Log data loading errors in conversion / mapping application

CHANGELOG.unreleased.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Reading image files on datastore filesystem is now done asynchronously. [#8126](https://github.com/scalableminds/webknossos/pull/8126)
 - Improved error messages for starting jobs on datasets from other organizations. [#8181](https://github.com/scalableminds/webknossos/pull/8181)
 - Removed bounding box size restriction for inferral jobs for super users. [#8200](https://github.com/scalableminds/webknossos/pull/8200)
+- Improved logging for errors when loading datasets and problems arise during a conversion step. [#8202](https://github.com/scalableminds/webknossos/pull/8202)
 
 ### Fixed
 - Fix performance bottleneck when deleting a lot of trees at once. [#8176](https://github.com/scalableminds/webknossos/pull/8176)

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataService.scala

@@ -10,7 +10,7 @@ import com.scalableminds.webknossos.datastore.models.datasource.{Category, DataL
 import com.scalableminds.webknossos.datastore.models.requests.{DataReadInstruction, DataServiceDataRequest}
 import com.scalableminds.webknossos.datastore.storage._
 import com.typesafe.scalalogging.LazyLogging
-import net.liftweb.common.{Box, Failure, Full}
+import net.liftweb.common.{Box, Full}
 import ucar.ma2.{Array => MultiArray}
 import net.liftweb.common.Box.tryo
 
@@ -20,7 +20,6 @@ import scala.concurrent.ExecutionContext
 class BinaryDataService(val dataBaseDir: Path,
                         val agglomerateServiceOpt: Option[AgglomerateService],
                         remoteSourceDescriptorServiceOpt: Option[RemoteSourceDescriptorService],
-                        val applicationHealthService: Option[ApplicationHealthService],
                         sharedChunkContentsCache: Option[AlfuCache[String, MultiArray]],
                         datasetErrorLoggingService: Option[DatasetErrorLoggingService])(implicit ec: ExecutionContext)
     extends FoxImplicits
@@ -55,22 +54,28 @@ class BinaryDataService(val dataBaseDir: Path,
   def handleDataRequests(requests: List[DataServiceDataRequest]): Fox[(Array[Byte], List[Int])] = {
     def convertIfNecessary(isNecessary: Boolean,
                            inputArray: Array[Byte],
-                           conversionFunc: Array[Byte] => Box[Array[Byte]]): Box[Array[Byte]] =
-      if (isNecessary) conversionFunc(inputArray) else Full(inputArray)
+                           conversionFunc: Array[Byte] => Fox[Array[Byte]],
+                           request: DataServiceDataRequest): Fox[Array[Byte]] =
+      if (isNecessary) datasetErrorLoggingService match {
+        case Some(value) => value.withErrorLogging(request.dataSource.id, "converting bucket data", conversionFunc(inputArray))
+        case None        => conversionFunc(inputArray)
+      } else Full(inputArray)
 
     val requestsCount = requests.length
     val requestData = requests.zipWithIndex.map {
       case (request, index) =>
         for {
           data <- handleDataRequest(request)
-          mappedData <- agglomerateServiceOpt.map { agglomerateService =>
+          mappedDataFox <- agglomerateServiceOpt.map { agglomerateService =>
             convertIfNecessary(
               request.settings.appliedAgglomerate.isDefined && request.dataLayer.category == Category.segmentation && request.cuboid.mag.maxDim <= MaxMagForAgglomerateMapping,
               data,
-              agglomerateService.applyAgglomerate(request)
+              agglomerateService.applyAgglomerate(request),
+              request
             )
-          }.getOrElse(Full(data)) ?~> "Failed to apply agglomerate mapping"
-          resultData <- convertIfNecessary(request.settings.halfByte, mappedData, convertToHalfByte)
+          }.fillEmpty(Fox.successful(data)) ?~> "Failed to apply agglomerate mapping"
+          mappedData <- mappedDataFox
+          resultData <- convertIfNecessary(request.settings.halfByte, mappedData, convertToHalfByte, request)
         } yield (resultData, index)
     }
 
@@ -91,28 +96,14 @@ class BinaryDataService(val dataBaseDir: Path,
       val bucketProvider =
         bucketProviderCache.getOrLoadAndPut((dataSourceId, request.dataLayer.bucketProviderCacheKey))(_ =>
           request.dataLayer.bucketProvider(remoteSourceDescriptorServiceOpt, dataSourceId, sharedChunkContentsCache))
-      bucketProvider.load(readInstruction).futureBox.flatMap {
-        case Failure(msg, Full(e: InternalError), _) =>
-          applicationHealthService.foreach(a => a.pushError(e))
-          logger.error(
-            s"Caught internal error: $msg while loading a bucket for layer ${request.dataLayer.name} of dataset ${request.dataSource.id}")
-          Fox.failure(e.getMessage)
-        case f: Failure =>
-          if (datasetErrorLoggingService.exists(_.shouldLog(request.dataSource.id.team, request.dataSource.id.name))) {
-            logger.error(
-              s"Bucket loading for layer ${request.dataLayer.name} of dataset ${request.dataSource.id.team}/${request.dataSource.id.name} at ${readInstruction.bucket} failed: ${Fox
-                .failureChainAsString(f, includeStackTraces = true)}")
-            datasetErrorLoggingService.foreach(_.registerLogged(request.dataSource.id.team, request.dataSource.id.name))
-          }
-          f.toFox
-        case Full(data) =>
-          if (data.length == 0) {
-            val msg =
-              s"Bucket provider returned Full, but data is zero-length array. Layer ${request.dataLayer.name} of dataset ${request.dataSource.id}, ${request.cuboid}"
-            logger.warn(msg)
-            Fox.failure(msg)
-          } else Fox.successful(data)
-        case other => other.toFox
+      datasetErrorLoggingService match {
+        case Some(d) =>
+          d.withErrorLogging(
+            request.dataSource.id,
+            s"loading bucket for layer ${request.dataLayer.name} at ${readInstruction.bucket}, cuboid: ${request.cuboid}",
+            bucketProvider.load(readInstruction)
+          )
+        case None => bucketProvider.load(readInstruction)
       }
     } else Fox.empty
 
