Remove store dependency from scheduler api

build.sbt

@@ -530,7 +530,7 @@ val schedulerApi = project
       Dependencies.fs2Core ++
         Dependencies.circeCore
   )
-  .dependsOn(loggingApi, common, store, pubsubApi)
+  .dependsOn(loggingApi, common, pubsubApi)
 
 val schedulerImpl = project
   .in(file("modules/scheduler/impl"))
@@ -540,7 +540,7 @@ val schedulerImpl = project
   .settings(
     name := "docspell-scheduler-impl"
   )
-  .dependsOn(schedulerApi, notificationApi, pubsubApi)
+  .dependsOn(store, schedulerApi, notificationApi, pubsubApi)
 
 val extract = project
   .in(file("modules/extract"))

modules/joex/src/main/scala/docspell/joex/JoexAppImpl.scala

@@ -149,91 +149,91 @@ object JoexAppImpl extends MailAddressCodec {
           .withTask(
             JobTask.json(
               ProcessItemArgs.taskName,
-              ItemHandler.newItem[F](cfg, itemOps, fts, analyser, regexNer),
+              ItemHandler.newItem[F](cfg,store, itemOps, fts, analyser, regexNer),
-              ItemHandler.onCancel[F]
+              ItemHandler.onCancel[F](store)
             )
           )
           .withTask(
             JobTask.json(
               ReProcessItemArgs.taskName,
-              ReProcessItem[F](cfg, fts, itemOps, analyser, regexNer),
+              ReProcessItem[F](cfg, fts, itemOps, analyser, regexNer, store),
               ReProcessItem.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               ScanMailboxArgs.taskName,
-              ScanMailboxTask[F](cfg.userTasks.scanMailbox, javaEmil, upload, joex),
+              ScanMailboxTask[F](cfg.userTasks.scanMailbox, store, javaEmil, upload, joex),
               ScanMailboxTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               MigrationTask.taskName,
-              MigrationTask[F](cfg.fullTextSearch, fts, createIndex),
+              MigrationTask[F](cfg.fullTextSearch, store, fts, createIndex),
               MigrationTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               ReIndexTask.taskName,
-              ReIndexTask[F](cfg.fullTextSearch, fts, createIndex),
+              ReIndexTask[F](cfg.fullTextSearch, store, fts, createIndex),
               ReIndexTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               HouseKeepingTask.taskName,
-              HouseKeepingTask[F](cfg, fileRepo),
+              HouseKeepingTask[F](cfg, store, fileRepo),
               HouseKeepingTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               PdfConvTask.taskName,
-              PdfConvTask[F](cfg),
+              PdfConvTask[F](cfg, store),
               PdfConvTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               ConvertAllPdfArgs.taskName,
-              ConvertAllPdfTask[F](jobStoreModule.jobs, joex),
+              ConvertAllPdfTask[F](jobStoreModule.jobs, joex, store),
               ConvertAllPdfTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               LearnClassifierArgs.taskName,
-              LearnClassifierTask[F](cfg.textAnalysis, analyser),
+              LearnClassifierTask[F](cfg.textAnalysis, store, analyser),
               LearnClassifierTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               MakePreviewArgs.taskName,
-              MakePreviewTask[F](cfg.extraction.preview),
+              MakePreviewTask[F](cfg.extraction.preview, store),
               MakePreviewTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               AllPreviewsArgs.taskName,
-              AllPreviewsTask[F](jobStoreModule.jobs, joex),
+              AllPreviewsTask[F](jobStoreModule.jobs, joex, store),
               AllPreviewsTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               MakePageCountArgs.taskName,
-              MakePageCountTask[F](),
+              MakePageCountTask[F](store),
               MakePageCountTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               AllPageCountTask.taskName,
-              AllPageCountTask[F](jobStoreModule.jobs, joex),
+              AllPageCountTask[F](store, jobStoreModule.jobs, joex),
               AllPageCountTask.onCancel[F]
             )
           )
@@ -250,6 +250,7 @@ object JoexAppImpl extends MailAddressCodec {
               UpdateCheckTask[F](
                 cfg.updateCheck,
                 cfg.sendMail,
+                store,
                 javaEmil,
                 updateCheck,
                 ThisVersion.default
@@ -260,28 +261,28 @@ object JoexAppImpl extends MailAddressCodec {
           .withTask(
             JobTask.json(
               PeriodicQueryTask.taskName,
-              PeriodicQueryTask[F](notification),
+              PeriodicQueryTask[F](store, notification),
               PeriodicQueryTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               PeriodicDueItemsTask.taskName,
-              PeriodicDueItemsTask[F](notification),
+              PeriodicDueItemsTask[F](store, notification),
               PeriodicDueItemsTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               FileCopyTaskArgs.taskName,
-              FileCopyTask[F](cfg),
+              FileCopyTask[F](cfg, store),
               FileCopyTask.onCancel[F]
             )
           )
           .withTask(
             JobTask.json(
               FileIntegrityCheckArgs.taskName,
-              FileIntegrityCheckTask[F](fileRepo),
+              FileIntegrityCheckTask[F](fileRepo, store),
               FileIntegrityCheckTask.onCancel[F]
             )
           )

modules/joex/src/main/scala/docspell/joex/filecopy/FileCopyTask.scala

@@ -17,6 +17,7 @@ import docspell.logging.Logger
 import docspell.store.file.{BinnyUtils, FileRepository, FileRepositoryConfig}
 import binny.CopyTool.Counter
 import binny.{BinaryId, BinaryStore, CopyTool}
+import docspell.store.Store
 import io.circe.generic.semiauto.deriveCodec
 import io.circe.{Codec, Decoder, Encoder}
 
@@ -69,7 +70,7 @@ object FileCopyTask {
   def onCancel[F[_]]: Task[F, Args, Unit] =
     Task.log(_.warn(s"Cancelling ${FileCopyTaskArgs.taskName.id} task"))
 
-  def apply[F[_]: Async](cfg: Config): Task[F, Args, CopyResult] =
+  def apply[F[_]: Async](cfg: Config, store: Store[F]): Task[F, Args, CopyResult] =
     Task { ctx =>
       val src = ctx.args.from
         .map(id =>
@@ -93,8 +94,8 @@ object FileCopyTask {
             .fromList(targets.filter(_ != srcConfig))
             .toRight(CopyResult.noTargetStore)
 
-          srcRepo = ctx.store.createFileRepository(srcConfig, true)
+          srcRepo = store.createFileRepository(srcConfig, true)
-          targetRepos = trgConfig.map(ctx.store.createFileRepository(_, false))
+          targetRepos = trgConfig.map(store.createFileRepository(_, false))
         } yield (srcRepo, targetRepos)
 
       data match {

modules/joex/src/main/scala/docspell/joex/filecopy/FileIntegrityCheckTask.scala

@@ -13,6 +13,7 @@ import docspell.backend.ops.OFileRepository
 import docspell.backend.ops.OFileRepository.IntegrityResult
 import docspell.common.{FileIntegrityCheckArgs, FileKey}
 import docspell.scheduler.{JobTaskResultEncoder, Task}
+import docspell.store.Store
 import docspell.store.records.RFileMeta
 import io.circe.Encoder
 import io.circe.generic.semiauto.deriveEncoder
@@ -54,9 +55,9 @@ object FileIntegrityCheckTask {
       }
   }
 
-  def apply[F[_]: Sync](ops: OFileRepository[F]): Task[F, Args, Result] =
+  def apply[F[_]: Sync](ops: OFileRepository[F], store: Store[F]): Task[F, Args, Result] =
     Task { ctx =>
-      ctx.store
+      store
         .transact(
           RFileMeta
             .findAll(ctx.args.pattern, 50)

modules/joex/src/main/scala/docspell/joex/fts/FtsContext.scala

@@ -9,25 +9,13 @@ package docspell.joex.fts
 import docspell.backend.fulltext.CreateIndex
 import docspell.ftsclient.FtsClient
 import docspell.joex.Config
-import docspell.scheduler.Context
 import docspell.logging.Logger
 import docspell.store.Store
 
-case class FtsContext[F[_]](
+final case class FtsContext[F[_]](
     cfg: Config.FullTextSearch,
     store: Store[F],
     fulltext: CreateIndex[F],
     fts: FtsClient[F],
     logger: Logger[F]
 )
-
-object FtsContext {
-
-  def apply[F[_]](
-      cfg: Config.FullTextSearch,
-      fts: FtsClient[F],
-      fulltext: CreateIndex[F],
-      ctx: Context[F, _]
-  ): FtsContext[F] =
-    FtsContext(cfg, ctx.store, fulltext, fts, ctx.logger)
-}

modules/joex/src/main/scala/docspell/joex/fts/FtsWork.scala

@@ -9,13 +9,13 @@ package docspell.joex.fts
 import cats._
 import cats.data.{Kleisli, NonEmptyList}
 import cats.implicits._
-
 import docspell.backend.fulltext.CreateIndex
 import docspell.common._
 import docspell.ftsclient._
 import docspell.joex.Config
 import docspell.scheduler.Context
 import docspell.logging.Logger
+import docspell.store.Store
 
 object FtsWork {
   import syntax._
@@ -106,10 +106,11 @@ object FtsWork {
 
       def forContext(
           cfg: Config.FullTextSearch,
+          store: Store[F],
           fts: FtsClient[F],
           fulltext: CreateIndex[F]
       ): Kleisli[F, Context[F, _], Unit] =
-        mt.local(ctx => FtsContext(cfg, fts, fulltext, ctx))
+        mt.local(ctx => FtsContext(cfg, store, fulltext, fts, ctx.logger))
     }
   }
 }

modules/joex/src/main/scala/docspell/joex/fts/MigrationTask.scala

@@ -13,12 +13,14 @@ import docspell.common._
 import docspell.ftsclient._
 import docspell.joex.Config
 import docspell.scheduler.{Job, Task}
+import docspell.store.Store
 
 object MigrationTask {
   val taskName = Ident.unsafe("full-text-index")
 
   def apply[F[_]: Async](
       cfg: Config.FullTextSearch,
+      store: Store[F],
       fts: FtsClient[F],
       createIndex: CreateIndex[F]
   ): Task[F, Unit, Unit] =
@@ -28,7 +30,7 @@ object MigrationTask {
         Task(ctx =>
           for {
             migs <- migrationTasks[F](fts)
-            res <- Migration[F](cfg, fts, ctx.store, createIndex, ctx.logger).run(migs)
+            res <- Migration[F](cfg, fts, store, createIndex, ctx.logger).run(migs)
           } yield res
         )
       )

modules/joex/src/main/scala/docspell/joex/fts/ReIndexTask.scala

@@ -8,13 +8,13 @@ package docspell.joex.fts
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.backend.fulltext.CreateIndex
 import docspell.common._
 import docspell.ftsclient._
 import docspell.joex.Config
 import docspell.joex.fts.FtsWork.syntax._
 import docspell.scheduler.Task
+import docspell.store.Store
 
 object ReIndexTask {
   type Args = ReIndexTaskArgs
@@ -24,6 +24,7 @@ object ReIndexTask {
 
   def apply[F[_]: Async](
       cfg: Config.FullTextSearch,
+      store: Store[F],
       fts: FtsClient[F],
       fulltext: CreateIndex[F]
   ): Task[F, Args, Unit] =
@@ -31,7 +32,7 @@ object ReIndexTask {
       .log[F, Args](_.info(s"Running full-text re-index now"))
       .flatMap(_ =>
         Task(ctx =>
-          clearData[F](ctx.args.collective).forContext(cfg, fts, fulltext).run(ctx)
+          clearData[F](ctx.args.collective).forContext(cfg, store, fts, fulltext).run(ctx)
         )
       )
 

modules/joex/src/main/scala/docspell/joex/hk/CheckNodesTask.scala

@@ -8,18 +8,18 @@ package docspell.joex.hk
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
-import docspell.scheduler.{Context, Task}
+import docspell.scheduler.Task
 import docspell.logging.Logger
+import docspell.store.Store
 import docspell.store.records._
-
 import org.http4s.blaze.client.BlazeClientBuilder
 import org.http4s.client.Client
 
 object CheckNodesTask {
   def apply[F[_]: Async](
-      cfg: HouseKeepingConfig.CheckNodes
+      cfg: HouseKeepingConfig.CheckNodes,
+      store: Store[F]
   ): Task[F, Unit, CleanupResult] =
     Task { ctx =>
       if (cfg.enabled)
@@ -27,12 +27,12 @@ object CheckNodesTask {
           _ <- ctx.logger.info("Check nodes reachability")
           ec = scala.concurrent.ExecutionContext.global
           _ <- BlazeClientBuilder[F].withExecutionContext(ec).resource.use { client =>
-            checkNodes(ctx, client)
+            checkNodes(ctx.logger, store, client)
           }
           _ <- ctx.logger.info(
             s"Remove nodes not found more than ${cfg.minNotFound} times"
           )
-          n <- removeNodes(ctx, cfg)
+          n <- removeNodes(store, cfg)
           _ <- ctx.logger.info(s"Removed $n nodes")
         } yield CleanupResult.of(n)
       else
@@ -41,14 +41,18 @@ object CheckNodesTask {
 
