Fix the Suggestions Database Updates Handling (#1161)

Misc updates to the Suggestions database updates handling algorithm
2024-12-22 13:41:39 +03:00 · 2020-10-05 17:22:13 +03:00 · 2020-10-05 17:22:13 +03:00 · 3d65ffd3cd
commit 3d65ffd3cd
parent 8e07e0347f
13 changed files with 439 additions and 415 deletions
--- a/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
@ -90,11 +90,7 @@ final class SuggestionsHandler(
    context.system.eventStream
      .subscribe(self, classOf[Api.ExpressionValuesComputed])
    context.system.eventStream
-      .subscribe(self, classOf[Api.SuggestionsDatabaseUpdateNotification])
-    context.system.eventStream
-      .subscribe(self, classOf[Api.SuggestionsDatabaseReIndexNotification])
-    context.system.eventStream
-      .subscribe(self, classOf[Api.SuggestionsDatabaseIndexUpdateNotification])
+      .subscribe(self, classOf[Api.SuggestionsDatabaseModuleUpdateNotification])
    context.system.eventStream.subscribe(self, classOf[ProjectNameChangedEvent])
    context.system.eventStream.subscribe(self, classOf[FileDeletedEvent])
    context.system.eventStream
@ -143,24 +139,7 @@ final class SuggestionsHandler(
      sender() ! CapabilityReleased
      context.become(initialized(projectName, clients - client.clientId))

-    case msg: Api.SuggestionsDatabaseIndexUpdateNotification =>
-      applyIndexedModuleUpdates(msg.updates.toSeq)
-        .onComplete {
-          case Success(notification) =>
-            if (notification.updates.nonEmpty) {
-              clients.foreach { clientId =>
-                sessionRouter ! DeliverToJsonController(clientId, notification)
-              }
-            }
-          case Failure(ex) =>
-            log.error(
-              ex,
-              "Error applying suggestion database updates: {}",
-              msg.updates.map(_.file)
-            )
-        }
-
-    case msg: Api.SuggestionsDatabaseUpdateNotification =>
+    case msg: Api.SuggestionsDatabaseModuleUpdateNotification =>
      applyDatabaseUpdates(msg)
        .onComplete {
          case Success(notification) =>
@ -173,25 +152,7 @@ final class SuggestionsHandler(
            log.error(
              ex,
              "Error applying suggestion database updates: {}",
-              msg.updates
-            )
-        }
-
-    case msg: Api.SuggestionsDatabaseReIndexNotification =>
-      log.debug(s"ReIndex ${msg.moduleName} ${msg.updates.map(_.suggestion)}")
-      applyReIndexUpdates(msg.updates)
-        .onComplete {
-          case Success(notification) =>
-            if (notification.updates.nonEmpty) {
-              clients.foreach { clientId =>
-                sessionRouter ! DeliverToJsonController(clientId, notification)
-              }
-            }
-          case Failure(ex) =>
-            log.error(
-              ex,
-              "Error applying suggestion re-index updates: {}",
-              msg.updates
+              msg.file
            )
        }

@ -211,6 +172,20 @@ final class SuggestionsHandler(
            }
            SuggestionsDatabaseUpdateNotification(version, updates)
        }
+        .onComplete {
+          case Success(notification) =>
+            if (notification.updates.nonEmpty) {
+              clients.foreach { clientId =>
+                sessionRouter ! DeliverToJsonController(clientId, notification)
+              }
+            }
+          case Failure(ex) =>
+            log.error(
+              ex,
+              "Error applying changes from computed values: {}",
+              updates
+            )
+        }

    case GetSuggestionsDatabaseVersion =>
      suggestionsRepo.currentVersion
@ -314,68 +289,6 @@ final class SuggestionsHandler(
    }
  }

