Show Annotation Segment Counts in Dashboard (#7548)

* WIP: save annotation stats per layer * store annotation stats per layer in postgres * generalize annotation stats and send segmentCount for volume tracings * sql migration * add zeros for new annotation layers * integrate segment stats into dashboard and unify with stats in dataset-info-sidebar * remove obsolete stats property from annotation object * changelog * don't show segment or tree count if a skeleton-only or volume-only annotation is present * fix unit tests * test db, snapshots * rename stats to statistics in listExplorationals json * fix typing * rename statistics to stats in annotation json * re-add stats property to type definition * use pluralize for segment and tree count formatting * add missing import * DRY helper type --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]>
scalableminds · Jan 22, 2024 · d8a2931 · d8a2931
1 parent 9187eff
commit d8a2931
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -22,6 +22,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - When setting up WEBKNOSSOS from the git repository for development, the organization directory for storing datasets is now automatically created on startup. [#7517](https://github.com/scalableminds/webknossos/pull/7517)
 - Multiple segments can be dragged and dropped in the segments tab. [#7536](https://github.com/scalableminds/webknossos/pull/7536)
 - Added the option to convert agglomerate skeletons to freely modifiable skeletons in the context menu of the Skeleton tab. [#7537](https://github.com/scalableminds/webknossos/pull/7537)
+- The annotation list in the dashboard now also shows segment counts of volume annotations (after they have been edited). [#7548](https://github.com/scalableminds/webknossos/pull/7548)
 
 ### Changed
 - Improved loading speed of the annotation list. [#7410](https://github.com/scalableminds/webknossos/pull/7410)

diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -7,7 +7,11 @@ import com.scalableminds.util.geometry.BoundingBox
 import com.scalableminds.util.time.Instant
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.scalableminds.webknossos.datastore.models.annotation.AnnotationLayerType.AnnotationLayerType
-import com.scalableminds.webknossos.datastore.models.annotation.{AnnotationLayer, AnnotationLayerType}
+import com.scalableminds.webknossos.datastore.models.annotation.{
+  AnnotationLayer,
+  AnnotationLayerStatistics,
+  AnnotationLayerType
+}
 import com.scalableminds.webknossos.datastore.models.datasource.AdditionalAxis
 import com.scalableminds.webknossos.datastore.rpc.RPC
 import com.scalableminds.webknossos.tracingstore.tracings.volume.ResolutionRestrictions
@@ -283,7 +287,8 @@ class AnnotationController @Inject()(
           List(
             AnnotationLayer(TracingIds.dummyTracingId,
                             AnnotationLayerType.Skeleton,
-                            AnnotationLayer.defaultSkeletonLayerName))
+                            AnnotationLayer.defaultSkeletonLayerName,
+                            AnnotationLayerStatistics.unknown))
         )
         json <- annotationService.publicWrites(annotation, request.identity) ?~> "annotation.write.failed"
       } yield JsonOk(json)

diff --git a/app/controllers/AnnotationIOController.scala b/app/controllers/AnnotationIOController.scala
@@ -13,6 +13,7 @@ import com.scalableminds.webknossos.datastore.VolumeTracing.{VolumeTracing, Volu
 import com.scalableminds.webknossos.datastore.helpers.ProtoGeometryImplicits
 import com.scalableminds.webknossos.datastore.models.annotation.{
   AnnotationLayer,
+  AnnotationLayerStatistics,
   AnnotationLayerType,
   FetchedAnnotationLayer
 }
@@ -159,7 +160,8 @@ class AnnotationIOController @Inject()(
           AnnotationLayer(
             savedTracingId,
             AnnotationLayerType.Volume,
-            uploadedVolumeLayer.name.getOrElse(AnnotationLayer.defaultVolumeLayerName + idx.toString)
+            uploadedVolumeLayer.name.getOrElse(AnnotationLayer.defaultVolumeLayerName + idx.toString),
+            AnnotationLayerStatistics.unknown
           )
       }
     } else { // Multiple annotations with volume layers (but at most one each) was uploaded merge those volume layers into one
@@ -175,7 +177,8 @@ class AnnotationIOController @Inject()(
           AnnotationLayer(
             mergedTracingId,
             AnnotationLayerType.Volume,
-            AnnotationLayer.defaultVolumeLayerName
+            AnnotationLayer.defaultVolumeLayerName,
+            AnnotationLayerStatistics.unknown
           ))
     }
 