     }
 
-  def checkNodes[F[_]: Async](ctx: Context[F, _], client: Client[F]): F[Unit] =
+  def checkNodes[F[_]: Async](
-    ctx.store
+      logger: Logger[F],
+      store: Store[F],
+      client: Client[F]
+  ): F[Unit] =
+    store
       .transact(RNode.streamAll)
       .evalMap(node =>
-        checkNode(ctx.logger, client)(node.url)
+        checkNode(logger, client)(node.url)
           .flatMap(seen =>
-            if (seen) ctx.store.transact(RNode.resetNotFound(node.id))
+            if (seen) store.transact(RNode.resetNotFound(node.id))
-            else ctx.store.transact(RNode.incrementNotFound(node.id))
+            else store.transact(RNode.incrementNotFound(node.id))
           )
       )
       .compile
@@ -68,9 +72,9 @@ object CheckNodesTask {
   }
 
   def removeNodes[F[_]](
-      ctx: Context[F, _],
+      store: Store[F],
       cfg: HouseKeepingConfig.CheckNodes
   ): F[Int] =
-    ctx.store.transact(RNode.deleteNotFound(cfg.minNotFound))
+    store.transact(RNode.deleteNotFound(cfg.minNotFound))
 
 }

modules/joex/src/main/scala/docspell/joex/hk/CleanupInvitesTask.scala

@@ -8,15 +8,16 @@ package docspell.joex.hk
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records._
 
 object CleanupInvitesTask {
 
   def apply[F[_]: Sync](
-      cfg: HouseKeepingConfig.CleanupInvites
+      cfg: HouseKeepingConfig.CleanupInvites,
+      store: Store[F]
   ): Task[F, Unit, CleanupResult] =
     Task { ctx =>
       if (cfg.enabled)
@@ -24,7 +25,7 @@ object CleanupInvitesTask {
           now <- Timestamp.current[F]
           ts = now - cfg.olderThan
           _ <- ctx.logger.info(s"Cleanup invitations older than $ts")
-          n <- ctx.store.transact(RInvitation.deleteOlderThan(ts))
+          n <- store.transact(RInvitation.deleteOlderThan(ts))
           _ <- ctx.logger.info(s"Removed $n invitations")
         } yield CleanupResult.of(n)
       else

modules/joex/src/main/scala/docspell/joex/hk/CleanupJobsTask.scala

@@ -18,7 +18,8 @@ import docspell.store.records._
 object CleanupJobsTask {
 
   def apply[F[_]: Sync](
-      cfg: HouseKeepingConfig.CleanupJobs
+      cfg: HouseKeepingConfig.CleanupJobs,
+      store: Store[F]
   ): Task[F, Unit, CleanupResult] =
     Task { ctx =>
       if (cfg.enabled)
@@ -26,7 +27,7 @@ object CleanupJobsTask {
           now <- Timestamp.current[F]
           ts = now - cfg.olderThan
           _ <- ctx.logger.info(s"Cleanup jobs older than $ts")
-          n <- deleteDoneJobs(ctx.store, ts, cfg.deleteBatch)
+          n <- deleteDoneJobs(store, ts, cfg.deleteBatch)
           _ <- ctx.logger.info(s"Removed $n jobs")
         } yield CleanupResult.of(n)
       else

modules/joex/src/main/scala/docspell/joex/hk/CleanupRememberMeTask.scala

@@ -8,14 +8,15 @@ package docspell.joex.hk
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records._
 
 object CleanupRememberMeTask {
   def apply[F[_]: Sync](
-      cfg: HouseKeepingConfig.CleanupRememberMe
+      cfg: HouseKeepingConfig.CleanupRememberMe,
+      store: Store[F]
   ): Task[F, Unit, CleanupResult] =
     Task { ctx =>
       if (cfg.enabled)
@@ -23,7 +24,7 @@ object CleanupRememberMeTask {
           now <- Timestamp.current[F]
           ts = now - cfg.olderThan
           _ <- ctx.logger.info(s"Cleanup remember-me tokens older than $ts")
-          n <- ctx.store.transact(RRememberMe.deleteOlderThan(ts))
+          n <- store.transact(RRememberMe.deleteOlderThan(ts))
           _ <- ctx.logger.info(s"Removed $n tokens")
         } yield CleanupResult.of(n)
       else

modules/joex/src/main/scala/docspell/joex/hk/HouseKeepingTask.scala

@@ -15,6 +15,7 @@ import docspell.joex.filecopy.FileIntegrityCheckTask
 import docspell.scheduler.{JobTaskResultEncoder, Task}
 import com.github.eikek.calev._
 import docspell.scheduler.usertask.UserTask
+import docspell.store.Store
 import io.circe.Encoder
 import io.circe.generic.semiauto.deriveEncoder
 
@@ -25,15 +26,16 @@ object HouseKeepingTask {
 
   def apply[F[_]: Async](
       cfg: Config,
+      store: Store[F],
       fileRepo: OFileRepository[F]
   ): Task[F, Unit, Result] = {
     val combined =
       (
-        CheckNodesTask(cfg.houseKeeping.checkNodes),
+        CheckNodesTask(cfg.houseKeeping.checkNodes, store),
-        CleanupInvitesTask(cfg.houseKeeping.cleanupInvites),
+        CleanupInvitesTask(cfg.houseKeeping.cleanupInvites, store),
-        CleanupJobsTask(cfg.houseKeeping.cleanupJobs),
+        CleanupJobsTask(cfg.houseKeeping.cleanupJobs, store),
-        CleanupRememberMeTask(cfg.houseKeeping.cleanupRememberMe),
+        CleanupRememberMeTask(cfg.houseKeeping.cleanupRememberMe, store),
-        IntegrityCheckTask(cfg.houseKeeping.integrityCheck, fileRepo)
+        IntegrityCheckTask(cfg.houseKeeping.integrityCheck, store, fileRepo)
       ).mapN(Result.apply)
 
     Task

modules/joex/src/main/scala/docspell/joex/hk/IntegrityCheckTask.scala

@@ -8,21 +8,22 @@ package docspell.joex.hk
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.backend.ops.OFileRepository
 import docspell.common._
 import docspell.joex.filecopy.FileIntegrityCheckTask
 import docspell.scheduler.Task
+import docspell.store.Store
 
 object IntegrityCheckTask {
 
   def apply[F[_]: Sync](
       cfg: HouseKeepingConfig.IntegrityCheck,
+      store: Store[F],
       fileRepo: OFileRepository[F]
   ): Task[F, Unit, FileIntegrityCheckTask.Result] =
     Task { ctx =>
       if (cfg.enabled)
-        FileIntegrityCheckTask(fileRepo).run(
+        FileIntegrityCheckTask(fileRepo, store).run(
           ctx.map(_ => FileIntegrityCheckArgs(FileKeyPart.Empty))
         )
       else

modules/joex/src/main/scala/docspell/joex/learn/LearnClassifierTask.scala

@@ -9,13 +9,13 @@ package docspell.joex.learn
 import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
-
 import docspell.analysis.TextAnalyser
 import docspell.backend.ops.OCollective
 import docspell.common._
 import docspell.joex.Config
 import docspell.scheduler._
 import docspell.logging.Logger
+import docspell.store.Store
 import docspell.store.records.{RClassifierModel, RClassifierSetting}
 
 object LearnClassifierTask {
@@ -29,14 +29,16 @@ object LearnClassifierTask {
 
   def apply[F[_]: Async](
       cfg: Config.TextAnalysis,
+      store: Store[F],
       analyser: TextAnalyser[F]
   ): Task[F, Args, Unit] =
-    learnTags(cfg, analyser)
+    learnTags(cfg, store, analyser)
-      .flatMap(_ => learnItemEntities(cfg, analyser))
+      .flatMap(_ => learnItemEntities(cfg, store, analyser))
       .flatMap(_ => Task(_ => Sync[F].delay(System.gc())))
 
   private def learnItemEntities[F[_]: Async](
       cfg: Config.TextAnalysis,
+      store: Store[F],
       analyser: TextAnalyser[F]
   ): Task[F, Args, Unit] =
     Task { ctx =>
@@ -44,6 +46,7 @@ object LearnClassifierTask {
         LearnItemEntities
           .learnAll(
             analyser,
+            store,
             ctx.args.collective,
             cfg.classification.itemCount,
             cfg.maxLength
@@ -54,16 +57,17 @@ object LearnClassifierTask {
 
   private def learnTags[F[_]: Async](
       cfg: Config.TextAnalysis,
+      store: Store[F],
       analyser: TextAnalyser[F]
   ): Task[F, Args, Unit] =
     Task { ctx =>
       val learnTags =
         for {
-          sett <- findActiveSettings[F](ctx, cfg)
+          sett <- findActiveSettings[F](ctx, store, cfg)
           maxItems = cfg.classification.itemCountOrWhenLower(sett.itemCount)
           _ <- OptionT.liftF(
             LearnTags
-              .learnAllTagCategories(analyser)(
+              .learnAllTagCategories(analyser, store)(
                 ctx.args.collective,
                 maxItems,
                 cfg.maxLength
@@ -74,34 +78,38 @@ object LearnClassifierTask {
       // learn classifier models from active tag categories
       learnTags.getOrElseF(logInactiveWarning(ctx.logger)) *>
         // delete classifier model files for categories that have been removed
-        clearObsoleteTagModels(ctx) *>
+        clearObsoleteTagModels(ctx, store) *>
         // when tags are deleted, categories may get removed. fix the json array
-        ctx.store
+        store
           .transact(RClassifierSetting.fixCategoryList(ctx.args.collective))
           .map(_ => ())
     }
 
-  private def clearObsoleteTagModels[F[_]: Sync](ctx: Context[F, Args]): F[Unit] =
+  private def clearObsoleteTagModels[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F]
+  ): F[Unit] =
     for {
-      list <- ctx.store.transact(
+      list <- store.transact(
         ClassifierName.findOrphanTagModels(ctx.args.collective)
       )
       _ <- ctx.logger.info(
         s"Found ${list.size} obsolete model files that are deleted now."
       )
-      n <- ctx.store.transact(RClassifierModel.deleteAll(list.map(_.id)))
+      n <- store.transact(RClassifierModel.deleteAll(list.map(_.id)))
       _ <- list
         .map(_.fileId)
-        .traverse(id => ctx.store.fileRepo.delete(id))
+        .traverse(id => store.fileRepo.delete(id))
       _ <- ctx.logger.debug(s"Deleted $n model files.")
     } yield ()
 
   private def findActiveSettings[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: Config.TextAnalysis
   ): OptionT[F, OCollective.Classifier] =
     if (cfg.classification.enabled)
-      OptionT(ctx.store.transact(RClassifierSetting.findById(ctx.args.collective)))
+      OptionT(store.transact(RClassifierSetting.findById(ctx.args.collective)))
         .filter(_.autoTagEnabled)
         .map(OCollective.Classifier.fromRecord)
     else

modules/joex/src/main/scala/docspell/joex/learn/LearnItemEntities.scala

@@ -10,76 +10,84 @@ import cats.data.Kleisli
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.analysis.TextAnalyser
 import docspell.analysis.classifier.TextClassifier.Data
 import docspell.common._
 import docspell.scheduler._
+import docspell.store.Store
 
 object LearnItemEntities {
   def learnAll[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
-    learnCorrOrg[F, A](analyser, collective, maxItems, maxTextLen)
+    learnCorrOrg[F, A](analyser, store, collective, maxItems, maxTextLen)
-      .flatMap(_ => learnCorrPerson[F, A](analyser, collective, maxItems, maxTextLen))
+      .flatMap(_ =>
-      .flatMap(_ => learnConcPerson(analyser, collective, maxItems, maxTextLen))
+        learnCorrPerson[F, A](analyser, store, collective, maxItems, maxTextLen)
-      .flatMap(_ => learnConcEquip(analyser, collective, maxItems, maxTextLen))
+      )
+      .flatMap(_ => learnConcPerson(analyser, store, collective, maxItems, maxTextLen))
+      .flatMap(_ => learnConcEquip(analyser, store, collective, maxItems, maxTextLen))
 
   def learnCorrOrg[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
-    learn(analyser, collective)(
+    learn(store, analyser, collective)(
       ClassifierName.correspondentOrg,
-      ctx => SelectItems.forCorrOrg(ctx.store, collective, maxItems, maxTextLen)
+      _ => SelectItems.forCorrOrg(store, collective, maxItems, maxTextLen)
     )
 