-  private def applyIndexedModuleUpdates(
-    updates: Seq[Api.IndexedModule]
-  ): Future[SuggestionsDatabaseUpdateNotification] = {
-    def createIndexedModuleUpdatesBatch(
-      contents: String,
-      file: java.io.File,
-      updates: Seq[Api.SuggestionsDatabaseUpdate.Add]
-    ): Future[Seq[Api.SuggestionsDatabaseUpdate.Add]] =
-      fileVersionsRepo
-        .updateVersion(file, versionCalculator.evalDigest(contents))
-        .map(versionChanged => if (versionChanged) updates else Seq())
-    def getBatches =
-      Future
-        .traverse(updates) { indexed =>
-          createIndexedModuleUpdatesBatch(
-            indexed.contents,
-            indexed.file,
-            indexed.updates
-          )
-        }
-        .map(_.flatten)
-    for {
-      batch  <- getBatches
-      update <- applyReIndexUpdates(batch)
-    } yield update
-  }
-
-  /**
-    * Handle the suggestions database re-index update.
-    *
-    * Function clears existing module suggestions from the database, inserts new
-    * suggestions and builds the notification containing combined removed and
-    * added suggestions.
-    *
-    * @param updates the list of updates after the full module re-index
-    * @return the API suggestions database update notification
-    */
-  private def applyReIndexUpdates(
-    updates: Seq[Api.SuggestionsDatabaseUpdate.Add]
-  ): Future[SuggestionsDatabaseUpdateNotification] = {
-    val added   = updates.map(_.suggestion)
-    val modules = updates.map(_.suggestion.module).distinct
-    log.debug(s"Applying re-index updates; modules=$modules")
-    for {
-      (_, removedIds)     <- suggestionsRepo.removeAllByModule(modules)
-      (version, addedIds) <- suggestionsRepo.insertAll(added)
-    } yield {
-      val updatesRemoved = removedIds.map(SuggestionsDatabaseUpdate.Remove)
-      val updatesAdded = (addedIds zip added).flatMap {
-        case (Some(id), suggestion) =>
-          Some(SuggestionsDatabaseUpdate.Add(id, suggestion))
-        case (None, suggestion) =>
-          log.error("Failed to insert re-index suggestion: {}", suggestion)
-          None
-      }
-      SuggestionsDatabaseUpdateNotification(
-        version,
-        updatesRemoved :++ updatesAdded
-      )
-    }
-  }
-
  /**
    * Handle the suggestions database update.
    *
@ -386,28 +299,42 @@ final class SuggestionsHandler(
    * @return the API suggestions database update notification
    */
  private def applyDatabaseUpdates(
-    msg: Api.SuggestionsDatabaseUpdateNotification
+    msg: Api.SuggestionsDatabaseModuleUpdateNotification
  ): Future[SuggestionsDatabaseUpdateNotification] = {
-    val (added, removed) = msg.updates
-      .foldLeft((Seq[Suggestion](), Seq[Suggestion]())) {
-        case ((add, remove), msg: Api.SuggestionsDatabaseUpdate.Add) =>
-          (add :+ msg.suggestion, remove)
-        case ((add, remove), msg: Api.SuggestionsDatabaseUpdate.Remove) =>
-          (add, remove :+ msg.suggestion)
+    val (addCmds, removeCmds, cleanCmds) = msg.updates
+      .foldLeft(
+        (Vector[Suggestion](), Vector[Suggestion](), Vector[String]())
+      ) {
+        case ((add, remove, clean), m: Api.SuggestionsDatabaseUpdate.Add) =>
+          (add :+ m.suggestion, remove, clean)
+        case ((add, remove, clean), m: Api.SuggestionsDatabaseUpdate.Remove) =>
+          (add, remove :+ m.suggestion, clean)
+        case ((add, remove, clean), m: Api.SuggestionsDatabaseUpdate.Clean) =>
+          (add, remove, clean :+ m.module)
      }
+    val fileVersion = versionCalculator.evalDigest(msg.contents)
    log.debug(
-      s"Applying suggestion updates; added=${added
-        .map(_.name)}; removed=${removed.map(_.name)}"
+      s"Applying suggestion updates: Add(${addCmds.map(_.name).mkString(",")}); Remove(${removeCmds
+        .map(_.name)
+        .mkString(",")}); Clean(${cleanCmds.mkString(",")})"
    )
    for {
-      (_, removedIds)     <- suggestionsRepo.removeAll(removed)
-      (version, addedIds) <- suggestionsRepo.insertAll(added)
+      (_, cleanedIds)     <- suggestionsRepo.removeAllByModule(cleanCmds)
+      (_, removedIds)     <- suggestionsRepo.removeAll(removeCmds)
+      (version, addedIds) <- suggestionsRepo.insertAll(addCmds)
+      _                   <- fileVersionsRepo.setVersion(msg.file, fileVersion)
    } yield {
-      val updatesRemoved = removedIds.collect {
-        case Some(id) => SuggestionsDatabaseUpdate.Remove(id)
-      }
+      val updatesCleaned = cleanedIds.map(SuggestionsDatabaseUpdate.Remove)
+      val updatesRemoved =
+        (removedIds zip removeCmds).flatMap {
+          case (Some(id), _) =>
+            Some(SuggestionsDatabaseUpdate.Remove(id))
+          case (None, suggestion) =>
+            log.error("Failed to remove suggestion: {}", suggestion)
+            None
+        }
      val updatesAdded =
-        (addedIds zip added).flatMap {
+        (addedIds zip addCmds).flatMap {
          case (Some(id), suggestion) =>
            Some(SuggestionsDatabaseUpdate.Add(id, suggestion))
          case (None, suggestion) =>
@ -416,7 +343,7 @@ final class SuggestionsHandler(
        }
      SuggestionsDatabaseUpdateNotification(
        version,
-        updatesRemoved :++ updatesAdded
+        updatesCleaned :++ updatesRemoved :++ updatesAdded
      )
    }
  }
--- a/engine/language-server/src/test/scala/org/enso/languageserver/search/SuggestionsHandlerSpec.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/search/SuggestionsHandlerSpec.scala
@ -71,7 +71,9 @@ class SuggestionsHandlerSpec
        expectMsg(CapabilityAcquired)

        // receive updates
-        handler ! Api.SuggestionsDatabaseUpdateNotification(
+        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Suggestions.all.map(Api.SuggestionsDatabaseUpdate.Add)
        )

@ -105,7 +107,9 @@ class SuggestionsHandlerSpec
        expectMsg(CapabilityAcquired)

        // receive updates
-        handler ! Api.SuggestionsDatabaseUpdateNotification(
+        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Suggestions.all.map(Api.SuggestionsDatabaseUpdate.Add) ++
          Suggestions.all.map(Api.SuggestionsDatabaseUpdate.Remove)
        )
@ -178,7 +182,7 @@ class SuggestionsHandlerSpec

    "search entries by empty search query" taggedAs Retry in withDb {
      (config, repo, _, _, handler) =>
-        Await.ready(repo.insertAll(Suggestions.all), Timeout)
+        val (_, inserted) = Await.result(repo.insertAll(Suggestions.all), Timeout)
        handler ! SearchProtocol.Completion(
          file       = mkModulePath(config, "Foo", "Main.enso"),
          position   = Position(0, 0),
@ -187,7 +191,12 @@ class SuggestionsHandlerSpec
          tags       = None
        )

-        expectMsg(SearchProtocol.CompletionResult(4L, Seq()))
+      expectMsg(
+        SearchProtocol.CompletionResult(
+          4L,
+          Seq(inserted(0).get, inserted(1).get)
+        )
+      )
    }

    "search entries by self type" taggedAs Retry in withDb {
--- a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/SuggestionsHandlerEventsTest.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/SuggestionsHandlerEventsTest.scala
@ -1,5 +1,7 @@
 package org.enso.languageserver.websocket.json

+import java.io.File
+
 import io.circe.literal._
 import org.enso.languageserver.refactoring.ProjectNameChangedEvent
 import org.enso.languageserver.search.Suggestions
@ -20,7 +22,9 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {

      // add atom
      system.eventStream.publish(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Seq(Api.SuggestionsDatabaseUpdate.Add(Suggestions.atom))
        )
      )
@ -56,7 +60,9 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {

      // add method
      system.eventStream.publish(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Seq(Api.SuggestionsDatabaseUpdate.Add(Suggestions.method))
        )
      )
@ -102,7 +108,9 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {

      // add function
      system.eventStream.publish(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Seq(Api.SuggestionsDatabaseUpdate.Add(Suggestions.function))
        )
      )
@ -142,7 +150,9 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {

      // add local
      system.eventStream.publish(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Seq(Api.SuggestionsDatabaseUpdate.Add(Suggestions.local))
        )
      )
@ -281,7 +291,9 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {

      // remove items
      system.eventStream.publish(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          new File("/tmp/foo"),
+          "",
          Seq(
            Api.SuggestionsDatabaseUpdate.Remove(Suggestions.method),
            Api.SuggestionsDatabaseUpdate.Remove(Suggestions.function)
--- a/engine/polyglot-api/src/main/scala/org/enso/polyglot/Suggestion.scala
+++ b/engine/polyglot-api/src/main/scala/org/enso/polyglot/Suggestion.scala
@ -28,8 +28,10 @@ import com.fasterxml.jackson.annotation.{JsonSubTypes, JsonTypeInfo}
 )
 sealed trait Suggestion {

-  def name:   String
+  def externalId: Option[Suggestion.ExternalId]
  def module: String
+  def name: String
+  def returnType: String
 }

 object Suggestion {
--- a/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala
+++ b/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala
@ -165,12 +165,8 @@ object Runtime {
        name  = "runtimeServerShutDown"
      ),
      new JsonSubTypes.Type(
-        value = classOf[Api.SuggestionsDatabaseUpdateNotification],
-        name  = "suggestionsDatabaseUpdateNotification"
-      ),
-      new JsonSubTypes.Type(
-        value = classOf[Api.SuggestionsDatabaseReIndexNotification],
-        name  = "suggestionsDatabaseReindexNotification"
+        value = classOf[Api.SuggestionsDatabaseModuleUpdateNotification],
+        name  = "suggestionsDatabaseModuleUpdateNotification"
      ),
      new JsonSubTypes.Type(
        value = classOf[Api.InvalidateModulesIndexRequest],
@ -179,10 +175,6 @@ object Runtime {
      new JsonSubTypes.Type(
        value = classOf[Api.InvalidateModulesIndexResponse],
        name  = "invalidateModulesIndexResponse"
-      ),
-      new JsonSubTypes.Type(
-        value = classOf[Api.SuggestionsDatabaseIndexUpdateNotification],
-        name  = "suggestionsDatabaseIndexUpdateNotification"
      )
    )
  )
@ -343,24 +335,37 @@ object Runtime {
        new JsonSubTypes.Type(
          value = classOf[SuggestionsDatabaseUpdate.Remove],
          name  = "suggestionsDatabaseUpdateRemove"
+        ),
+        new JsonSubTypes.Type(
+          value = classOf[SuggestionsDatabaseUpdate.Clean],
+          name  = "suggestionsDatabaseUpdateClean"
        )
      )
    )
    sealed trait SuggestionsDatabaseUpdate
    object SuggestionsDatabaseUpdate {

-      /** Create or replace the database entry.
+      /**
+        * Create or replace the database entry.
        *
        * @param suggestion the new suggestion
        */
      case class Add(suggestion: Suggestion) extends SuggestionsDatabaseUpdate

-      /** Remove the database entry.
+      /**
+        * Remove the database entry.
        *
        * @param suggestion the suggestion to remove
        */
      case class Remove(suggestion: Suggestion)
          extends SuggestionsDatabaseUpdate
+
+      /**
+        * Remove all module entries from the database.
+        *
+        * @param module the module name
+        */
+      case class Clean(module: String) extends SuggestionsDatabaseUpdate
    }

    /**
@ -711,53 +716,24 @@ object Runtime {
    case class ProjectRenamed(newName: String) extends ApiResponse

    /**
-      * A notification about the change in the suggestions database.
+      * A notification about the changes in the suggestions database.
      *
-      * @param updates the list of database updates
+      * @param file the module file path
+      * @param contents the module source
+      * @param updates the list of suggestions extracted from module
      */
-    case class SuggestionsDatabaseUpdateNotification(
+    case class SuggestionsDatabaseModuleUpdateNotification(
+      file: File,
+      contents: String,
      updates: Seq[SuggestionsDatabaseUpdate]
    ) extends ApiNotification

-    /**
-      * A notification about the re-indexed module updates.
-      *
-      * @param moduleName the name of re-indexed module
-      * @param updates the list of database updates
-      */
-    case class SuggestionsDatabaseReIndexNotification(
-      moduleName: String,
-      updates: Seq[SuggestionsDatabaseUpdate.Add]
-    ) extends ApiNotification
-
    /** A request to invalidate the indexed flag of the modules. */
    case class InvalidateModulesIndexRequest() extends ApiRequest

    /** Signals that the module indexes has been invalidated. */
    case class InvalidateModulesIndexResponse() extends ApiResponse

