 @@ class CachedVideoReferenceInfoDAOImpl(entityManager: EntityManager)
   override def findByVideoReferenceUUID(uuid: UUID): Option[CachedVideoReferenceInfoImpl] =
     findByNamedQuery("VideoReferenceInfo.findByVideoReferenceUUID", Map("uuid" -> uuid)).headOption
 
-  override def findAll(): Iterable[CachedVideoReferenceInfoImpl] =
-    findByNamedQuery("VideoReferenceInfo.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[CachedVideoReferenceInfoImpl] =
-    findByNamedQuery("VideoReferenceInfo.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[CachedVideoReferenceInfoImpl] =
+    findByNamedQuery("VideoReferenceInfo.findAll", limit = limit, offset = offset)
 
   override def findAllVideoReferenceUUIDs(): Iterable[UUID] =
     fetchUsing("VideoReferenceInfo.findAllVideoReferenceUUIDs")

src/main/scala/org/mbari/vars/annotation/dao/jpa/ImageReferenceDAOImpl.scala

@@ -48,11 +48,9 @@ class ImageReferenceDAOImpl(entityManager: EntityManager)
     imageReference
   }
 
-  override def findAll(): Iterable[ImageReferenceImpl] =
-    findByNamedQuery("ImageReference.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[ImageReferenceImpl] =
-    findByNamedQuery("ImageReference.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[ImageReferenceImpl] =
+    findByNamedQuery("ImageReference.findAll", limit = limit, offset = offset)
 
   override def findByURL(url: URL): Option[ImageReferenceImpl] =
     findByNamedQuery("ImageReference.findByURL", Map("url" -> url)).headOption

src/main/scala/org/mbari/vars/annotation/dao/jpa/ImagedMomentDAOImpl.scala

@@ -202,11 +202,9 @@ class ImagedMomentDAOImpl(entityManager: EntityManager)
   //  override def findByUUID(primaryKey: UUID): Option[ImagedMomentImpl] =
   //    findByNamedQuery("ImagedMoment.findByUUID", Map("uuid" -> primaryKey)).headOption
 
-  override def findAll(): Iterable[ImagedMomentImpl] =
-    findByNamedQuery("ImagedMoment.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[ImagedMomentImpl] =
-    findByNamedQuery("ImagedMoment.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[ImagedMomentImpl] =
+    findByNamedQuery("ImagedMoment.findAll", limit = limit, offset = offset)
 
   override def findByVideoReferenceUUIDAndElapsedTime(uuid: UUID, elapsedTime: Duration): Option[ImagedMomentImpl] =
     findByNamedQuery(

src/main/scala/org/mbari/vars/annotation/dao/jpa/ImagedMomentImpl.scala

@@ -137,7 +137,7 @@ import scala.collection.JavaConverters._
     ),
     new NamedQuery(
       name = "ImagedMoment.findByVideoReferenceUUIDAndTimestamps",
-      query = "SELECT i FROM ImagedMoment i WHERE i.videoReferenceUUID = :uuid AND i.recordedDate BETWEEN :start AND :end"
+      query = "SELECT i FROM ImagedMoment i WHERE i.videoReferenceUUID = :uuid AND i.recordedDate BETWEEN :start AND :end ORDER BY i.recordedDate"
     ),
     new NamedQuery(
       name = "ImagedMoment.findWithImageReferences",

src/main/scala/org/mbari/vars/annotation/dao/jpa/IndexDAOImpl.scala

@@ -40,9 +40,7 @@ class IndexDAOImpl(entityManager: EntityManager)
 
   // --- These methods are deliberately overridden ---
 
-  override def findAll(): Iterable[IndexImpl] = ???
-
-  override def findAll(limit: Int, offset: Int): Iterable[IndexImpl] = ???
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[IndexImpl] = ???
 
   override def deleteByUUID(primaryKey: UUID): Unit = ???
 

src/main/scala/org/mbari/vars/annotation/dao/jpa/ObservationDAOImpl.scala

@@ -94,11 +94,9 @@ class ObservationDAOImpl(entityManager: EntityManager)
     .filter(_ != null)
     .map(_.toString)
 
-  override def findAll(): Iterable[ObservationImpl] =
-    findByNamedQuery("Observation.findAll")
 