   def learnCorrPerson[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
-    learn(analyser, collective)(
+    learn(store, analyser, collective)(
       ClassifierName.correspondentPerson,
-      ctx => SelectItems.forCorrPerson(ctx.store, collective, maxItems, maxTextLen)
+      _ => SelectItems.forCorrPerson(store, collective, maxItems, maxTextLen)
     )
 
   def learnConcPerson[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
-    learn(analyser, collective)(
+    learn(store, analyser, collective)(
       ClassifierName.concernedPerson,
-      ctx => SelectItems.forConcPerson(ctx.store, collective, maxItems, maxTextLen)
+      _ => SelectItems.forConcPerson(store, collective, maxItems, maxTextLen)
     )
 
   def learnConcEquip[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
-    learn(analyser, collective)(
+    learn(store, analyser, collective)(
       ClassifierName.concernedEquip,
-      ctx => SelectItems.forConcEquip(ctx.store, collective, maxItems, maxTextLen)
+      _ => SelectItems.forConcEquip(store, collective, maxItems, maxTextLen)
     )
 
   private def learn[F[_]: Async, A](
+      store: Store[F],
       analyser: TextAnalyser[F],
       collective: Ident
   )(cname: ClassifierName, data: Context[F, _] => Stream[F, Data]): Task[F, A, Unit] =
     Task { ctx =>
       ctx.logger.info(s"Learn classifier ${cname.name}") *>
         analyser.classifier.trainClassifier(ctx.logger, data(ctx))(
-          Kleisli(StoreClassifierModel.handleModel(ctx, collective, cname))
+          Kleisli(StoreClassifierModel.handleModel(store, ctx.logger, collective, cname))
         )
     }
 }

modules/joex/src/main/scala/docspell/joex/learn/LearnTags.scala

@@ -9,16 +9,17 @@ package docspell.joex.learn
 import cats.data.Kleisli
 import cats.effect._
 import cats.implicits._
-
 import docspell.analysis.TextAnalyser
 import docspell.common._
 import docspell.scheduler._
+import docspell.store.Store
 import docspell.store.records.RClassifierSetting
 
 object LearnTags {
 
   def learnTagCategory[F[_]: Async, A](
       analyser: TextAnalyser[F],
+      store: Store[F],
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
@@ -26,12 +27,14 @@ object LearnTags {
       category: String
   ): Task[F, A, Unit] =
     Task { ctx =>
-      val data = SelectItems.forCategory(ctx, collective)(maxItems, category, maxTextLen)
+      val data =
+        SelectItems.forCategory(store, collective)(maxItems, category, maxTextLen)
       ctx.logger.info(s"Learn classifier for tag category: $category") *>
         analyser.classifier.trainClassifier(ctx.logger, data)(
           Kleisli(
             StoreClassifierModel.handleModel(
-              ctx,
+              store,
+              ctx.logger,
               collective,
               ClassifierName.tagCategory(category)
             )
@@ -39,15 +42,15 @@ object LearnTags {
         )
     }
 
-  def learnAllTagCategories[F[_]: Async, A](analyser: TextAnalyser[F])(
+  def learnAllTagCategories[F[_]: Async, A](analyser: TextAnalyser[F], store: Store[F])(
       collective: Ident,
       maxItems: Int,
       maxTextLen: Int
   ): Task[F, A, Unit] =
     Task { ctx =>
       for {
-        cats <- ctx.store.transact(RClassifierSetting.getActiveCategories(collective))
+        cats <- store.transact(RClassifierSetting.getActiveCategories(collective))
-        task = learnTagCategory[F, A](analyser, collective, maxItems, maxTextLen) _
+        task = learnTagCategory[F, A](analyser, store, collective, maxItems, maxTextLen) _
         _ <- cats.map(task).traverse(_.run(ctx))
       } yield ()
     }

modules/joex/src/main/scala/docspell/joex/learn/SelectItems.scala

@@ -10,7 +10,6 @@ import fs2.{Pipe, Stream}
 
 import docspell.analysis.classifier.TextClassifier.Data
 import docspell.common._
-import docspell.scheduler.Context
 import docspell.store.Store
 import docspell.store.qb.Batch
 import docspell.store.queries.{QItem, TextAndTag}
@@ -21,16 +20,7 @@ object SelectItems {
   val pageSep = LearnClassifierTask.pageSep
   val noClass = LearnClassifierTask.noClass
 
-  def forCategory[F[_]](ctx: Context[F, _], collective: Ident)(
+  def forCategory[F[_]](store: Store[F], collective: Ident)(
-      maxItems: Int,
-      category: String,
-      maxTextLen: Int
-  ): Stream[F, Data] =
-    forCategory(ctx.store, collective, maxItems, category, maxTextLen)
-
-  def forCategory[F[_]](
-      store: Store[F],
-      collective: Ident,
       maxItems: Int,
       category: String,
       maxTextLen: Int

modules/joex/src/main/scala/docspell/joex/learn/StoreClassifierModel.scala

@@ -12,7 +12,6 @@ import fs2.io.file.Files
 
 import docspell.analysis.classifier.ClassifierModel
 import docspell.common._
-import docspell.scheduler._
 import docspell.logging.Logger
 import docspell.store.Store
 import docspell.store.records.RClassifierModel
@@ -20,21 +19,12 @@ import docspell.store.records.RClassifierModel
 object StoreClassifierModel {
 
   def handleModel[F[_]: Async](
-      ctx: Context[F, _],
+      store: Store[F],
+      logger: Logger[F],
       collective: Ident,
       modelName: ClassifierName
   )(
       trainedModel: ClassifierModel
-  ): F[Unit] =
-    handleModel(ctx.store, ctx.logger)(collective, modelName, trainedModel)
-
-  def handleModel[F[_]: Async](
-      store: Store[F],
-      logger: Logger[F]
-  )(
-      collective: Ident,
-      modelName: ClassifierName,
-      trainedModel: ClassifierModel
   ): F[Unit] =
     for {
       oldFile <- store.transact(

modules/joex/src/main/scala/docspell/joex/mail/ReadMail.scala

@@ -70,7 +70,7 @@ object ReadMail {
           HtmlBodyViewConfig.default.copy(
             textToHtml = MarkdownBody.makeHtml(markdownCfg)
           )
-        ).map(makeHtmlBinary[F] _).map(b => Some(b))
+        ).map(makeHtmlBinary[F]).map(b => Some(b))
       }
 
     for {

modules/joex/src/main/scala/docspell/joex/notify/PeriodicDueItemsTask.scala

@@ -9,7 +9,6 @@ package docspell.joex.notify
 import cats.data.NonEmptyList
 import cats.effect._
 import cats.implicits._
-
 import docspell.backend.ops.ONotification
 import docspell.common._
 import docspell.scheduler.Context
@@ -20,6 +19,7 @@ import docspell.notification.api.PeriodicDueItemsArgs
 import docspell.query.Date
 import docspell.query.ItemQuery._
 import docspell.query.ItemQueryDsl._
+import docspell.store.Store
 import docspell.store.qb.Batch
 import docspell.store.queries.ListItem
 import docspell.store.queries.{QItem, Query}
@@ -32,11 +32,14 @@ object PeriodicDueItemsTask {
   def onCancel[F[_]]: Task[F, Args, Unit] =
     Task.log(_.warn(s"Cancelling ${taskName.id} task"))
 
-  def apply[F[_]: Sync](notificationOps: ONotification[F]): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](
+      store: Store[F],
+      notificationOps: ONotification[F]
+  ): Task[F, Args, Unit] =
     Task { ctx =>
       val limit = 7
       Timestamp.current[F].flatMap { now =>
-        withItems(ctx, limit, now) { items =>
+        withItems(ctx, store, limit, now) { items =>
           withEventContext(ctx, items, limit, now) { eventCtx =>
             withChannel(ctx, notificationOps) { channels =>
               notificationOps.sendMessage(ctx.logger, eventCtx, channels)
@@ -51,7 +54,12 @@ object PeriodicDueItemsTask {
   ): F[Unit] =
     TaskOperations.withChannel(ctx.logger, ctx.args.channels, ctx.args.account, ops)(cont)
 
-  def withItems[F[_]: Sync](ctx: Context[F, Args], limit: Int, now: Timestamp)(
+  def withItems[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F],
+      limit: Int,
+      now: Timestamp
+  )(
       cont: Vector[ListItem] => F[Unit]
   ): F[Unit] = {
     val rightDate = Date((now + Duration.days(ctx.args.remindDays.toLong)).toMillis)
@@ -77,7 +85,7 @@ object PeriodicDueItemsTask {
 
     for {
       res <-
-        ctx.store
+        store
           .transact(
             QItem
               .findItems(q, now.toUtcDate, 0, Batch.limit(limit))

modules/joex/src/main/scala/docspell/joex/notify/PeriodicQueryTask.scala

@@ -10,7 +10,6 @@ import cats.data.OptionT
 import cats.data.{NonEmptyList => Nel}
 import cats.effect._
 import cats.implicits._
-
 import docspell.backend.ops.ONotification
 import docspell.common._
 import docspell.scheduler.Context
@@ -22,6 +21,7 @@ import docspell.query.ItemQuery
 import docspell.query.ItemQuery.Expr
 import docspell.query.ItemQuery.Expr.AndExpr
 import docspell.query.ItemQueryParser
+import docspell.store.Store
 import docspell.store.qb.Batch
 import docspell.store.queries.ListItem
 import docspell.store.queries.{QItem, Query}
@@ -36,11 +36,14 @@ object PeriodicQueryTask {
   def onCancel[F[_]]: Task[F, Args, Unit] =
     Task.log(_.warn(s"Cancelling ${taskName.id} task"))
 
-  def apply[F[_]: Sync](notificationOps: ONotification[F]): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](
+      store: Store[F],
+      notificationOps: ONotification[F]
+  ): Task[F, Args, Unit] =
     Task { ctx =>
       val limit = 7
       Timestamp.current[F].flatMap { now =>
-        withItems(ctx, limit, now) { items =>
+        withItems(ctx, store, limit, now) { items =>
           withEventContext(ctx, items, limit, now) { eventCtx =>
             withChannel(ctx, notificationOps) { channels =>
               notificationOps.sendMessage(ctx.logger, eventCtx, channels)
@@ -58,9 +61,11 @@ object PeriodicQueryTask {
   private def queryString(q: ItemQuery.Expr) =
     ItemQueryParser.asString(q)
 
-  def withQuery[F[_]: Sync](ctx: Context[F, Args])(cont: Query => F[Unit]): F[Unit] = {
+  def withQuery[F[_]: Sync](ctx: Context[F, Args], store: Store[F])(
+      cont: Query => F[Unit]
+  ): F[Unit] = {
     def fromBookmark(id: String) =
-      ctx.store
+      store
         .transact(RQueryBookmark.findByNameOrId(ctx.args.account, id))
         .map(_.map(_.query))
         .flatTap(q =>
@@ -68,7 +73,7 @@ object PeriodicQueryTask {
         )
 
     def fromShare(id: String) =
-      ctx.store
+      store
         .transact(RShare.findOneByCollective(ctx.args.account.collective, Some(true), id))
         .map(_.map(_.query))
         .flatTap(q =>
@@ -120,11 +125,16 @@ object PeriodicQueryTask {
     }
   }
 
-  def withItems[F[_]: Sync](ctx: Context[F, Args], limit: Int, now: Timestamp)(
+  def withItems[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F],
+      limit: Int,
+      now: Timestamp
+  )(
       cont: Vector[ListItem] => F[Unit]
   ): F[Unit] =
-    withQuery(ctx) { query =>
+    withQuery(ctx, store) { query =>
-      val items = ctx.store
+      val items = store
         .transact(QItem.findItems(query, now.toUtcDate, 0, Batch.limit(limit)))
         .compile
         .to(Vector)

modules/joex/src/main/scala/docspell/joex/pagecount/AllPageCountTask.scala

@@ -13,6 +13,7 @@ import docspell.backend.JobFactory
 import docspell.backend.ops.OJoex
 import docspell.common._
 import docspell.scheduler.{Context, Job, JobStore, Task}
+import docspell.store.Store
 import docspell.store.records.RAttachment
 
 object AllPageCountTask {
@@ -20,11 +21,15 @@ object AllPageCountTask {
   val taskName = Ident.unsafe("all-page-count")
   type Args = Unit
 