-    /**
-      * An indexed module.
-      *
-      * @param file the module file path
-      * @param contents the module source
-      * @param updates the list of suggestions extracted from module
-      */
-    case class IndexedModule(
-      file: File,
-      contents: String,
-      updates: Seq[SuggestionsDatabaseUpdate.Add]
-    ) extends ApiNotification
-
-    /**
-      * A notification about new indexed modules.
-      *
-      * @param updates the list of suggestions database updates
-      */
-    case class SuggestionsDatabaseIndexUpdateNotification(
-      updates: Iterable[IndexedModule]
-    ) extends ApiNotification
-
    private lazy val mapper = {
      val factory = new CBORFactory()
      val mapper  = new ObjectMapper(factory) with ScalaObjectMapper
--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala
@ -92,33 +92,40 @@ class EnsureCompiledJob(protected val files: Iterable[File])
      ctx.executionService.getContext.getTopScope.getModules.asScala
    ctx.executionService.getLogger
      .finest(s"Modules in scope: ${modulesInScope.map(_.getName)}")
-    val updates = modulesInScope.flatMap { module =>
+    modulesInScope.foreach { module =>
      compile(module)
      analyzeModuleInScope(module)
    }
-    sendIndexUpdateNotification(
-      Api.SuggestionsDatabaseIndexUpdateNotification(updates)
-    )
  }

  private def analyzeImport(
    module: Module
  )(implicit ctx: RuntimeContext): Unit = {
-    if (!module.isIndexed && module.getLiteralSource != null) {
+    if (
+      !module.isIndexed &&
+      module.getLiteralSource != null &&
+      module.getPath != null
+    ) {
      ctx.executionService.getLogger
        .finest(s"Analyzing imported ${module.getName}")
      val moduleName = module.getName.toString
      val addedSuggestions = SuggestionBuilder(module.getLiteralSource)
        .build(module.getName.toString, module.getIr)
        .filter(isSuggestionGlobal)
-      sendReIndexNotification(moduleName, addedSuggestions)
+      val update = Api.SuggestionsDatabaseModuleUpdateNotification(
+        new File(module.getPath),
+        module.getLiteralSource.toString,
+        Api.SuggestionsDatabaseUpdate.Clean(moduleName) +:
+        addedSuggestions.map(Api.SuggestionsDatabaseUpdate.Add)
+      )
+      sendModuleUpdate(update)
      module.setIndexed(true)
    }
  }

  private def analyzeModuleInScope(module: Module)(implicit
    ctx: RuntimeContext
-  ): Option[Api.IndexedModule] = {
+  ): Unit = {
    try module.getSource
    catch {
      case e: IOException =>
@ -139,16 +146,14 @@ class EnsureCompiledJob(protected val files: Iterable[File])
      val addedSuggestions = SuggestionBuilder(module.getLiteralSource)
        .build(moduleName, module.getIr)
        .filter(isSuggestionGlobal)
-      module.setIndexed(true)
-      Some(
-        Api.IndexedModule(
-          new File(module.getPath),
-          module.getSource.getCharacters.toString,
-          addedSuggestions.map(Api.SuggestionsDatabaseUpdate.Add)
-        )
+      val update = Api.SuggestionsDatabaseModuleUpdateNotification(
+        new File(module.getPath),
+        module.getLiteralSource.toString,
+        Api.SuggestionsDatabaseUpdate.Clean(moduleName) +:
+        addedSuggestions.map(Api.SuggestionsDatabaseUpdate.Add)
      )
-    } else {
-      None
+      sendModuleUpdate(update)
+      module.setIndexed(true)
    }
  }

@ -165,17 +170,30 @@ class EnsureCompiledJob(protected val files: Iterable[File])
      val addedSuggestions =
        SuggestionBuilder(module.getLiteralSource)
          .build(moduleName, module.getIr)
-      sendSuggestionsUpdateNotification(
-        removedSuggestions diff addedSuggestions,
-        addedSuggestions diff removedSuggestions
+      val update = Api.SuggestionsDatabaseModuleUpdateNotification(
+        new File(module.getPath),
+        module.getLiteralSource.toString,
+        removedSuggestions
+          .diff(addedSuggestions)
+          .map(Api.SuggestionsDatabaseUpdate.Remove) :++
+        addedSuggestions
+          .diff(removedSuggestions)
+          .map(Api.SuggestionsDatabaseUpdate.Add)
      )
+      sendModuleUpdate(update)
    } else {
      ctx.executionService.getLogger
        .finest(s"Analyzing not-indexed module ${module.getName}")
      val addedSuggestions =
        SuggestionBuilder(module.getLiteralSource)
          .build(moduleName, module.getIr)
-      sendReIndexNotification(moduleName, addedSuggestions)
+      val update = Api.SuggestionsDatabaseModuleUpdateNotification(
+        new File(module.getPath),
+        module.getLiteralSource.toString,
+        Api.SuggestionsDatabaseUpdate.Clean(moduleName) +:
+        addedSuggestions.map(Api.SuggestionsDatabaseUpdate.Add)
+      )
+      sendModuleUpdate(update)
      module.setIndexed(true)
    }
  }
@ -209,7 +227,7 @@ class EnsureCompiledJob(protected val files: Iterable[File])
    val prevStage = module.getCompilationStage
    module.compileScope(ctx.executionService.getContext).getModule
    if (prevStage != module.getCompilationStage) {
-      ctx.executionService.getLogger.finer(
+      ctx.executionService.getLogger.finest(
        s"Compiled ${module.getName} $prevStage->${module.getCompilationStage}"
      )
    }
@ -289,58 +307,18 @@ class EnsureCompiledJob(protected val files: Iterable[File])
  }

  /**
-    * Send notification about the suggestions database updates.
+    * Send notification about module updates.
    *
-    * @param removed the list of suggestions to remove
-    * @param added the list of suggestions to add
+    * @param payload the module update
    * @param ctx the runtime context
    */
-  private def sendSuggestionsUpdateNotification(
-    removed: Seq[Suggestion],
-    added: Seq[Suggestion]
+  private def sendModuleUpdate(
+    payload: Api.SuggestionsDatabaseModuleUpdateNotification
  )(implicit ctx: RuntimeContext): Unit =
-    if (added.nonEmpty || removed.nonEmpty) {
-      ctx.endpoint.sendToClient(
-        Api.Response(
-          Api.SuggestionsDatabaseUpdateNotification(
-            removed.map(Api.SuggestionsDatabaseUpdate.Remove) :++
-            added.map(Api.SuggestionsDatabaseUpdate.Add)
-          )
-        )
-      )
+    if (payload.updates.nonEmpty) {
+      ctx.endpoint.sendToClient(Api.Response(payload))
    }