@@ -197,5 +188,4 @@ class BinaryDataService(val dataBaseDir: Path,
 
     (closedAgglomerateFileHandleCount, clearedBucketProviderCount, removedChunksCount)
   }
-
 }

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataServiceHolder.scala

@@ -22,7 +22,6 @@ import scala.concurrent.ExecutionContext
 class BinaryDataServiceHolder @Inject()(
     config: DataStoreConfig,
     agglomerateService: AgglomerateService,
-    applicationHealthService: ApplicationHealthService,
     remoteSourceDescriptorService: RemoteSourceDescriptorService,
     datasetErrorLoggingService: DatasetErrorLoggingService)(implicit ec: ExecutionContext)
     extends LazyLogging {
@@ -46,7 +45,6 @@ class BinaryDataServiceHolder @Inject()(
     Paths.get(config.Datastore.baseFolder),
     Some(agglomerateService),
     Some(remoteSourceDescriptorService),
-    Some(applicationHealthService),
     Some(sharedChunkContentsCache),
     Some(datasetErrorLoggingService)
   )

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DatasetErrorLoggingService.scala

@@ -2,8 +2,12 @@ package com.scalableminds.webknossos.datastore.services
 
 import org.apache.pekko.actor.ActorSystem
 import com.google.inject.name.Named
+import com.scalableminds.util.tools.{Fox, TextUtils}
+import com.scalableminds.util.tools.Fox.box2Fox
 import com.scalableminds.webknossos.datastore.helpers.IntervalScheduler
+import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId
 import com.typesafe.scalalogging.LazyLogging
+import net.liftweb.common.{Empty, Failure, Full}
 import play.api.inject.ApplicationLifecycle
 
 import javax.inject.Inject
@@ -12,6 +16,7 @@ import scala.concurrent.duration._
 
 class DatasetErrorLoggingService @Inject()(
     val lifecycle: ApplicationLifecycle,
+    val applicationHealthService: ApplicationHealthService,
     @Named("webknossos-datastore") val system: ActorSystem)(implicit val ec: ExecutionContext)
     extends IntervalScheduler
     with LazyLogging {
@@ -41,4 +46,36 @@ class DatasetErrorLoggingService @Inject()(
     recentErrors.remove((organizationId, datasetName))
 
   override protected def tick(): Unit = recentErrors.clear()
+
+  def withErrorLogging(dataSourceId: DataSourceId, label: String, resultFox: Fox[Array[Byte]]): Fox[Array[Byte]] =
+    resultFox.futureBox.flatMap {
+      case Full(data) =>
+        if (data.length == 0) {
+          val msg = s"Zero-length array returned while $label for $dataSourceId"
+          if (shouldLog(dataSourceId.team, dataSourceId.name)) {
+            logger.warn(msg)
+            registerLogged(dataSourceId.team, dataSourceId.name)
+          }
+          Fox.failure(msg)
+        } else {
+          Fox.successful(data)
+        }
+      case Failure(msg, Full(e: InternalError), _) =>
+        logger.error(s"Caught internal error while $label for $dataSourceId:", e)
+        applicationHealthService.pushError(e)
+        Fox.failure(msg, Full(e))
+      case Failure(msg, Full(exception), _) =>
+        if (shouldLog(dataSourceId.team, dataSourceId.name)) {
+          logger.error(s"Error while $label for $dataSourceId Stack trace: ${TextUtils.stackTraceAsString(exception)} ")
+          registerLogged(dataSourceId.team, dataSourceId.name)
+        }
+        Fox.failure(msg, Full(exception))
+      case Failure(msg, Empty, _) =>
+        if (shouldLog(dataSourceId.team, dataSourceId.name)) {
+          logger.error(s"Error while $label for $dataSourceId, Empty failure")
+          registerLogged(dataSourceId.team, dataSourceId.name)
+        }
+        Fox.failure(msg)
+      case other => other.toFox
+    }
 }

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/editablemapping/EditableMappingService.scala

@@ -103,7 +103,7 @@ class EditableMappingService @Inject()(
 
   private def generateId: String = UUID.randomUUID.toString
 
-  val binaryDataService = new BinaryDataService(Paths.get(""), None, None, None, None, None)
+  val binaryDataService = new BinaryDataService(Paths.get(""), None, None, None, None)
   adHocMeshServiceHolder.tracingStoreAdHocMeshConfig = (binaryDataService, 30 seconds, 1)
   private val adHocMeshService: AdHocMeshService = adHocMeshServiceHolder.tracingStoreAdHocMeshService
 

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingService.scala

@@ -88,7 +88,7 @@ class VolumeTracingService @Inject()(
 
   /* We want to reuse the bucket loading methods from binaryDataService for the volume tracings, however, it does not
      actually load anything from disk, unlike its “normal” instance in the datastore (only from the volume tracing store) */
-  private val binaryDataService = new BinaryDataService(Paths.get(""), None, None, None, None, None)
+  private val binaryDataService = new BinaryDataService(Paths.get(""), None, None, None, None)
 
   adHocMeshServiceHolder.tracingStoreAdHocMeshConfig = (binaryDataService, 30 seconds, 1)
   val adHocMeshService: AdHocMeshService = adHocMeshServiceHolder.tracingStoreAdHocMeshService