-  def apply[F[_]: Sync](jobStore: JobStore[F], joex: OJoex[F]): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](
+      store: Store[F],
+      jobStore: JobStore[F],
+      joex: OJoex[F]
+  ): Task[F, Args, Unit] =
     Task { ctx =>
       for {
         _ <- ctx.logger.info("Generating previews for attachments")
-        n <- submitConversionJobs(ctx, jobStore)
+        n <- submitConversionJobs(ctx, store, jobStore)
         _ <- ctx.logger.info(s"Submitted $n jobs")
         _ <- joex.notifyAllNodes
       } yield ()
@@ -35,9 +40,10 @@ object AllPageCountTask {
 
   def submitConversionJobs[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       jobStore: JobStore[F]
   ): F[Int] =
-    ctx.store
+    store
       .transact(findAttachments)
       .chunks
       .flatMap(createJobs[F])

modules/joex/src/main/scala/docspell/joex/pagecount/MakePageCountTask.scala

@@ -8,11 +8,11 @@ package docspell.joex.pagecount
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.joex.process.AttachmentPageCount
 import docspell.scheduler.Context
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records.RAttachment
 import docspell.store.records.RAttachmentMeta
 
@@ -20,10 +20,10 @@ object MakePageCountTask {
 
   type Args = MakePageCountArgs
 
-  def apply[F[_]: Sync](): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](store: Store[F]): Task[F, Args, Unit] =
     Task { ctx =>
       for {
-        exists <- pageCountExists(ctx)
+        exists <- pageCountExists(ctx, store)
         _ <-
           if (exists)
             ctx.logger.info(
@@ -32,7 +32,7 @@ object MakePageCountTask {
           else
             ctx.logger.info(
               s"Reading page-count for attachment ${ctx.args.attachment}"
-            ) *> generatePageCount(ctx)
+            ) *> generatePageCount(ctx, store)
       } yield ()
     }
 
@@ -40,19 +40,20 @@ object MakePageCountTask {
     Task.log(_.warn("Cancelling make-page-count task"))
 
   private def generatePageCount[F[_]: Sync](
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[Unit] =
     for {
-      ra <- ctx.store.transact(RAttachment.findById(ctx.args.attachment))
+      ra <- store.transact(RAttachment.findById(ctx.args.attachment))
       _ <- ra
-        .map(AttachmentPageCount.createPageCount(ctx))
+        .map(AttachmentPageCount.createPageCount(ctx, store))
         .getOrElse(
           ctx.logger.warn(s"No attachment found with id: ${ctx.args.attachment}")
         )
     } yield ()
 
-  private def pageCountExists[F[_]](ctx: Context[F, Args]): F[Boolean] =
+  private def pageCountExists[F[_]](ctx: Context[F, Args], store: Store[F]): F[Boolean] =
-    ctx.store.transact(
+    store.transact(
       RAttachmentMeta
         .findPageCountById(ctx.args.attachment)
         .map(_.exists(_ > 0))

modules/joex/src/main/scala/docspell/joex/pdfconv/ConvertAllPdfTask.scala

@@ -12,6 +12,7 @@ import fs2.{Chunk, Stream}
 import docspell.backend.ops.OJoex
 import docspell.common._
 import docspell.scheduler.{Context, Job, JobStore, Task}
+import docspell.store.Store
 import docspell.store.records.RAttachment
 
 /* A task to find all non-converted pdf files (of a collective, or
@@ -21,11 +22,15 @@ import docspell.store.records.RAttachment
 object ConvertAllPdfTask {
   type Args = ConvertAllPdfArgs
 
-  def apply[F[_]: Sync](jobStore: JobStore[F], joex: OJoex[F]): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](
+      jobStore: JobStore[F],
+      joex: OJoex[F],
+      store: Store[F]
+  ): Task[F, Args, Unit] =
     Task { ctx =>
       for {
         _ <- ctx.logger.info("Converting pdfs using ocrmypdf")
-        n <- submitConversionJobs(ctx, jobStore)
+        n <- submitConversionJobs(ctx, store, jobStore)
         _ <- ctx.logger.info(s"Submitted $n file conversion jobs")
         _ <- joex.notifyAllNodes
       } yield ()
@@ -36,9 +41,10 @@ object ConvertAllPdfTask {
 
   def submitConversionJobs[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       jobStore: JobStore[F]
   ): F[Int] =
-    ctx.store
+    store
       .transact(RAttachment.findNonConvertedPdf(ctx.args.collective, 50))
       .chunks
       .flatMap(createJobs[F](ctx))

modules/joex/src/main/scala/docspell/joex/pdfconv/PdfConvTask.scala

@@ -11,14 +11,13 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.common._
 import docspell.convert.ConversionResult
 import docspell.convert.extern.OcrMyPdf
 import docspell.joex.Config
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.records._
-
 import io.circe.generic.semiauto._
 import io.circe.{Decoder, Encoder}
 
@@ -36,12 +35,12 @@ object PdfConvTask {
 
   val taskName = Ident.unsafe("pdf-files-migration")
 
-  def apply[F[_]: Async](cfg: Config): Task[F, Args, Unit] =
+  def apply[F[_]: Async](cfg: Config, store: Store[F]): Task[F, Args, Unit] =
     Task { ctx =>
       for {
         _ <- ctx.logger.info(s"Converting pdf file ${ctx.args} using ocrmypdf")
-        meta <- checkInputs(cfg, ctx)
+        meta <- checkInputs(cfg, ctx, store)
-        _ <- meta.traverse(fm => convert(cfg, ctx, fm))
+        _ <- meta.traverse(fm => convert(cfg, ctx, store, fm))
       } yield ()
     }
 
@@ -53,19 +52,20 @@ object PdfConvTask {
   // check if file exists and if it is pdf and if source id is the same and if ocrmypdf is enabled
   def checkInputs[F[_]: Sync](
       cfg: Config,
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[Option[RFileMeta]] = {
     val none: Option[RFileMeta] = None
     val checkSameFiles =
       (for {
-        ra <- OptionT(ctx.store.transact(RAttachment.findById(ctx.args.attachId)))
+        ra <- OptionT(store.transact(RAttachment.findById(ctx.args.attachId)))
         isSame <- OptionT.liftF(
-          ctx.store.transact(RAttachmentSource.isSameFile(ra.id, ra.fileId))
+          store.transact(RAttachmentSource.isSameFile(ra.id, ra.fileId))
         )
       } yield isSame).getOrElse(false)
     val existsPdf =
       for {
-        meta <- ctx.store.transact(RAttachment.findMeta(ctx.args.attachId))
+        meta <- store.transact(RAttachment.findMeta(ctx.args.attachId))
         res = meta.filter(_.mimetype.matches(MimeType.pdf))
         _ <-
           if (res.isEmpty)
@@ -90,18 +90,19 @@ object PdfConvTask {
   def convert[F[_]: Async](
       cfg: Config,
       ctx: Context[F, Args],
+      store: Store[F],
       in: RFileMeta
   ): F[Unit] = {
-    val fs = ctx.store.fileRepo
+    val fs = store.fileRepo
     val data = fs.getBytes(in.id)
 
     val storeResult: ConversionResult.Handler[F, Unit] =
       Kleisli {
         case ConversionResult.SuccessPdf(file) =>
-          storeToAttachment(ctx, in, file)
+          storeToAttachment(ctx, store, in, file)
 
         case ConversionResult.SuccessPdfTxt(file, _) =>
-          storeToAttachment(ctx, in, file)
+          storeToAttachment(ctx, store, in, file)
 
         case ConversionResult.UnsupportedFormat(mime) =>
           ctx.logger.warn(
@@ -124,19 +125,20 @@ object PdfConvTask {
       )(data, storeResult)
 
     for {
-      lang <- getLanguage(ctx)
+      lang <- getLanguage(ctx, store)
       _ <- ocrMyPdf(lang)
     } yield ()
   }
 
-  def getLanguage[F[_]: Sync](ctx: Context[F, Args]): F[Language] =
+  def getLanguage[F[_]: Sync](ctx: Context[F, Args], store: Store[F]): F[Language] =
     (for {
-      coll <- OptionT(ctx.store.transact(RCollective.findByAttachment(ctx.args.attachId)))
+      coll <- OptionT(store.transact(RCollective.findByAttachment(ctx.args.attachId)))
       lang = coll.language
     } yield lang).getOrElse(Language.German)
 
   def storeToAttachment[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       meta: RFileMeta,
       newFile: Stream[F, Byte]
   ): F[Unit] = {
@@ -146,10 +148,10 @@ object PdfConvTask {
     for {
       fid <-
         newFile
-          .through(ctx.store.fileRepo.save(collective, cat, mimeHint))
+          .through(store.fileRepo.save(collective, cat, mimeHint))
           .compile
           .lastOrError
-      _ <- ctx.store.transact(RAttachment.updateFileId(ctx.args.attachId, fid))
+      _ <- store.transact(RAttachment.updateFileId(ctx.args.attachId, fid))
     } yield ()
   }
 }

modules/joex/src/main/scala/docspell/joex/preview/AllPreviewsTask.scala

@@ -14,17 +14,22 @@ import docspell.backend.ops.OJoex
 import docspell.common.MakePreviewArgs.StoreMode
 import docspell.common._
 import docspell.scheduler.{Context, Job, JobStore, Task}
+import docspell.store.Store
 import docspell.store.records.RAttachment
 
 object AllPreviewsTask {
 
   type Args = AllPreviewsArgs
 
-  def apply[F[_]: Sync](jobStore: JobStore[F], joex: OJoex[F]): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](
+      jobStore: JobStore[F],
+      joex: OJoex[F],
+      store: Store[F]
+  ): Task[F, Args, Unit] =
     Task { ctx =>
       for {
         _ <- ctx.logger.info("Generating previews for attachments")
-        n <- submitConversionJobs(ctx, jobStore)
+        n <- submitConversionJobs(ctx, store, jobStore)
         _ <- ctx.logger.info(s"Submitted $n jobs")
         _ <- joex.notifyAllNodes
       } yield ()
@@ -35,9 +40,10 @@ object AllPreviewsTask {
 
   def submitConversionJobs[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       jobStore: JobStore[F]
   ): F[Int] =
-    ctx.store
+    store
       .transact(findAttachments(ctx))
       .chunks
       .flatMap(createJobs[F](ctx))

modules/joex/src/main/scala/docspell/joex/preview/MakePreviewTask.scala

@@ -8,13 +8,13 @@ package docspell.joex.preview
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.extract.pdfbox.PdfboxPreview
 import docspell.extract.pdfbox.PreviewConfig
 import docspell.joex.process.AttachmentPreview
 import docspell.scheduler.Context
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records.RAttachment
 import docspell.store.records.RAttachmentPreview
 
@@ -22,10 +22,10 @@ object MakePreviewTask {
 
   type Args = MakePreviewArgs
 
-  def apply[F[_]: Sync](pcfg: PreviewConfig): Task[F, Args, Unit] =
+  def apply[F[_]: Sync](pcfg: PreviewConfig, store: Store[F]): Task[F, Args, Unit] =
     Task { ctx =>
       for {
-        exists <- previewExists(ctx)
+        exists <- previewExists(ctx, store)
         preview <- PdfboxPreview(pcfg)
         _ <-
           if (exists)
@@ -35,7 +35,7 @@ object MakePreviewTask {
           else
             ctx.logger.info(
               s"Generating preview image for attachment ${ctx.args.attachment}"
-            ) *> generatePreview(ctx, preview)
+            ) *> generatePreview(ctx, store, preview)
       } yield ()
     }
 
@@ -44,20 +44,24 @@ object MakePreviewTask {
 
   private def generatePreview[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       preview: PdfboxPreview[F]
   ): F[Unit] =
     for {
-      ra <- ctx.store.transact(RAttachment.findById(ctx.args.attachment))
+      ra <- store.transact(RAttachment.findById(ctx.args.attachment))
       _ <- ra
-        .map(AttachmentPreview.createPreview(ctx, preview))
+        .map(AttachmentPreview.createPreview(ctx, store, preview))
         .getOrElse(
           ctx.logger.error(s"No attachment found with id: ${ctx.args.attachment}")
         )
     } yield ()
 
-  private def previewExists[F[_]: Sync](ctx: Context[F, Args]): F[Boolean] =
+  private def previewExists[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F]
+  ): F[Boolean] =
     if (ctx.args.store == MakePreviewArgs.StoreMode.WhenMissing)
-      ctx.store.transact(
+      store.transact(
         RAttachmentPreview.findById(ctx.args.attachment).map(_.isDefined)
       )
     else

modules/joex/src/main/scala/docspell/joex/process/AttachmentPageCount.scala

@@ -11,11 +11,11 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.common._
 import docspell.extract.pdfbox.PdfMetaData
 import docspell.extract.pdfbox.PdfboxExtract
 import docspell.scheduler._
+import docspell.store.Store
 import docspell.store.records.RAttachment
 import docspell.store.records._
 
@@ -24,7 +24,7 @@ import docspell.store.records._
   */
 object AttachmentPageCount {
 