-  /**
-    * Send notification about the re-indexed module updates.
-    *
-    * @param moduleName the name of re-indexed module
-    * @param added the list of suggestions to add
-    * @param ctx the runtime context
-    */
-  private def sendReIndexNotification(
-    moduleName: String,
-    added: Seq[Suggestion]
-  )(implicit ctx: RuntimeContext): Unit = {
-    ctx.endpoint.sendToClient(
-      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
-          added.map(Api.SuggestionsDatabaseUpdate.Add)
-        )
-      )
-    )
-  }
-
-  private def sendIndexUpdateNotification(
-    msg: Api.SuggestionsDatabaseIndexUpdateNotification
-  )(implicit
-    ctx: RuntimeContext
-  ): Unit = {
-    if (msg.updates.nonEmpty) {
-      ctx.endpoint.sendToClient(Api.Response(msg))
-    }
-  }
-
  private def isSuggestionGlobal(suggestion: Suggestion): Boolean =
    suggestion match {
      case _: Suggestion.Atom     => true
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
@ -454,9 +454,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
@ -557,9 +559,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
@ -660,9 +664,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -761,9 +767,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -862,9 +870,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
@ -946,9 +956,11 @@ class RuntimeServerTest
      context.Main.Update.mainZ(contextId),
      idMainUpdate,
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -1136,9 +1148,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -1270,9 +1284,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -1621,9 +1637,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -1877,6 +1895,7 @@ class RuntimeServerTest
      Api.Response(requestId, Api.CreateContextResponse(contextId))
    )

+    val moduleName = "Test.Main"
    val code =
      """from Builtins import all
        |
@ -1899,7 +1918,7 @@ class RuntimeServerTest
          contextId,
          Api.StackItem
            .ExplicitCall(
-              Api.MethodPointer("Test.Main", "Main", "main"),
+              Api.MethodPointer(moduleName, "Main", "main"),
              None,
              Vector()
            )
@ -1909,9 +1928,11 @@ class RuntimeServerTest
    context.receive(3) should contain theSameElementsAs Seq(
      Api.Response(requestId, Api.PushContextResponse(contextId)),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          "Test.Main",
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          code,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
@ -1953,11 +1974,12 @@ class RuntimeServerTest
  }

  it should "support file modification operations with attached ids" in {
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
-    val metadata  = new Metadata
-    val idMain    = metadata.addItem(7, 2)
-    val code      = metadata.appendToCode("main = 84")
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()
+    val moduleName = "Test.Main"
+    val metadata   = new Metadata
+    val idMain     = metadata.addItem(7, 2)
+    val code       = metadata.appendToCode("main = 84")

    context.send(Api.Request(requestId, Api.CreateContextRequest(contextId)))
    context.receive shouldEqual Some(
@ -1987,7 +2009,7 @@ class RuntimeServerTest
          contextId,
          Api.StackItem
            .ExplicitCall(
-              Api.MethodPointer("Test.Main", "Main", "main"),
+              Api.MethodPointer(moduleName, "Main", "main"),
              None,
              Vector()
            )
@ -2005,9 +2027,11 @@ class RuntimeServerTest
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          "Test.Main",
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          code,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
@ -2043,9 +2067,10 @@ class RuntimeServerTest
  }

  it should "send suggestion notifications when file is executed" in {
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
-    val idMain    = context.Main.metadata.addItem(33, 47)
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()
+    val moduleName = "Test.Main"
+    val idMain     = context.Main.metadata.addItem(33, 47)
    val idMainUpdate =
      Api.Response(
        Api.ExpressionValuesComputed(
@ -2076,7 +2101,7 @@ class RuntimeServerTest

    // push main
    val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer("Test.Main", "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
      None,
      Vector()
    )
@ -2090,13 +2115,15 @@ class RuntimeServerTest
      context.Main.Update.mainZ(contextId),
      idMainUpdate,
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          "Test.Main",
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          context.Main.code,
          List(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                Some(idMain),
-                "Test.Main",
+                moduleName,
                "main",
                List(Suggestion.Argument("this", "Any", false, false, None)),
                "Main",
@ -2107,7 +2134,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
-                "Test.Main",
+                moduleName,
                "foo",
                List(
                  Suggestion.Argument("this", "Any", false, false, None),
@ -2121,7 +2148,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Local(
                Some(context.Main.idMainX),
-                "Test.Main",
+                moduleName,
                "x",
                "Any",
                Suggestion
@ -2131,7 +2158,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Local(
                Some(context.Main.idMainY),
-                "Test.Main",
+                moduleName,
                "y",
                "Any",
                Suggestion
@ -2141,7 +2168,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Local(
                Some(context.Main.idMainZ),
-                "Test.Main",
+                moduleName,
                "z",
                "Any",
                Suggestion
@ -2151,7 +2178,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Local(
                Some(context.Main.idFooY),
-                "Test.Main",
+                moduleName,
                "y",
                "Any",
                Suggestion
@ -2161,7 +2188,7 @@ class RuntimeServerTest
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Local(
                Some(context.Main.idFooZ),
-                "Test.Main",
+                moduleName,
                "z",
                "Any",
                Suggestion
@ -2219,8 +2246,10 @@ class RuntimeServerTest
  }

  it should "send suggestion notifications when file is modified" in {
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()
+    val moduleName = "Test.Main"
+    val newline    = System.lineSeparator()

    context.send(Api.Request(requestId, Api.CreateContextRequest(contextId)))
    context.receive shouldEqual Some(
@ -2237,15 +2266,7 @@ class RuntimeServerTest
    val mainFile = context.writeMain(code)