-  override def findAll(limit: Int, offset: Int): Iterable[ObservationImpl] =
-    findByNamedQuery("Observation.findAll", limit = Some(limit), offset = Some(offset))
+  override def findAll(limit: Option[Int] = None, offset: Option[Int] = None): Iterable[ObservationImpl] =
+    findByNamedQuery("Observation.findAll", limit = limit, offset = offset)
 
   override def findAllConceptsByVideoReferenceUUID(uuid: UUID): Seq[String] = {
     val query = entityManager.createNamedQuery("Observation.findAllNamesByVideoReferenceUUID")

src/main/scala/org/mbari/vars/annotation/dao/jpa/ObservationImpl.scala

@@ -79,7 +79,7 @@ import org.mbari.vars.annotation.model.{Association, ImagedMoment, Observation}
     query = "SELECT o FROM Observation o LEFT JOIN o.imagedMoment i WHERE i.videoReferenceUUID = :uuid ORDER BY o.uuid"),
   new NamedQuery(
     name = "Observation.findByVideoReferenceUUIDAndTimestamps",
-    query = "SELECT o FROM Observation o LEFT JOIN o.imagedMoment i WHERE i.videoReferenceUUID = :uuid AND i.recordedDate BETWEEN :start AND :end ORDER BY o.uuid")))
+    query = "SELECT o FROM Observation o LEFT JOIN o.imagedMoment i WHERE i.videoReferenceUUID = :uuid AND i.recordedDate BETWEEN :start AND :end ORDER BY i.recordedDate")))
 class ObservationImpl extends Observation with JPAPersistentObject {
 
   @Expose(serialize = true)

src/test/scala/org/mbari/vars/annotation/api/v1/AnnotationV1ApiSpec.scala

@@ -43,8 +43,6 @@ class AnnotationV1ApiSpec extends WebApiStack {
     new AnnotationV1Api(controller)
   }
 
-  protected[this] override val gson = Constants.GSON_FOR_ANNOTATION
-
   addServlet(annotationV1Api, "/v1/annotations")
 
   var annotation: Annotation = _

src/test/scala/org/mbari/vars/annotation/api/v1/CachedAncillaryDatumV1ApiSpec.scala

@@ -40,7 +40,6 @@ class CachedAncillaryDatumV1ApiSpec extends WebApiStack {
     val controller = new CachedAncillaryDatumController(daoFactory)
     new CachedAncillaryDatumV1Api(controller)
   }
-  protected[this] override val gson = Constants.GSON
 
   private[this] val path = "/v1/ancillarydata"
   addServlet(datumV1Api, path)

src/test/scala/org/mbari/vars/annotation/api/v1/IndexV1ApiSpec.scala

@@ -36,8 +36,6 @@ import scala.concurrent.duration.{Duration => SDuration}
  */
 class IndexV1ApiSpec extends WebApiStack {
 
-  private[this] val startTimestamp = Instant.now()
-
   private[this] val indexController = new IndexController(daoFactory)
 
   private[this] val indexV1Api = new IndexV1Api(indexController)

src/test/scala/org/mbari/vars/annotation/controllers/AnnotationControllerSpec.scala

@@ -39,7 +39,7 @@ class AnnotationControllerSpec extends FlatSpec with Matchers with BeforeAndAfte
   private[this] val controller = new AnnotationController(daoFactory.asInstanceOf[BasicDAOFactory])
   private[this] val timeout = SDuration(200, TimeUnit.SECONDS)
   private[this] val recordedDate = Instant.now()
-  private[this] val log = LoggerFactory.getLogger(getClass)
+//  private[this] val log = LoggerFactory.getLogger(getClass)
 
   def exec[R](fn: () => Future[R]): R = Await.result(fn.apply(), timeout)
 
@@ -103,6 +103,8 @@ class AnnotationControllerSpec extends FlatSpec with Matchers with BeforeAndAfte
         recordedDate = Some(recordedDate.plusSeconds(i * 3600))))
     }
 
+    xs.size should be (5)
+
     val (closeable, stream) = controller.streamByVideoReferenceUUIDAndTimestamps(videoReferenceUuid,
         recordedDate,
       recordedDate.plusSeconds(4000))