-  def apply[F[_]: Sync]()(
+  def apply[F[_]: Sync](store: Store[F])(
       item: ItemData
   ): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
@@ -33,7 +33,7 @@ object AttachmentPageCount {
           s"Retrieving page count for ${item.attachments.size} files…"
         )
         _ <- item.attachments
-          .traverse(createPageCount(ctx))
+          .traverse(createPageCount(ctx, store))
           .attempt
           .flatMap {
             case Right(_) => ().pure[F]
@@ -46,14 +46,15 @@ object AttachmentPageCount {
     }
 
   def createPageCount[F[_]: Sync](
-      ctx: Context[F, _]
+      ctx: Context[F, _],
+      store: Store[F]
   )(ra: RAttachment): F[Option[PdfMetaData]] =
-    findMime[F](ctx)(ra).flatMap {
+    findMime[F](store)(ra).flatMap {
       case MimeType.PdfMatch(_) =>
-        PdfboxExtract.getMetaData(loadFile(ctx)(ra)).flatMap {
+        PdfboxExtract.getMetaData(loadFile(store)(ra)).flatMap {
           case Right(md) =>
             ctx.logger.debug(s"Found number of pages: ${md.pageCount}") *>
-              updatePageCount(ctx, md, ra).map(_.some)
+              updatePageCount(ctx, store, md, ra).map(_.some)
           case Left(ex) =>
             ctx.logger.warn(s"Error obtaining pages count: ${ex.getMessage}") *>
               (None: Option[PdfMetaData]).pure[F]
@@ -66,6 +67,7 @@ object AttachmentPageCount {
 
   private def updatePageCount[F[_]: Sync](
       ctx: Context[F, _],
+      store: Store[F],
       md: PdfMetaData,
       ra: RAttachment
   ): F[PdfMetaData] =
@@ -73,12 +75,12 @@ object AttachmentPageCount {
       _ <- ctx.logger.debug(
         s"Update attachment ${ra.id.id} with page count ${md.pageCount.some}"
       )
-      n <- ctx.store.transact(RAttachmentMeta.updatePageCount(ra.id, md.pageCount.some))
+      n <- store.transact(RAttachmentMeta.updatePageCount(ra.id, md.pageCount.some))
       m <-
         if (n == 0)
           ctx.logger.warn(
             s"No attachmentmeta record exists for ${ra.id.id}. Creating new."
-          ) *> ctx.store.transact(
+          ) *> store.transact(
             RAttachmentMeta.insert(
               RAttachmentMeta(
                 ra.id,
@@ -94,11 +96,11 @@ object AttachmentPageCount {
       _ <- ctx.logger.debug(s"Stored page count (${n + m}).")
     } yield md
 
-  def findMime[F[_]: Functor](ctx: Context[F, _])(ra: RAttachment): F[MimeType] =
+  def findMime[F[_]: Functor](store: Store[F])(ra: RAttachment): F[MimeType] =
-    OptionT(ctx.store.transact(RFileMeta.findById(ra.fileId)))
+    OptionT(store.transact(RFileMeta.findById(ra.fileId)))
       .map(_.mimetype)
       .getOrElse(MimeType.octetStream)
 
-  def loadFile[F[_]](ctx: Context[F, _])(ra: RAttachment): Stream[F, Byte] =
+  def loadFile[F[_]](store: Store[F])(ra: RAttachment): Stream[F, Byte] =
-    ctx.store.fileRepo.getBytes(ra.fileId)
+    store.fileRepo.getBytes(ra.fileId)
 }

modules/joex/src/main/scala/docspell/joex/process/AttachmentPreview.scala

@@ -11,11 +11,11 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.common._
 import docspell.extract.pdfbox.PdfboxPreview
 import docspell.extract.pdfbox.PreviewConfig
 import docspell.scheduler._
+import docspell.store.Store
 import docspell.store.queries.QAttachment
 import docspell.store.records.RAttachment
 import docspell.store.records._
@@ -26,7 +26,7 @@ import docspell.store.records._
   */
 object AttachmentPreview {
 
-  def apply[F[_]: Sync](pcfg: PreviewConfig)(
+  def apply[F[_]: Sync](pcfg: PreviewConfig, store: Store[F])(
       item: ItemData
   ): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
@@ -36,7 +36,7 @@ object AttachmentPreview {
         )
         preview <- PdfboxPreview(pcfg)
         _ <- item.attachments
-          .traverse(createPreview(ctx, preview))
+          .traverse(createPreview(ctx, store, preview))
           .attempt
           .flatMap {
             case Right(_) => ().pure[F]
@@ -50,16 +50,17 @@ object AttachmentPreview {
 
   def createPreview[F[_]: Sync](
       ctx: Context[F, _],
+      store: Store[F],
       preview: PdfboxPreview[F]
   )(
       ra: RAttachment
   ): F[Option[RAttachmentPreview]] =
-    findMime[F](ctx)(ra).flatMap {
+    findMime[F](store)(ra).flatMap {
       case MimeType.PdfMatch(_) =>
-        preview.previewPNG(loadFile(ctx)(ra)).flatMap {
+        preview.previewPNG(loadFile(store)(ra)).flatMap {
           case Some(out) =>
             ctx.logger.debug("Preview generated, saving to database…") *>
-              createRecord(ctx, ra.fileId.collective, out, ra).map(_.some)
+              createRecord(store, ra.fileId.collective, out, ra).map(_.some)
           case None =>
             ctx.logger
               .info(s"Preview could not be generated. Maybe the pdf has no pages?") *>
@@ -72,7 +73,7 @@ object AttachmentPreview {
     }
 
   private def createRecord[F[_]: Sync](
-      ctx: Context[F, _],
+      store: Store[F],
       collective: Ident,
       png: Stream[F, Byte],
       ra: RAttachment
@@ -83,7 +84,7 @@ object AttachmentPreview {
     for {
       fileId <- png
         .through(
-          ctx.store.fileRepo.save(
+          store.fileRepo.save(
             collective,
             FileCategory.PreviewImage,
             MimeTypeHint(name.map(_.fullName), Some("image/png"))
@@ -93,16 +94,16 @@ object AttachmentPreview {
         .lastOrError
       now <- Timestamp.current[F]
       rp = RAttachmentPreview(ra.id, fileId, name.map(_.fullName), now)
-      _ <- QAttachment.deletePreview(ctx.store)(ra.id)
+      _ <- QAttachment.deletePreview(store)(ra.id)
-      _ <- ctx.store.transact(RAttachmentPreview.insert(rp))
+      _ <- store.transact(RAttachmentPreview.insert(rp))
     } yield rp
   }
 
-  def findMime[F[_]: Functor](ctx: Context[F, _])(ra: RAttachment): F[MimeType] =
+  def findMime[F[_]: Functor](store: Store[F])(ra: RAttachment): F[MimeType] =
-    OptionT(ctx.store.transact(RFileMeta.findById(ra.fileId)))
+    OptionT(store.transact(RFileMeta.findById(ra.fileId)))
       .map(_.mimetype)
       .getOrElse(MimeType.octetStream)
 
-  def loadFile[F[_]](ctx: Context[F, _])(ra: RAttachment): Stream[F, Byte] =
+  def loadFile[F[_]](store: Store[F])(ra: RAttachment): Stream[F, Byte] =
-    ctx.store.fileRepo.getBytes(ra.fileId)
+    store.fileRepo.getBytes(ra.fileId)
 }

modules/joex/src/main/scala/docspell/joex/process/ConvertPdf.scala

@@ -11,13 +11,13 @@ import cats.data.{Kleisli, OptionT}
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.common._
 import docspell.convert.ConversionResult.Handler
 import docspell.convert.SanitizeHtml
 import docspell.convert._
 import docspell.joex.extract.JsoupSanitizer
 import docspell.scheduler._
+import docspell.store.Store
 import docspell.store.records._
 
 /** Goes through all attachments and creates a PDF version of it where supported.
@@ -36,21 +36,22 @@ object ConvertPdf {
 
   def apply[F[_]: Async](
       cfg: ConvertConfig,
+      store: Store[F],
       item: ItemData
   ): Task[F, Args, ItemData] =
     Task { ctx =>
       def convert(ra: RAttachment): F[(RAttachment, Option[RAttachmentMeta])] =
-        isConverted(ctx)(ra).flatMap {
+        isConverted(store)(ra).flatMap {
           case true if ctx.args.isNormalProcessing =>
             ctx.logger.info(
               s"Conversion to pdf already done for attachment ${ra.name}."
             ) *>
-              ctx.store
+              store
                 .transact(RAttachmentMeta.findById(ra.id))
                 .map(rmOpt => (ra, rmOpt))
           case _ =>
-            findMime(ctx)(ra).flatMap(m =>
+            findMime(store)(ra).flatMap(m =>
-              convertSafe(cfg, JsoupSanitizer.clean, ctx, item)(ra, m)
+              convertSafe(cfg, JsoupSanitizer.clean, ctx, store, item)(ra, m)
             )
         }
 
@@ -62,13 +63,15 @@ object ConvertPdf {
 
     }
 
-  def isConverted[F[_]](ctx: Context[F, Args])(
+  def isConverted[F[_]](store: Store[F])(
       ra: RAttachment
   ): F[Boolean] =
-    ctx.store.transact(RAttachmentSource.isConverted(ra.id))
+    store.transact(RAttachmentSource.isConverted(ra.id))
 
-  def findMime[F[_]: Functor](ctx: Context[F, _])(ra: RAttachment): F[MimeType] =
+  def findMime[F[_]: Functor](store: Store[F])(
-    OptionT(ctx.store.transact(RFileMeta.findById(ra.fileId)))
+      ra: RAttachment
+  ): F[MimeType] =
+    OptionT(store.transact(RFileMeta.findById(ra.fileId)))
       .map(_.mimetype)
       .getOrElse(MimeType.octetStream)
 
@@ -76,14 +79,15 @@ object ConvertPdf {
       cfg: ConvertConfig,
       sanitizeHtml: SanitizeHtml,
       ctx: Context[F, Args],
+      store: Store[F],
       item: ItemData
   )(ra: RAttachment, mime: MimeType): F[(RAttachment, Option[RAttachmentMeta])] =
-    loadCollectivePasswords(ctx).flatMap(collPass =>
+    loadCollectivePasswords(ctx, store).flatMap(collPass =>
       Conversion.create[F](cfg, sanitizeHtml, collPass, ctx.logger).use { conv =>
         mime match {
           case mt =>
-            val data = ctx.store.fileRepo.getBytes(ra.fileId)
+            val data = store.fileRepo.getBytes(ra.fileId)
-            val handler = conversionHandler[F](ctx, cfg, ra, item)
+            val handler = conversionHandler[F](ctx, store, cfg, ra, item)
             ctx.logger
               .info(s"Converting file ${ra.name} (${mime.asString}) into a PDF") *>
               conv.toPDF(DataType(mt), ctx.args.meta.language, handler)(
@@ -94,14 +98,16 @@ object ConvertPdf {
     )
 
   private def loadCollectivePasswords[F[_]: Async](
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[List[Password]] =
-    ctx.store
+    store
       .transact(RCollectivePassword.findAll(ctx.args.meta.collective))
       .map(_.map(_.password).distinct)
 
   private def conversionHandler[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: ConvertConfig,
       ra: RAttachment,
       item: ItemData
@@ -109,12 +115,12 @@ object ConvertPdf {
     Kleisli {
       case ConversionResult.SuccessPdf(pdf) =>
         ctx.logger.info(s"Conversion to pdf successful. Saving file.") *>
-          storePDF(ctx, cfg, ra, pdf)
+          storePDF(ctx, store, cfg, ra, pdf)
             .map(r => (r, None))
 
       case ConversionResult.SuccessPdfTxt(pdf, txt) =>
         ctx.logger.info(s"Conversion to pdf+txt successful. Saving file.") *>
-          storePDF(ctx, cfg, ra, pdf)
+          storePDF(ctx, store, cfg, ra, pdf)
             .flatMap(r =>
               txt.map(t =>
                 (
@@ -148,6 +154,7 @@ object ConvertPdf {
 
   private def storePDF[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: ConvertConfig,
       ra: RAttachment,
       pdf: Stream[F, Byte]
@@ -162,7 +169,7 @@ object ConvertPdf {
 
     pdf
       .through(
-        ctx.store.fileRepo.save(
+        store.fileRepo.save(
           ctx.args.meta.collective,
           FileCategory.AttachmentConvert,
           MimeTypeHint(hint.filename, hint.advertised)
@@ -170,32 +177,33 @@ object ConvertPdf {
       )
       .compile
       .lastOrError
-      .flatMap(fmId => updateAttachment[F](ctx, ra, fmId, newName).map(_ => fmId))
+      .flatMap(fmId => updateAttachment[F](ctx, store, ra, fmId, newName).map(_ => fmId))
       .map(fmId => ra.copy(fileId = fmId, name = newName))
   }
 
   private def updateAttachment[F[_]: Sync](
       ctx: Context[F, _],
+      store: Store[F],
       ra: RAttachment,
       fmId: FileKey,
       newName: Option[String]
   ): F[Unit] =
     for {
-      oldFile <- ctx.store.transact(RAttachment.findById(ra.id))
+      oldFile <- store.transact(RAttachment.findById(ra.id))
       _ <-
-        ctx.store
+        store
           .transact(RAttachment.updateFileIdAndName(ra.id, fmId, newName))
       _ <- oldFile match {
         case Some(raPrev) =>
           for {
             sameFile <-
-              ctx.store
+              store
                 .transact(RAttachmentSource.isSameFile(ra.id, raPrev.fileId))
             _ <-
               if (sameFile) ().pure[F]
               else
                 ctx.logger.info("Deleting previous attachment file") *>
-                  ctx.store.fileRepo
+                  store.fileRepo
                     .delete(raPrev.fileId)
                     .attempt
                     .flatMap {

modules/joex/src/main/scala/docspell/joex/process/CreateItem.scala

@@ -11,9 +11,9 @@ import cats.data.OptionT
 import cats.effect.Sync
 import cats.implicits._
 import fs2.Stream
-
 import docspell.common._
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.file.FileMetadata
 import docspell.store.queries.QItem
 import docspell.store.records._
@@ -21,13 +21,13 @@ import docspell.store.records._
 /** Task that creates the item. */
 object CreateItem {
 