    // Open the new file
-    context.send(
-      Api.Request(
-        Api.OpenFileNotification(
-          mainFile,
-          code,
-          false
-        )
-      )
-    )
+    context.send(Api.Request(Api.OpenFileNotification(mainFile, code, false)))
    context.receiveNone shouldEqual None
    context.consumeOut shouldEqual List()

@ -2257,7 +2278,7 @@ class RuntimeServerTest
          contextId,
          Api.StackItem
            .ExplicitCall(
-              Api.MethodPointer("Test.Main", "Main", "main"),
+              Api.MethodPointer(moduleName, "Main", "main"),
              None,
              Vector()
            )
@ -2267,13 +2288,15 @@ class RuntimeServerTest
    context.receive(3) should contain theSameElementsAs Seq(
      Api.Response(requestId, Api.PushContextResponse(contextId)),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          "Test.Main",
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          code,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
-                "Test.Main",
+                moduleName,
                "main",
                Seq(Suggestion.Argument("this", "Any", false, false, None)),
                "Main",
@ -2300,20 +2323,29 @@ class RuntimeServerTest
            ),
            TextEdit(
              model.Range(model.Position(2, 0), model.Position(2, 0)),
-              "Number.lucky = 42\n\n"
+              s"Number.lucky = 42$newline$newline"
            )
          )
        )
      )
    )
+    val codeModified =
+      """from Builtins import all
+        |
+        |Number.lucky = 42
+        |
+        |main = IO.println "I'm a modified!"
+        |""".stripMargin
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
-        Api.SuggestionsDatabaseUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          codeModified,
          Seq(
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
-                "Test.Main",
+                moduleName,
                "lucky",
                Seq(Suggestion.Argument("this", "Any", false, false, None)),
                "Number",
@ -2335,10 +2367,11 @@ class RuntimeServerTest
  }

  it should "recompute expressions without invalidation" in {
-    val contents  = context.Main.code
-    val mainFile  = context.writeMain(contents)
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
+    val contents   = context.Main.code
+    val mainFile   = context.writeMain(contents)
+    val moduleName = "Test.Main"
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()

    // create context
    context.send(Api.Request(requestId, Api.CreateContextRequest(contextId)))
@ -2354,7 +2387,7 @@ class RuntimeServerTest

    // push main
    val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer("Test.Main", "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
      None,
      Vector()
    )
@ -2380,10 +2413,11 @@ class RuntimeServerTest
  }

  it should "recompute expressions invalidating all" in {
-    val contents  = context.Main.code
-    val mainFile  = context.writeMain(contents)
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
+    val contents   = context.Main.code
+    val mainFile   = context.writeMain(contents)
+    val moduleName = "Test.Main"
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()

    // create context
    context.send(Api.Request(requestId, Api.CreateContextRequest(contextId)))
@ -2399,7 +2433,7 @@ class RuntimeServerTest

    // push main
    val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer("Test.Main", "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
      None,
      Vector()
    )
@ -2431,10 +2465,11 @@ class RuntimeServerTest
  }

  it should "recompute expressions invalidating some" in {
-    val contents  = context.Main.code
-    val mainFile  = context.writeMain(contents)
-    val contextId = UUID.randomUUID()
-    val requestId = UUID.randomUUID()
+    val contents   = context.Main.code
+    val mainFile   = context.writeMain(contents)
+    val moduleName = "Test.Main"
+    val contextId  = UUID.randomUUID()
+    val requestId  = UUID.randomUUID()

    // create context
    context.send(Api.Request(requestId, Api.CreateContextRequest(contextId)))
@ -2450,7 +2485,7 @@ class RuntimeServerTest
    context.receiveNone shouldEqual None
    // push main
    val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer("Test.Main", "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
      None,
      Vector()
    )
@ -2849,8 +2884,9 @@ class RuntimeServerTest
  }

  it should "emit visualisation update when expression is evaluated" in {
-    val contents = context.Main.code
-    val mainFile = context.writeMain(context.Main.code)
+    val contents   = context.Main.code
+    val mainFile   = context.writeMain(context.Main.code)
+    val moduleName = "Test.Main"
    val visualisationFile =
      context.writeInSrcDir("Visualisation", context.Visualisation.code)