@@ -189,7 +192,11 @@ class AnnotationIOController @Inject()(
           SkeletonTracings(skeletonTracings.map(t => SkeletonTracingOpt(Some(t)))),
           persistTracing = true)
       } yield
-        List(AnnotationLayer(mergedTracingId, AnnotationLayerType.Skeleton, AnnotationLayer.defaultSkeletonLayerName))
+        List(
+          AnnotationLayer(mergedTracingId,
+                          AnnotationLayerType.Skeleton,
+                          AnnotationLayer.defaultSkeletonLayerName,
+                          AnnotationLayerStatistics.unknown))
     }
 
   private def assertNonEmpty(parseSuccesses: List[NmlParseSuccess]) =

diff --git a/app/controllers/WKRemoteTracingStoreController.scala b/app/controllers/WKRemoteTracingStoreController.scala
@@ -9,7 +9,13 @@ import com.scalableminds.webknossos.tracingstore.TracingUpdatesReport
 import javax.inject.Inject
 import models.analytics.{AnalyticsService, UpdateAnnotationEvent, UpdateAnnotationViewOnlyEvent}
 import models.annotation.AnnotationState._
-import models.annotation.{Annotation, AnnotationDAO, AnnotationInformationProvider, TracingStoreService}
+import models.annotation.{
+  Annotation,
+  AnnotationDAO,
+  AnnotationInformationProvider,
+  AnnotationLayerDAO,
+  TracingStoreService
+}
 import models.dataset.{DatasetDAO, DatasetService}
 import models.organization.OrganizationDAO
 import models.user.UserDAO
@@ -31,7 +37,8 @@ class WKRemoteTracingStoreController @Inject()(
     annotationInformationProvider: AnnotationInformationProvider,
     analyticsService: AnalyticsService,
     datasetDAO: DatasetDAO,
-    annotationDAO: AnnotationDAO)(implicit ec: ExecutionContext, playBodyParsers: PlayBodyParsers)
+    annotationDAO: AnnotationDAO,
+    annotationLayerDAO: AnnotationLayerDAO)(implicit ec: ExecutionContext, playBodyParsers: PlayBodyParsers)
     extends Controller
     with FoxImplicits {
 
@@ -46,10 +53,10 @@ class WKRemoteTracingStoreController @Inject()(
         for {
           annotation <- annotationDAO.findOneByTracingId(report.tracingId)
           _ <- ensureAnnotationNotFinished(annotation)
+          _ <- annotationDAO.updateModified(annotation._id, Instant.now)
           _ <- Fox.runOptional(report.statistics) { statistics =>
-            annotationDAO.updateStatistics(annotation._id, statistics)
+            annotationLayerDAO.updateStatistics(annotation._id, report.tracingId, statistics)
           }
-          _ <- annotationDAO.updateModified(annotation._id, Instant.now)
           userBox <- bearerTokenService.userForTokenOpt(report.userToken).futureBox
           _ <- Fox.runOptional(userBox)(user => timeSpanService.logUserInteraction(report.timestamps, user, annotation))
           _ <- Fox.runOptional(userBox)(user =>

diff --git a/app/models/annotation/Annotation.scala b/app/models/annotation/Annotation.scala
@@ -33,7 +33,6 @@ case class Annotation(
     name: String = "",
     viewConfiguration: Option[JsObject] = None,
     state: AnnotationState.Value = Active,
-    statistics: JsObject = Json.obj(),
     tags: Set[String] = Set.empty,
     tracingTime: Option[Long] = None,
     typ: AnnotationType.Value = AnnotationType.Explorational,
@@ -83,7 +82,6 @@ case class AnnotationCompactInfo(id: ObjectId,
                                  teamNames: Seq[String],
                                  teamOrganizationIds: Seq[ObjectId],
                                  modified: Instant,
-                                 stats: JsObject,
                                  tags: Set[String],
                                  state: AnnotationState.Value = Active,
                                  dataSetName: String,
@@ -92,7 +90,8 @@ case class AnnotationCompactInfo(id: ObjectId,
                                  organizationName: String,
                                  tracingIds: Seq[String],
                                  annotationLayerNames: Seq[String],
-                                 annotationLayerTypes: Seq[String])
+                                 annotationLayerTypes: Seq[String],
+                                 annotationLayerStatistics: Seq[JsObject])
 
 object AnnotationCompactInfo {
   implicit val jsonFormat: Format[AnnotationCompactInfo] = Json.format[AnnotationCompactInfo]
@@ -108,14 +107,15 @@ class AnnotationLayerDAO @Inject()(SQLClient: SqlClient)(implicit ec: ExecutionC
       AnnotationLayer(
         r.tracingid,
         typ,
-        r.name
+        r.name,
+        Json.parse(r.statistics).as[JsObject],
       )
     }
 
   def findAnnotationLayersFor(annotationId: ObjectId): Fox[List[AnnotationLayer]] =
     for {
       rows <- run(
-        q"select _annotation, tracingId, typ, name from webknossos.annotation_layers where _annotation = $annotationId order by tracingId"
+        q"select _annotation, tracingId, typ, name, statistics from webknossos.annotation_layers where _annotation = $annotationId order by tracingId"
           .as[AnnotationLayersRow])
       parsed <- Fox.serialCombined(rows.toList)(parse)
     } yield parsed
@@ -137,8 +137,8 @@ class AnnotationLayerDAO @Inject()(SQLClient: SqlClient)(implicit ec: ExecutionC
     }
 