-  def apply[F[_]: Sync]: Task[F, ProcessItemArgs, ItemData] =
+  def apply[F[_]: Sync](store: Store[F]): Task[F, ProcessItemArgs, ItemData] =
-    findExisting[F].flatMap {
+    findExisting[F](store).flatMap {
       case Some(ri) => Task.pure(ri)
-      case None     => createNew[F]
+      case None     => createNew[F](store)
     }
 
-  def createNew[F[_]: Sync]: Task[F, ProcessItemArgs, ItemData] =
+  def createNew[F[_]: Sync](store: Store[F]): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
       def isValidFile(fm: FileMetadata) =
         ctx.args.meta.validFileTypes.isEmpty ||
@@ -36,11 +36,11 @@ object CreateItem {
 
       def fileMetas(itemId: Ident, now: Timestamp) =
         Stream
-          .eval(ctx.store.transact(RAttachment.nextPosition(itemId)))
+          .eval(store.transact(RAttachment.nextPosition(itemId)))
           .flatMap { offset =>
             Stream
               .emits(ctx.args.files)
-              .evalMap(f => ctx.store.fileRepo.findMeta(f.fileMetaId).map(fm => (f, fm)))
+              .evalMap(f => store.fileRepo.findMeta(f.fileMetaId).map(fm => (f, fm)))
               .collect { case (f, Some(fm)) if isValidFile(fm) => f }
               .zipWithIndex
               .evalMap { case (f, index) =>
@@ -67,11 +67,11 @@ object CreateItem {
             (for {
               _ <- OptionT.liftF(
                 ctx.logger.info(
-                  s"Loading item with id ${id.id} to ammend"
+                  s"Loading item with id ${id.id} to amend"
                 )
               )
               item <- OptionT(
-                ctx.store
+                store
                   .transact(RItem.findByIdAndCollective(id, ctx.args.meta.collective))
               )
             } yield (1, item))
@@ -88,7 +88,7 @@ object CreateItem {
                 ctx.args.meta.direction.getOrElse(Direction.Incoming),
                 ItemState.Premature
               )
-              n <- ctx.store.transact(RItem.insert(item))
+              n <- store.transact(RItem.insert(item))
             } yield (n, item)
         }
 
@@ -98,7 +98,7 @@ object CreateItem {
         _ <- if (it._1 != 1) storeItemError[F](ctx) else ().pure[F]
         now <- Timestamp.current[F]
         fm <- fileMetas(it._2.id, now)
-        k <- fm.traverse(insertAttachment(ctx))
+        k <- fm.traverse(insertAttachment(store))
         _ <- logDifferences(ctx, fm, k.sum)
         dur <- time
         _ <- ctx.logger.info(s"Creating item finished in ${dur.formatExact}")
@@ -115,25 +115,27 @@ object CreateItem {
       )
     }
 
-  def insertAttachment[F[_]](ctx: Context[F, _])(ra: RAttachment): F[Int] = {
+  def insertAttachment[F[_]](store: Store[F])(ra: RAttachment): F[Int] = {
     val rs = RAttachmentSource.of(ra)
-    ctx.store.transact(for {
+    store.transact(for {
       n <- RAttachment.insert(ra)
       _ <- RAttachmentSource.insert(rs)
     } yield n)
   }
 
-  private def findExisting[F[_]: Sync]: Task[F, ProcessItemArgs, Option[ItemData]] =
+  private def findExisting[F[_]: Sync](
+      store: Store[F]
+  ): Task[F, ProcessItemArgs, Option[ItemData]] =
     Task { ctx =>
       val states = ItemState.invalidStates
       val fileMetaIds = ctx.args.files.map(_.fileMetaId).toSet
       for {
-        cand <- ctx.store.transact(QItem.findByFileIds(fileMetaIds.toSeq, states))
+        cand <- store.transact(QItem.findByFileIds(fileMetaIds.toSeq, states))
         _ <-
           if (cand.nonEmpty)
             ctx.logger.warn(s"Found ${cand.size} existing item with these files.")
           else ().pure[F]
-        ht <- cand.drop(1).traverse(ri => QItem.delete(ctx.store)(ri.id, ri.cid))
+        ht <- cand.drop(1).traverse(ri => QItem.delete(store)(ri.id, ri.cid))
         _ <-
           if (ht.sum > 0)
             ctx.logger.warn(s"Removed ${ht.sum} items with same attachments")
@@ -144,7 +146,7 @@ object CreateItem {
             OptionT(
               // load attachments but only those mentioned in the task's arguments
               cand.headOption.traverse(ri =>
-                ctx.store
+                store
                   .transact(RAttachment.findByItemCollectiveSource(ri.id, ri.cid, fids))
                   .flatTap(ats =>
                     ctx.logger.debug(
@@ -156,7 +158,7 @@ object CreateItem {
           )
           .getOrElse(Vector.empty)
         orig <- rms.traverse(a =>
-          ctx.store.transact(RAttachmentSource.findById(a.id)).map(s => (a, s))
+          store.transact(RAttachmentSource.findById(a.id)).map(s => (a, s))
         )
         origMap =
           orig

modules/joex/src/main/scala/docspell/joex/process/CrossCheckProposals.scala

@@ -10,10 +10,10 @@ import cats.data.NonEmptyList
 import cats.data.OptionT
 import cats.effect.Sync
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.Task
 import docspell.logging.Logger
+import docspell.store.Store
 
 /** After candidates have been determined, the set is reduced by doing some cross checks.
   * For example: if a organization is suggested as correspondent, the correspondent person
@@ -22,13 +22,15 @@ import docspell.logging.Logger
   */
 object CrossCheckProposals {
 
-  def apply[F[_]: Sync](data: ItemData): Task[F, ProcessItemArgs, ItemData] =
+  def apply[F[_]: Sync](
+      store: Store[F]
+  )(data: ItemData): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
       val proposals = data.finalProposals
       val corrOrg = proposals.find(MetaProposalType.CorrOrg)
       (for {
         orgRef <- OptionT.fromOption[F](corrOrg)
-        persRefs <- OptionT.liftF(EvalProposals.findOrganizationRelation(data, ctx))
+        persRefs <- OptionT.liftF(EvalProposals.findOrganizationRelation(data, store))
         clProps <- OptionT.liftF(
           personOrgCheck[F](ctx.logger, data.classifyProposals, persRefs)(orgRef)
         )
@@ -53,7 +55,7 @@ object CrossCheckProposals {
     mpl.find(MetaProposalType.CorrPerson) match {
       case Some(ppl) =>
         val list = ppl.values.filter(c =>
-          persRefs.get(c.ref.id).exists(_.organization == Some(orgId))
+          persRefs.get(c.ref.id).exists(_.organization.contains(orgId))
         )
 
         if (ppl.values.toList == list) mpl.pure[F]

modules/joex/src/main/scala/docspell/joex/process/DuplicateCheck.scala

@@ -8,58 +8,63 @@ package docspell.joex.process
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.queries.QItem
 import docspell.store.records.RFileMeta
 import docspell.store.records.RJob
-
 import doobie._
 
 object DuplicateCheck {
   type Args = ProcessItemArgs
 
-  def apply[F[_]: Sync]: Task[F, Args, Args] =
+  def apply[F[_]: Sync](store: Store[F]): Task[F, Args, Args] =
     Task { ctx =>
       if (ctx.args.meta.skipDuplicate)
         for {
-          retries <- getRetryCount(ctx)
+          retries <- getRetryCount(ctx, store)
           res <-
             if (retries == 0)
-              ctx.logger.debug("Checking for duplicate files") *> removeDuplicates(ctx)
+              ctx.logger
+                .debug("Checking for duplicate files") *> removeDuplicates(ctx, store)
             else ctx.args.pure[F]
         } yield res
       else ctx.logger.debug("Not checking for duplicates") *> ctx.args.pure[F]
     }
 
-  def removeDuplicates[F[_]: Sync](ctx: Context[F, Args]): F[ProcessItemArgs] =
+  def removeDuplicates[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F]
+  ): F[ProcessItemArgs] =
     for {
-      fileMetas <- findDuplicates(ctx)
+      fileMetas <- findDuplicates(ctx, store)
-      _ <- fileMetas.traverse(deleteDuplicate(ctx))
+      _ <- fileMetas.traverse(deleteDuplicate(ctx, store))
       ids = fileMetas.filter(_.exists).map(_.fm.id).toSet
     } yield ctx.args.copy(files =
       ctx.args.files.filterNot(f => ids.contains(f.fileMetaId))
     )
 
-  private def getRetryCount[F[_]: Sync](ctx: Context[F, Args]): F[Int] =
+  private def getRetryCount[F[_]: Sync](ctx: Context[F, _], store: Store[F]): F[Int] =
-    ctx.store.transact(RJob.getRetries(ctx.jobId)).map(_.getOrElse(0))
+    store.transact(RJob.getRetries(ctx.jobId)).map(_.getOrElse(0))
 
   private def deleteDuplicate[F[_]: Sync](
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   )(fd: FileMetaDupes): F[Unit] = {
     val fname = ctx.args.files.find(_.fileMetaId == fd.fm.id).flatMap(_.name)
     if (fd.exists)
       ctx.logger
-        .info(s"Deleting duplicate file $fname!") *> ctx.store.fileRepo
+        .info(s"Deleting duplicate file $fname!") *> store.fileRepo
         .delete(fd.fm.id)
     else ().pure[F]
   }
 
   private def findDuplicates[F[_]](
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[Vector[FileMetaDupes]] =
-    ctx.store.transact(for {
+    store.transact(for {
       fileMetas <- RFileMeta.findByIds(ctx.args.files.map(_.fileMetaId))
       dupes <- fileMetas.traverse(checkDuplicate(ctx))
     } yield dupes)

modules/joex/src/main/scala/docspell/joex/process/EvalProposals.scala

@@ -7,30 +7,31 @@
 package docspell.joex.process
 
 import java.time.{LocalDate, Period}
-
 import cats.effect.Sync
 import cats.implicits._
-
 import docspell.common._
-import docspell.scheduler.{Context, Task}
+import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records.{RAttachmentMeta, RPerson}
 
 /** Calculate weights for candidates that adds the most likely candidate a lower number.
   */
 object EvalProposals {
 
-  def apply[F[_]: Sync](data: ItemData): Task[F, ProcessItemArgs, ItemData] =
+  def apply[F[_]: Sync](
-    Task { ctx =>
+      store: Store[F]
+  )(data: ItemData): Task[F, ProcessItemArgs, ItemData] =
+    Task { _ =>
       for {
         now <- Timestamp.current[F]
-        personRefs <- findOrganizationRelation[F](data, ctx)
+        personRefs <- findOrganizationRelation[F](data, store)
         metas = data.metas.map(calcCandidateWeight(now.toUtcDate, personRefs))
       } yield data.copy(metas = metas)
     }
 
   def findOrganizationRelation[F[_]: Sync](
       data: ItemData,
-      ctx: Context[F, _]
+      store: Store[F]
   ): F[Map[Ident, PersonRef]] = {
     val corrPersIds = data.metas
       .map(_.proposals)
@@ -38,7 +39,7 @@ object EvalProposals {
       .flatMap(_.find(MetaProposalType.CorrPerson))
       .flatMap(_.values.toList.map(_.ref.id))
       .toSet
-    ctx.store
+    store
       .transact(RPerson.findOrganization(corrPersIds))
       .map(_.map(p => (p.id, p)).toMap)
   }

modules/joex/src/main/scala/docspell/joex/process/ExtractArchive.scala

@@ -14,13 +14,12 @@ import cats.implicits._
 import cats.kernel.Monoid
 import cats.kernel.Order
 import fs2.Stream
-
 import docspell.common._
 import docspell.files.Zip
 import docspell.joex.mail._
 import docspell.scheduler._
+import docspell.store.Store
 import docspell.store.records._
-
 import emil.Mail
 