@ -2882,7 +2918,7 @@ class RuntimeServerTest

    // push main
    val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer("Test.Main", "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
      None,
      Vector()
    )
@ -2895,40 +2931,37 @@ class RuntimeServerTest
      context.Main.Update.mainY(contextId),
      context.Main.Update.mainZ(contextId),
      Api.Response(
-        Api.SuggestionsDatabaseIndexUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          visualisationFile,
+          context.Visualisation.code,
          Seq(
-            Api.IndexedModule(
-              visualisationFile,
-              context.Visualisation.code,
-              Seq(
-                Api.SuggestionsDatabaseUpdate.Add(
-                  Suggestion.Method(
-                    None,
-                    "Test.Visualisation",
-                    "encode",
-                    List(
-                      Suggestion.Argument("this", "Any", false, false, None),
-                      Suggestion.Argument("x", "Any", false, false, None)
-                    ),
-                    "Visualisation",
-                    "Any",
-                    None
-                  )
+            Api.SuggestionsDatabaseUpdate.Clean("Test.Visualisation"),
+            Api.SuggestionsDatabaseUpdate.Add(
+              Suggestion.Method(
+                None,
+                "Test.Visualisation",
+                "encode",
+                List(
+                  Suggestion.Argument("this", "Any", false, false, None),
+                  Suggestion.Argument("x", "Any", false, false, None)
                ),
-                Api.SuggestionsDatabaseUpdate.Add(
-                  Suggestion.Method(
-                    None,
-                    "Test.Visualisation",
-                    "incAndEncode",
-                    List(
-                      Suggestion.Argument("this", "Any", false, false, None),
-                      Suggestion.Argument("x", "Any", false, false, None)
-                    ),
-                    "Visualisation",
-                    "Any",
-                    None
-                  )
-                )
+                "Visualisation",
+                "Any",
+                None
+              )
+            ),
+            Api.SuggestionsDatabaseUpdate.Add(
+              Suggestion.Method(
+                None,
+                "Test.Visualisation",
+                "incAndEncode",
+                List(
+                  Suggestion.Argument("this", "Any", false, false, None),
+                  Suggestion.Argument("x", "Any", false, false, None)
+                ),
+                "Visualisation",
+                "Any",
+                None
              )
            )
          )
@ -3066,49 +3099,48 @@ class RuntimeServerTest
      context.Main.Update.mainY(contextId),
      context.Main.Update.mainZ(contextId),
      Api.Response(
-        Api.SuggestionsDatabaseIndexUpdateNotification(
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          visualisationFile,
+          context.Visualisation.code,
          Seq(
-            Api.IndexedModule(
-              visualisationFile,
-              context.Visualisation.code,
-              Seq(
-                Api.SuggestionsDatabaseUpdate.Add(
-                  Suggestion.Method(
-                    None,
-                    "Test.Visualisation",
-                    "encode",
-                    List(
-                      Suggestion.Argument("this", "Any", false, false, None),
-                      Suggestion.Argument("x", "Any", false, false, None)
-                    ),
-                    "Visualisation",
-                    "Any",
-                    None
-                  )
+            Api.SuggestionsDatabaseUpdate.Clean("Test.Visualisation"),
+            Api.SuggestionsDatabaseUpdate.Add(
+              Suggestion.Method(
+                None,
+                "Test.Visualisation",
+                "encode",
+                List(
+                  Suggestion.Argument("this", "Any", false, false, None),
+                  Suggestion.Argument("x", "Any", false, false, None)
                ),
-                Api.SuggestionsDatabaseUpdate.Add(
-                  Suggestion.Method(
-                    None,
-                    "Test.Visualisation",
-                    "incAndEncode",
-                    List(
-                      Suggestion.Argument("this", "Any", false, false, None),
-                      Suggestion.Argument("x", "Any", false, false, None)
-                    ),
-                    "Visualisation",
-                    "Any",
-                    None
-                  )
-                )
+                "Visualisation",
+                "Any",
+                None
+              )
+            ),
+            Api.SuggestionsDatabaseUpdate.Add(
+              Suggestion.Method(
+                None,
+                "Test.Visualisation",
+                "incAndEncode",
+                List(
+                  Suggestion.Argument("this", "Any", false, false, None),
+                  Suggestion.Argument("x", "Any", false, false, None)
+                ),
+                "Visualisation",
+                "Any",
+                None
              )
            )
          )
        )
      ),
      Api.Response(
-        Api.SuggestionsDatabaseReIndexNotification(
-          moduleName,
+        Api.SuggestionsDatabaseModuleUpdateNotification(
+          mainFile,
+          contents,
          Seq(
+            Api.SuggestionsDatabaseUpdate.Clean(moduleName),
            Api.SuggestionsDatabaseUpdate.Add(
              Suggestion.Method(
                None,
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/StdlibRuntimeServerTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/StdlibRuntimeServerTest.scala
@ -112,6 +112,17 @@ class StdlibRuntimeServerTest
      Iterator.continually(receive(timeout)).take(n).flatten.toList
    }

+    def receiveAllUntil(
+      msg: Api.Response,
+      timeout: Long
+    ): List[Api.Response] = {
+      Iterator
+        .continually(receive(timeout))
+        .takeWhile(received => received.isDefined && received != Some(msg))
+        .flatten
+        .toList
+    }
+
    def consumeOut: List[String] = {
      val result = out.toString
      out.reset()
@ -169,22 +180,22 @@ class StdlibRuntimeServerTest
        )
      )
    )
-    val response = context.receiveN(3, timeout = 30)
-    response.length shouldEqual 3
-    response should contain allOf (
-      Api.Response(requestId, Api.PushContextResponse(contextId)),
-      context.executionSuccessful(contextId)
+    val response  =
+      context.receiveAllUntil(
+        context.executionSuccessful(contextId),
+        timeout = 30
+      )
+    response should contain (
+      Api.Response(requestId, Api.PushContextResponse(contextId))
    )
-    response.collect {
+    val collected = response.collect {
      case Api.Response(
            None,
-            Api.SuggestionsDatabaseIndexUpdateNotification(xs)
+            Api.SuggestionsDatabaseModuleUpdateNotification(_, _, xs)
          ) =>
        xs.nonEmpty shouldBe true
-        xs.flatMap(
-          _.updates.headOption.map(_.suggestion.module)
-        ) should not contain "Test.Main"
-    } should have length 1
+    }
+    collected.nonEmpty shouldBe true

    context.consumeOut shouldEqual List("Hello World!")
  }
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/FileVersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/FileVersionsRepo.scala
@ -28,6 +28,12 @@ trait FileVersionsRepo[F[_]] {
    */
  def updateVersion(file: File, digest: Array[Byte]): F[Boolean]

+  /** Update the versions in batch.
+    *
+    * @param versions files with corresponding digests
+    */
+  def updateVersions(versions: Seq[(File, Array[Byte])]): F[Unit]
+
  /** Remove the version record.
    *
    * @param file the file path
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
@ -269,6 +269,7 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  private def removeQuery(suggestion: Suggestion): DBIO[Option[Long]] = {
    val (raw, _) = toSuggestionRow(suggestion)
    val selectQuery = Suggestions
+      .filter(_.module === raw.module)
      .filter(_.kind === raw.kind)
      .filter(_.name === raw.name)
      .filter(_.scopeStartLine === raw.scopeStartLine)
@ -306,13 +307,18 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  private def removeAllByModuleQuery(
    modules: Seq[String]
  ): DBIO[(Long, Seq[Long])] = {
-    val selectQuery = Suggestions.filter(_.module inSet modules)
-    val deleteQuery = for {
-      rows    <- selectQuery.result
-      n       <- selectQuery.delete
-      version <- if (n > 0) incrementVersionQuery else currentVersionQuery
-    } yield version -> rows.flatMap(_.id)
-    deleteQuery
+    if (modules.nonEmpty) {
+      val selectQuery = Suggestions.filter(_.module inSet modules)
+      for {
+        rows    <- selectQuery.result
+        n       <- selectQuery.delete
+        version <- if (n > 0) incrementVersionQuery else currentVersionQuery
+      } yield version -> rows.flatMap(_.id)
+    } else {
+      for {
+        version <- currentVersionQuery
+      } yield (version, Seq())
+    }
  }