   private def insertOneQuery(annotationId: ObjectId, a: AnnotationLayer): SqlAction[Int, NoStream, Effect] =
-    q"""insert into webknossos.annotation_layers(_annotation, tracingId, typ, name)
-            values($annotationId, ${a.tracingId}, ${a.typ}, ${a.name})""".asUpdate
+    q"""insert into webknossos.annotation_layers(_annotation, tracingId, typ, name, statistics)
+            values($annotationId, ${a.tracingId}, ${a.typ}, ${a.name}, ${a.stats})""".asUpdate
 
   def deleteOne(annotationId: ObjectId, layerName: String): Fox[Unit] =
     for {
@@ -176,6 +176,13 @@ class AnnotationLayerDAO @Inject()(SQLClient: SqlClient)(implicit ec: ExecutionC
   def deleteAllForAnnotationQuery(annotationId: ObjectId): SqlAction[Int, NoStream, Effect] =
     q"delete from webknossos.annotation_layers where _annotation = $annotationId".asUpdate
 
+  def updateStatistics(annotationId: ObjectId, tracingId: String, statistics: JsObject): Fox[Unit] =
+    for {
+      _ <- run(q"""UPDATE webknossos.annotation_layers
+            SET statistics = $statistics
+            WHERE _annotation = $annotationId
+            AND tracingId = $tracingId""".asUpdate)
+    } yield ()
 }
 
 class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: AnnotationLayerDAO)(
@@ -206,7 +213,6 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
         r.name,
         viewconfigurationOpt,
         state,
-        Json.parse(r.statistics).as[JsObject],
         parseArrayLiteral(r.tags).toSet,
         r.tracingtime,
         typ,
@@ -332,7 +338,6 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
           STRING_AGG(t.name, ',') AS team_names,
           STRING_AGG(t._organization, ',') AS team_orgs,
           a.modified,
-          a.statistics,
           a.tags,
           a.state,
           d.name,
@@ -342,7 +347,8 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
           o.name,
           STRING_AGG(al.tracingid, ',') AS tracing_ids,
           STRING_AGG(al.name, ',') AS tracing_names,
-          STRING_AGG(al.typ :: varchar, ',') AS tracing_typs
+          STRING_AGG(al.typ :: varchar, ',') AS tracing_typs,
+          ARRAY_AGG(al.statistics) AS annotation_layer_statistics
       FROM webknossos.annotations as a
                LEFT JOIN webknossos.users_ u
                          ON u._id = a._user
@@ -378,11 +384,11 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
            String,
            String,
            String,
-           String,
            Long,
            String,
            String,
            String,
+           String,
            String)])
     } yield
       rows.toList.map(
@@ -399,17 +405,18 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
             teamNames = Option(r._9).map(_.split(",")).getOrElse(Array[String]()).toSeq,
             teamOrganizationIds = parseObjectIdArray(r._10),
             modified = r._11,
-            stats = Json.parse(r._12).validate[JsObject].getOrElse(Json.obj()),
-            tags = parseArrayLiteral(r._13).toSet,
-            state = AnnotationState.fromString(r._14).getOrElse(AnnotationState.Active),
-            dataSetName = r._15,
-            typ = AnnotationType.fromString(r._16).getOrElse(AnnotationType.Explorational),
-            visibility = AnnotationVisibility.fromString(r._17).getOrElse(AnnotationVisibility.Internal),
-            tracingTime = Option(r._18),
-            organizationName = r._19,
-            tracingIds = Option(r._20).map(_.split(",")).getOrElse(Array[String]()).toSeq,
-            annotationLayerNames = Option(r._21).map(_.split(",")).getOrElse(Array[String]()).toSeq,
-            annotationLayerTypes = Option(r._22).map(_.split(",")).getOrElse(Array[String]()).toSeq
+            tags = parseArrayLiteral(r._12).toSet,
+            state = AnnotationState.fromString(r._13).getOrElse(AnnotationState.Active),
+            dataSetName = r._14,
+            typ = AnnotationType.fromString(r._15).getOrElse(AnnotationType.Explorational),
+            visibility = AnnotationVisibility.fromString(r._16).getOrElse(AnnotationVisibility.Internal),
+            tracingTime = Option(r._17),
+            organizationName = r._18,
+            tracingIds = Option(r._19).map(_.split(",")).getOrElse(Array[String]()).toSeq,
+            annotationLayerNames = Option(r._20).map(_.split(",")).getOrElse(Array[String]()).toSeq,
+            annotationLayerTypes = Option(r._21).map(_.split(",")).getOrElse(Array[String]()).toSeq,
+            annotationLayerStatistics = parseArrayLiteral(r._22).map(layerStats =>
+              Json.parse(layerStats).validate[JsObject].getOrElse(Json.obj()))
           )
         }
       )
@@ -549,11 +556,11 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
   def insertOne(a: Annotation): Fox[Unit] = {
     val insertAnnotationQuery = q"""
         insert into webknossos.annotations(_id, _dataset, _task, _team, _user, description, visibility,
-                                           name, viewConfiguration, state, statistics, tags, tracingTime, typ, othersMayEdit, created, modified, isDeleted)
+                                           name, viewConfiguration, state, tags, tracingTime, typ, othersMayEdit, created, modified, isDeleted)
         values(${a._id}, ${a._dataset}, ${a._task}, ${a._team},
          ${a._user}, ${a.description}, ${a.visibility}, ${a.name},
          ${a.viewConfiguration},
-         ${a.state}, ${a.statistics},
+         ${a.state},
          ${a.tags}, ${a.tracingTime}, ${a.typ},
          ${a.othersMayEdit},
          ${a.created}, ${a.modified}, ${a.isDeleted})
@@ -577,7 +584,6 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
                name = ${a.name},
                viewConfiguration = ${a.viewConfiguration},
                state = ${a.state},
-               statistics = ${a.statistics},
                tags = ${a.tags.toList},
                tracingTime = ${a.tracingTime},
                typ = ${a.typ},
@@ -663,12 +669,6 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
       _ <- run(q"update webknossos.annotations set modified = $modified where _id = $id".asUpdate)
     } yield ()
 