 /** Goes through all attachments and extracts archive files, like zip files. The process
@@ -34,39 +33,41 @@ import emil.Mail
 object ExtractArchive {
   type Args = ProcessItemArgs
 
-  def apply[F[_]: Async](
+  def apply[F[_]: Async](store: Store[F])(
       item: ItemData
   ): Task[F, Args, ItemData] =
-    multiPass(item, None).map(_._2)
+    multiPass(store, item, None).map(_._2)
 
   def multiPass[F[_]: Async](
+      store: Store[F],
       item: ItemData,
       archive: Option[RAttachmentArchive]
   ): Task[F, Args, (Option[RAttachmentArchive], ItemData)] =
-    singlePass(item, archive).flatMap { t =>
+    singlePass(store, item, archive).flatMap { t =>
       if (t._1.isEmpty) Task.pure(t)
-      else multiPass(t._2, t._1)
+      else multiPass(store, t._2, t._1)
     }
 
   def singlePass[F[_]: Async](
+      store: Store[F],
       item: ItemData,
       archive: Option[RAttachmentArchive]
   ): Task[F, Args, (Option[RAttachmentArchive], ItemData)] =
     Task { ctx =>
       def extract(ra: RAttachment, pos: Int): F[Extracted] =
-        findMime(ctx)(ra).flatMap(m => extractSafe(ctx, archive)(ra, pos, m))
+        findMime(store)(ra).flatMap(m => extractSafe(ctx, store, archive)(ra, pos, m))
 
       for {
-        lastPos <- ctx.store.transact(RAttachment.nextPosition(item.item.id))
+        lastPos <- store.transact(RAttachment.nextPosition(item.item.id))
         extracts <-
           item.attachments.zipWithIndex
             .traverse(t => extract(t._1, lastPos + t._2))
             .map(Monoid[Extracted].combineAll)
             .map(fixPositions)
         nra = extracts.files
-        _ <- extracts.files.traverse(storeAttachment(ctx))
+        _ <- extracts.files.traverse(storeAttachment(store))
         naa = extracts.archives
-        _ <- naa.traverse(storeArchive(ctx))
+        _ <- naa.traverse(storeArchive(store))
       } yield naa.headOption -> item.copy(
         attachments = nra,
         originFile = item.originFile ++ nra.map(a => a.id -> a.fileId).toMap,
@@ -83,25 +84,26 @@ object ExtractArchive {
     if (extract.archives.isEmpty) extract
     else extract.updatePositions
 
-  def findMime[F[_]: Functor](ctx: Context[F, _])(ra: RAttachment): F[MimeType] =
+  def findMime[F[_]: Functor](store: Store[F])(ra: RAttachment): F[MimeType] =
-    OptionT(ctx.store.transact(RFileMeta.findById(ra.fileId)))
+    OptionT(store.transact(RFileMeta.findById(ra.fileId)))
       .map(_.mimetype)
       .getOrElse(MimeType.octetStream)
 
   def extractSafe[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       archive: Option[RAttachmentArchive]
   )(ra: RAttachment, pos: Int, mime: MimeType): F[Extracted] =
     mime match {
       case MimeType.ZipMatch(_) if ra.name.exists(_.toLowerCase.endsWith(".zip")) =>
         ctx.logger.info(s"Extracting zip archive ${ra.name.getOrElse("<noname>")}.") *>
-          extractZip(ctx, archive)(ra, pos)
+          extractZip(ctx, store, archive)(ra, pos)
-            .flatMap(cleanupParents(ctx, ra, archive))
+            .flatMap(cleanupParents(ctx, store, ra, archive))
 
       case MimeType.EmailMatch(_) =>
         ctx.logger.info(s"Reading e-mail ${ra.name.getOrElse("<noname>")}") *>
-          extractMail(ctx, archive)(ra, pos)
+          extractMail(ctx, store, archive)(ra, pos)
-            .flatMap(cleanupParents(ctx, ra, archive))
+            .flatMap(cleanupParents(ctx, store, ra, archive))
 
       case _ =>
         ctx.logger.debug(s"Not an archive: ${mime.asString}") *>
@@ -110,6 +112,7 @@ object ExtractArchive {
 
   def cleanupParents[F[_]: Sync](
       ctx: Context[F, _],
+      store: Store[F],
       ra: RAttachment,
       archive: Option[RAttachmentArchive]
   )(extracted: Extracted): F[Extracted] =
@@ -119,30 +122,31 @@ object ExtractArchive {
           _ <- ctx.logger.debug(
             s"Extracted inner attachment ${ra.name}. Remove it completely."
           )
-          _ <- ctx.store.transact(RAttachmentArchive.delete(ra.id))
+          _ <- store.transact(RAttachmentArchive.delete(ra.id))
-          _ <- ctx.store.transact(RAttachment.delete(ra.id))
+          _ <- store.transact(RAttachment.delete(ra.id))
-          _ <- ctx.store.fileRepo.delete(ra.fileId)
+          _ <- store.fileRepo.delete(ra.fileId)
         } yield extracted
       case None =>
         for {
           _ <- ctx.logger.debug(
             s"Extracted attachment ${ra.name}. Remove it from the item."
           )
-          _ <- ctx.store.transact(RAttachment.delete(ra.id))
+          _ <- store.transact(RAttachment.delete(ra.id))
         } yield extracted.copy(files = extracted.files.filter(_.id != ra.id))
     }
 
   def extractZip[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       archive: Option[RAttachmentArchive]
   )(ra: RAttachment, pos: Int): F[Extracted] = {
-    val zipData = ctx.store.fileRepo.getBytes(ra.fileId)
+    val zipData = store.fileRepo.getBytes(ra.fileId)
     val glob = ctx.args.meta.fileFilter.getOrElse(Glob.all)
     ctx.logger.debug(s"Filtering zip entries with '${glob.asString}'") *>
       zipData
         .through(Zip.unzipP[F](8192, glob))
         .zipWithIndex
-        .flatMap(handleEntry(ctx, ra, pos, archive, None))
+        .flatMap(handleEntry(ctx, store, ra, pos, archive, None))
         .foldMonoid
         .compile
         .lastOrError
@@ -150,9 +154,10 @@ object ExtractArchive {
 
   def extractMail[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       archive: Option[RAttachmentArchive]
   )(ra: RAttachment, pos: Int): F[Extracted] = {
-    val email: Stream[F, Byte] = ctx.store.fileRepo.getBytes(ra.fileId)
+    val email: Stream[F, Byte] = store.fileRepo.getBytes(ra.fileId)
 
     val glob = ctx.args.meta.fileFilter.getOrElse(Glob.all)
     val attachOnly = ctx.args.meta.attachmentsOnly.getOrElse(false)
@@ -170,7 +175,9 @@ object ExtractArchive {
           ReadMail
             .mailToEntries(ctx.logger, glob, attachOnly)(mail)
             .zipWithIndex
-            .flatMap(handleEntry(ctx, ra, pos, archive, mId)) ++ Stream.eval(givenMeta)
+            .flatMap(handleEntry(ctx, store, ra, pos, archive, mId)) ++ Stream.eval(
+            givenMeta
+          )
         }
         .foldMonoid
         .compile
@@ -185,6 +192,7 @@ object ExtractArchive {
 
   def handleEntry[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       ra: RAttachment,
       pos: Int,
       archive: Option[RAttachmentArchive],
@@ -195,7 +203,7 @@ object ExtractArchive {
     val (entry, subPos) = tentry
     val mimeHint = MimeTypeHint.filename(entry.name).withAdvertised(entry.mime.asString)
     val fileId = entry.data.through(
-      ctx.store.fileRepo
+      store.fileRepo
         .save(ctx.args.meta.collective, FileCategory.AttachmentSource, mimeHint)
     )
 
@@ -217,16 +225,16 @@ object ExtractArchive {
 
   }
 
-  def storeAttachment[F[_]: Sync](ctx: Context[F, _])(ra: RAttachment): F[Int] = {
+  def storeAttachment[F[_]: Sync](store: Store[F])(ra: RAttachment): F[Int] = {
-    val insert = CreateItem.insertAttachment(ctx)(ra)
+    val insert = CreateItem.insertAttachment(store)(ra)
     for {
-      n1 <- ctx.store.transact(RAttachment.updatePosition(ra.id, ra.position))
+      n1 <- store.transact(RAttachment.updatePosition(ra.id, ra.position))
       n2 <- if (n1 > 0) 0.pure[F] else insert
     } yield n1 + n2
   }
 
-  def storeArchive[F[_]](ctx: Context[F, _])(aa: RAttachmentArchive): F[Int] =
+  def storeArchive[F[_]](store: Store[F])(aa: RAttachmentArchive): F[Int] =
-    ctx.store.transact(RAttachmentArchive.insert(aa))
+    store.transact(RAttachmentArchive.insert(aa))
 
   case class Extracted(
       files: Vector[RAttachment],

modules/joex/src/main/scala/docspell/joex/process/FindProposal.scala

@@ -7,16 +7,15 @@
 package docspell.joex.process
 
 import java.time.ZoneId
-
 import cats.effect.Sync
 import cats.implicits._
 import cats.{Applicative, FlatMap}
-
 import docspell.analysis.contact._
 import docspell.common.MetaProposal.Candidate
 import docspell.common._
 import docspell.joex.Config
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.records._
 
 /** Super simple approach to find corresponding meta data to an item by looking up values
@@ -26,7 +25,8 @@ object FindProposal {
   type Args = ProcessItemArgs
 
   def apply[F[_]: Sync](
-      cfg: Config.TextAnalysis
+      cfg: Config.TextAnalysis,
+      store: Store[F]
   )(data: ItemData): Task[F, Args, ItemData] =
     Task { ctx =>
       val rmas = data.metas.map(rm => rm.copy(nerlabels = removeDuplicates(rm.nerlabels)))
@@ -34,15 +34,16 @@ object FindProposal {
         _ <- ctx.logger.info("Starting find-proposal")
         rmv <- rmas
           .traverse(rm =>
-            processAttachment(cfg, rm, data.findDates(rm), ctx)
+            processAttachment(cfg, rm, data.findDates(rm), ctx, store)
               .map(ml => rm.copy(proposals = ml))
           )
-        clp <- lookupClassifierProposals(ctx, data.classifyProposals)
+        clp <- lookupClassifierProposals(ctx, store, data.classifyProposals)
       } yield data.copy(metas = rmv, classifyProposals = clp)
     }
 
   def lookupClassifierProposals[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       mpList: MetaProposalList
   ): F[MetaProposalList] = {
     val coll = ctx.args.meta.collective
@@ -50,7 +51,7 @@ object FindProposal {
     def lookup(mp: MetaProposal): F[Option[IdRef]] =
       mp.proposalType match {
         case MetaProposalType.CorrOrg =>
-          ctx.store
+          store
             .transact(
               ROrganization
                 .findLike(coll, mp.values.head.ref.name.toLowerCase, OrgUse.notDisabled)
@@ -60,7 +61,7 @@ object FindProposal {
               ctx.logger.debug(s"Found classifier organization for $mp: $oref")
             )
         case MetaProposalType.CorrPerson =>
-          ctx.store
+          store
             .transact(
               RPerson
                 .findLike(
@@ -74,7 +75,7 @@ object FindProposal {
               ctx.logger.debug(s"Found classifier corr-person for $mp: $oref")
             )
         case MetaProposalType.ConcPerson =>
-          ctx.store
+          store
             .transact(
               RPerson
                 .findLike(
@@ -88,7 +89,7 @@ object FindProposal {
               ctx.logger.debug(s"Found classifier conc-person for $mp: $oref")
             )
         case MetaProposalType.ConcEquip =>
-          ctx.store
+          store
             .transact(
               REquipment
                 .findLike(
@@ -123,9 +124,10 @@ object FindProposal {
       cfg: Config.TextAnalysis,
       rm: RAttachmentMeta,
       rd: Vector[NerDateLabel],
-      ctx: Context[F, ProcessItemArgs]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[MetaProposalList] = {
-    val finder = Finder.searchExact(ctx).next(Finder.searchFuzzy(ctx))
+    val finder = Finder.searchExact(ctx, store).next(Finder.searchFuzzy(ctx, store))
     List(finder.find(rm.nerlabels), makeDateProposal(cfg, rd))
       .traverse(identity)
       .map(MetaProposalList.flatten)
@@ -215,19 +217,24 @@ object FindProposal {
     def unit[F[_]: Applicative](value: MetaProposalList): Finder[F] =
       _ => value.pure[F]
 