  /** The query to remove a list of suggestions.
@ -418,6 +424,9 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  }

  /** Create a search query by the provided parameters.
+    *
+    * Even if the module is specified, the response includes all available
+    * global symbols (atoms and method).
    *
    * @param module the module name search parameter
    * @param selfType the selfType search parameter
@ -435,7 +444,8 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  ): Query[SuggestionsTable, SuggestionRow, Seq] = {
    Suggestions
      .filterOpt(module) {
-        case (row, value) => row.module === value
+        case (row, value) =>
+          row.scopeStartLine === ScopeColumn.EMPTY || row.module === value
      }
      .filterOpt(selfType) {
        case (row, value) => row.selfType === value
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
@ -30,6 +30,12 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  override def updateVersion(file: File, digest: Array[Byte]): Future[Boolean] =
    db.run(updateVersionQuery(file, digest))

+  /** @inheritdoc */
+  override def updateVersions(
+    versions: Seq[(File, Array[Byte])]
+  ): Future[Unit] =
+    db.run(updateVersionsQuery(versions))
+
  /** @inheritdoc */
  override def remove(file: File): Future[Unit] =
    db.run(removeQuery(file))
@ -77,11 +83,10 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
  ): DBIO[Option[Array[Byte]]] = {
    val upsertQuery = FileVersions
      .insertOrUpdate(FileVersionRow(file.toString, version))
-    val query = for {
+    for {
      version <- getVersionQuery(file)
      _       <- upsertQuery
    } yield version
-    query.transactionally
  }

  /** The query to update the version if it differs from the recorded version.
@ -102,6 +107,23 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
        else DBIO.successful(None)
    } yield !versionsEquals

+
+  /** The query to update the versions in batch.
+    *
+    * @param versions files with corresponding digests
+    */
+  private def updateVersionsQuery(
+    versions: Seq[(File, Array[Byte])]
+  ): DBIO[Unit] =
+    if (versions.nonEmpty) {
+      def upsertQuery(file: File, version: Array[Byte]) = FileVersions
+        .insertOrUpdate(FileVersionRow(file.toString, version))
+      DBIO.sequence(versions.map(Function.tupled(upsertQuery))) >>
+      DBIO.successful(())
+    } else {
+      DBIO.successful(())
+    }
+
  /** The query to remove the version record.
    *
    * @param file the file path
--- a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/FileVersionsRepoTest.scala
+++ b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/FileVersionsRepoTest.scala
@ -108,6 +108,28 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
      b4 shouldBe false
    }

+    "batch update digest" taggedAs Retry in withRepo { repo =>
+      val file1   = new File("/foo/1")
+      val file2   = new File("/foo/2")
+      val digest0 = nextDigest()
+      val digest1 = nextDigest()
+      val digest2 = nextDigest()
+      val input   = Seq(file1 -> digest1, file2 -> digest2)
+      val action =
+        for {
+          _ <- repo.setVersion(file1, digest0)
+          _ <- repo.updateVersions(input)
+          v1 <- repo.getVersion(file1)
+          v2 <- repo.getVersion(file2)
+        } yield (v1, v2)
+
+      val (v1, v2) = Await.result(action, Timeout)
+      v1 shouldBe a[Some[_]]
+      v2 shouldBe a[Some[_]]
+      util.Arrays.equals(v1.get, digest1) shouldBe true
+      util.Arrays.equals(v2.get, digest2) shouldBe true
+    }
+
    "delete digest" taggedAs Retry in withRepo { repo =>
      val file   = new File("/foo/bar")
      val digest = nextDigest()
--- a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
+++ b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
@ -204,6 +204,23 @@ class SuggestionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
      inserted should contain theSameElementsAs removed
    }

+    "remove all suggestions by empty module" taggedAs Retry in withRepo { repo =>
+      val action = for {
+        (_, idsIns) <- repo.insertAll(
+          Seq(
+            suggestion.atom,
+            suggestion.method,
+            suggestion.function,
+            suggestion.local
+          )
+        )
+        (_, idsRem) <- repo.removeAllByModule(Seq())
+      } yield (idsIns.flatten, idsRem)
+
+      val (_, removed) = Await.result(action, Timeout)
+      removed.isEmpty shouldBe true
+    }
+
    "remove all suggestions" taggedAs Retry in withRepo { repo =>
      val action = for {
        (_, Seq(id1, _, _, id4)) <- repo.insertAll(
@ -492,15 +509,15 @@ class SuggestionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {

    "search suggestion by empty module" taggedAs Retry in withRepo { repo =>
      val action = for {
-        _   <- repo.insert(suggestion.atom)
-        _   <- repo.insert(suggestion.method)
+        id1 <- repo.insert(suggestion.atom)
+        id2 <- repo.insert(suggestion.method)
        _   <- repo.insert(suggestion.function)
        _   <- repo.insert(suggestion.local)
        res <- repo.search(Some(""), None, None, None, None)
-      } yield res._2
+      } yield (res._2, Seq(id1, id2))

-      val res = Await.result(action, Timeout)
-      res.isEmpty shouldEqual true
+      val (res, globals) = Await.result(action, Timeout)
+      res should contain theSameElementsAs globals.flatten
    }

    "search suggestion by self type" taggedAs Retry in withRepo { repo =>