-  def updateStatistics(id: ObjectId, statistics: JsObject)(implicit ctx: DBAccessContext): Fox[Unit] =
-    for {
-      _ <- assertUpdateAccess(id)
-      _ <- run(q"update webknossos.annotations set statistics = $statistics where _id = $id".asUpdate)
-    } yield ()
-
   def updateUser(id: ObjectId, userId: ObjectId)(implicit ctx: DBAccessContext): Fox[Unit] =
     updateObjectIdCol(id, _._User, userId)
 
@@ -689,15 +689,6 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
         q"insert into webknossos.annotation_contributors (_annotation, _user) values($id, $userId) on conflict do nothing".asUpdate)
     } yield ()
 
-  // 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(q"""select distinct ${columnsWithPrefix("a.")} from webknossos.annotations_ a
-                            join webknossos.annotation_sharedTeams l on a._id = l._annotation
-                            where l._team in ${SqlToken.tupleFromList(teams)}""".as[AnnotationsRow])
-      parsed <- Fox.combined(result.toList.map(parse))
-    } yield parsed
-
   def updateTeamsForSharedAnnotation(annotationId: ObjectId, teams: List[ObjectId])(
       implicit ctx: DBAccessContext): Fox[Unit] = {
     val clearQuery = q"delete from webknossos.annotation_sharedTeams where _annotation = $annotationId".asUpdate

diff --git a/app/models/annotation/AnnotationMerger.scala b/app/models/annotation/AnnotationMerger.scala
@@ -2,7 +2,11 @@ package models.annotation
 
 import com.scalableminds.util.accesscontext.DBAccessContext
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
-import com.scalableminds.webknossos.datastore.models.annotation.{AnnotationLayer, AnnotationLayerType}
+import com.scalableminds.webknossos.datastore.models.annotation.{
+  AnnotationLayer,
+  AnnotationLayerStatistics,
+  AnnotationLayerType
+}
 import com.typesafe.scalalogging.LazyLogging
 
 import javax.inject.Inject
@@ -78,12 +82,14 @@ class AnnotationMerger @Inject()(datasetDAO: DatasetDAO, tracingStoreService: Tr
         id =>
           AnnotationLayer(id,
                           AnnotationLayerType.Skeleton,
-                          mergedSkeletonName.getOrElse(AnnotationLayer.defaultSkeletonLayerName)))
+                          mergedSkeletonName.getOrElse(AnnotationLayer.defaultSkeletonLayerName),
+                          AnnotationLayerStatistics.unknown))
       mergedVolumeLayer = mergedVolumeTracingId.map(
         id =>
           AnnotationLayer(id,
                           AnnotationLayerType.Volume,
-                          mergedVolumeName.getOrElse(AnnotationLayer.defaultVolumeLayerName)))
+                          mergedVolumeName.getOrElse(AnnotationLayer.defaultVolumeLayerName),
+                          AnnotationLayerStatistics.unknown))
     } yield List(mergedSkeletonLayer, mergedVolumeLayer).flatten
 
   private def allEqual(str: List[String]): Option[String] =