-    def searchExact[F[_]: Sync](ctx: Context[F, ProcessItemArgs]): Finder[F] =
+    def searchExact[F[_]: Sync](ctx: Context[F, Args], store: Store[F]): Finder[F] =
       labels =>
-        labels.toList.traverse(nl => search(nl, true, ctx)).map(MetaProposalList.flatten)
+        labels.toList
+          .traverse(nl => search(nl, true, ctx, store))
+          .map(MetaProposalList.flatten)
 
-    def searchFuzzy[F[_]: Sync](ctx: Context[F, ProcessItemArgs]): Finder[F] =
+    def searchFuzzy[F[_]: Sync](ctx: Context[F, Args], store: Store[F]): Finder[F] =
       labels =>
-        labels.toList.traverse(nl => search(nl, false, ctx)).map(MetaProposalList.flatten)
+        labels.toList
+          .traverse(nl => search(nl, false, ctx, store))
+          .map(MetaProposalList.flatten)
   }
 
   private def search[F[_]: Sync](
       nt: NerLabel,
       exact: Boolean,
-      ctx: Context[F, ProcessItemArgs]
+      ctx: Context[F, ProcessItemArgs],
+      store: Store[F]
   ): F[MetaProposalList] = {
     val value =
       if (exact) normalizeSearchValue(nt.label)
@@ -243,7 +250,7 @@ object FindProposal {
       nt.tag match {
         case NerTag.Organization =>
           ctx.logger.debug(s"Looking for organizations: $value") *>
-            ctx.store
+            store
               .transact(
                 ROrganization
                   .findLike(ctx.args.meta.collective, value, OrgUse.notDisabled)
@@ -251,20 +258,20 @@ object FindProposal {
               .map(MetaProposalList.from(MetaProposalType.CorrOrg, nt))
 
         case NerTag.Person =>
-          val s1 = ctx.store
+          val s1 = store
             .transact(
               RPerson
                 .findLike(ctx.args.meta.collective, value, PersonUse.concerningAndBoth)
             )
             .map(MetaProposalList.from(MetaProposalType.ConcPerson, nt))
-          val s2 = ctx.store
+          val s2 = store
             .transact(
               RPerson
                 .findLike(ctx.args.meta.collective, value, PersonUse.correspondentAndBoth)
             )
             .map(MetaProposalList.from(MetaProposalType.CorrPerson, nt))
           val s3 =
-            ctx.store
+            store
               .transact(
                 ROrganization
                   .findLike(ctx.args.meta.collective, value, OrgUse.notDisabled)
@@ -283,7 +290,7 @@ object FindProposal {
 
         case NerTag.Misc =>
           ctx.logger.debug(s"Looking for equipments: $value") *>
-            ctx.store
+            store
               .transact(
                 REquipment
                   .findLike(ctx.args.meta.collective, value, EquipmentUse.notDisabled)
@@ -291,7 +298,7 @@ object FindProposal {
               .map(MetaProposalList.from(MetaProposalType.ConcEquip, nt))
 
         case NerTag.Email =>
-          searchContact(nt, ContactKind.Email, value, ctx)
+          searchContact(nt, ContactKind.Email, value, ctx, store)
 
         case NerTag.Website =>
           if (!exact) {
@@ -301,9 +308,9 @@ object FindProposal {
               .map(_.toPrimaryDomain.asString)
               .map(s => s"%$s%")
               .getOrElse(value)
-            searchContact(nt, ContactKind.Website, searchString, ctx)
+            searchContact(nt, ContactKind.Website, searchString, ctx, store)
           } else
-            searchContact(nt, ContactKind.Website, value, ctx)
+            searchContact(nt, ContactKind.Website, value, ctx, store)
 
         case NerTag.Date =>
           // There is no database search required for this tag
@@ -315,18 +322,19 @@ object FindProposal {
       nt: NerLabel,
       kind: ContactKind,
       value: String,
-      ctx: Context[F, ProcessItemArgs]
+      ctx: Context[F, ProcessItemArgs],
+      store: Store[F]
   ): F[MetaProposalList] = {
-    val orgs = ctx.store
+    val orgs = store
       .transact(ROrganization.findLike(ctx.args.meta.collective, kind, value))
       .map(MetaProposalList.from(MetaProposalType.CorrOrg, nt))
-    val corrP = ctx.store
+    val corrP = store
       .transact(
         RPerson
           .findLike(ctx.args.meta.collective, kind, value, PersonUse.correspondentAndBoth)
       )
       .map(MetaProposalList.from(MetaProposalType.CorrPerson, nt))
-    val concP = ctx.store
+    val concP = store
       .transact(
         RPerson
           .findLike(ctx.args.meta.collective, kind, value, PersonUse.concerningAndBoth)

modules/joex/src/main/scala/docspell/joex/process/ItemHandler.scala

@@ -10,7 +10,6 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import fs2.Stream
-
 import docspell.analysis.TextAnalyser
 import docspell.backend.ops.OItem
 import docspell.common.{ItemState, ProcessItemArgs}
@@ -18,49 +17,51 @@ import docspell.ftsclient.FtsClient
 import docspell.joex.Config
 import docspell.joex.analysis.RegexNerFile
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.queries.QItem
 import docspell.store.records.RItem
 
 object ItemHandler {
   type Args = ProcessItemArgs
 
-  def onCancel[F[_]: Sync]: Task[F, Args, Unit] =
+  def onCancel[F[_]: Sync](store: Store[F]): Task[F, Args, Unit] =
     logWarn[F]("Now cancelling.").flatMap(_ =>
-      markItemCreated.flatMap {
+      markItemCreated(store).flatMap {
         case true =>
           Task.pure(())
         case false =>
-          deleteByFileIds[F].flatMap(_ => deleteFiles)
+          deleteByFileIds[F](store).flatMap(_ => deleteFiles(store))
       }
     )
 
   def newItem[F[_]: Async](
       cfg: Config,
+      store: Store[F],
       itemOps: OItem[F],
       fts: FtsClient[F],
       analyser: TextAnalyser[F],
       regexNer: RegexNerFile[F]
   ): Task[F, Args, Option[ItemData]] =
     logBeginning[F].flatMap(_ =>
-      DuplicateCheck[F]
+      DuplicateCheck[F](store)
         .flatMap(args =>
           if (args.files.isEmpty) logNoFiles[F].map(_ => None)
           else {
             val create: Task[F, Args, ItemData] =
-              CreateItem[F].contramap(_ => args.pure[F])
+              CreateItem[F](store).contramap(_ => args.pure[F])
             create
-              .flatMap(itemStateTask(ItemState.Processing))
+              .flatMap(itemStateTask(store, ItemState.Processing))
-              .flatMap(safeProcess[F](cfg, itemOps, fts, analyser, regexNer))
+              .flatMap(safeProcess[F](cfg, store, itemOps, fts, analyser, regexNer))
               .map(_.some)
           }
         )
     )
 
-  def itemStateTask[F[_]: Sync, A](
+  def itemStateTask[F[_]: Sync, A](store: Store[F], state: ItemState)(
-      state: ItemState
+      data: ItemData
-  )(data: ItemData): Task[F, A, ItemData] =
+  ): Task[F, A, ItemData] =
-    Task(ctx =>
+    Task(_ =>
-      ctx.store
+      store
         .transact(RItem.updateState(data.item.id, state, ItemState.invalidStates))
         .map(_ => data)
     )
@@ -70,6 +71,7 @@ object ItemHandler {
 
   def safeProcess[F[_]: Async](
       cfg: Config,
+      store: Store[F],
       itemOps: OItem[F],
       fts: FtsClient[F],
       analyser: TextAnalyser[F],
@@ -77,30 +79,31 @@ object ItemHandler {
   )(data: ItemData): Task[F, Args, ItemData] =
     isLastRetry[F].flatMap {
       case true =>
-        ProcessItem[F](cfg, itemOps, fts, analyser, regexNer)(data).attempt.flatMap {
+        ProcessItem[F](cfg, itemOps, fts, analyser, regexNer, store)(data).attempt
-          case Right(d) =>
+          .flatMap {
-            Task.pure(d)
+            case Right(d) =>
-          case Left(ex) =>
+              Task.pure(d)
-            logWarn[F](
+            case Left(ex) =>
-              "Processing failed on last retry. Creating item but without proposals."
+              logWarn[F](
-            ).flatMap(_ => itemStateTask(ItemState.Created)(data))
+                "Processing failed on last retry. Creating item but without proposals."
-              .andThen(_ => Sync[F].raiseError(ex))
+              ).flatMap(_ => itemStateTask(store, ItemState.Created)(data))
-        }
+                .andThen(_ => Sync[F].raiseError(ex))
+          }
       case false =>
-        ProcessItem[F](cfg, itemOps, fts, analyser, regexNer)(data)
+        ProcessItem[F](cfg, itemOps, fts, analyser, regexNer, store)(data)
-          .flatMap(itemStateTask(ItemState.Created))
+          .flatMap(itemStateTask(store, ItemState.Created))
     }
 
-  private def markItemCreated[F[_]: Sync]: Task[F, Args, Boolean] =
+  private def markItemCreated[F[_]: Sync](store: Store[F]): Task[F, Args, Boolean] =
     Task { ctx =>
       val fileMetaIds = ctx.args.files.map(_.fileMetaId).toSet
       (for {
-        item <- OptionT(ctx.store.transact(QItem.findOneByFileIds(fileMetaIds.toSeq)))
+        item <- OptionT(store.transact(QItem.findOneByFileIds(fileMetaIds.toSeq)))
         _ <- OptionT.liftF(
           ctx.logger.info("Processing cancelled. Marking item as created anyways.")
         )
         _ <- OptionT.liftF(
-          ctx.store
+          store
             .transact(
               RItem.updateState(item.id, ItemState.Created, ItemState.invalidStates)
             )
@@ -111,11 +114,11 @@ object ItemHandler {
         )
     }
 
-  private def deleteByFileIds[F[_]: Sync]: Task[F, Args, Unit] =
+  private def deleteByFileIds[F[_]: Sync](store: Store[F]): Task[F, Args, Unit] =
     Task { ctx =>
       val states = ItemState.invalidStates
       for {
-        items <- ctx.store.transact(
+        items <- store.transact(
           QItem.findByFileIds(ctx.args.files.map(_.fileMetaId), states)
         )
         _ <-
@@ -124,16 +127,16 @@ object ItemHandler {
             ctx.logger.info(
               s"No items found for file ids ${ctx.args.files.map(_.fileMetaId)}"
             )
-        _ <- items.traverse(i => QItem.delete(ctx.store)(i.id, ctx.args.meta.collective))
+        _ <- items.traverse(i => QItem.delete(store)(i.id, ctx.args.meta.collective))
       } yield ()
     }
 
-  private def deleteFiles[F[_]: Sync]: Task[F, Args, Unit] =
+  private def deleteFiles[F[_]: Sync](store: Store[F]): Task[F, Args, Unit] =
     Task(ctx =>
       ctx.logger.info("Deleting input files …") *>
         Stream
           .emits(ctx.args.files.map(_.fileMetaId))
-          .evalMap(id => ctx.store.fileRepo.delete(id).attempt)
+          .evalMap(id => store.fileRepo.delete(id).attempt)
           .compile
           .drain
     )

modules/joex/src/main/scala/docspell/joex/process/LinkProposal.scala

@@ -9,22 +9,26 @@ package docspell.joex.process
 import cats.data.NonEmptyList
 import cats.effect.Sync
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.records.RItem
 
 object LinkProposal {
 
-  def onlyNew[F[_]: Sync](data: ItemData): Task[F, ProcessItemArgs, ItemData] =
+  def onlyNew[F[_]: Sync](
+      store: Store[F]
+  )(data: ItemData): Task[F, ProcessItemArgs, ItemData] =
     if (data.item.state.isValid)
       Task
         .log[F, ProcessItemArgs](_.debug(s"Not linking proposals on existing item"))
         .map(_ => data)
     else
-      LinkProposal[F](data)
+      LinkProposal[F](store)(data)
 
-  def apply[F[_]: Sync](data: ItemData): Task[F, ProcessItemArgs, ItemData] =
+  def apply[F[_]: Sync](
+      store: Store[F]
+  )(data: ItemData): Task[F, ProcessItemArgs, ItemData] =
     if (data.item.state == ItemState.Confirmed)
       Task
         .log[F, ProcessItemArgs](_.debug(s"Not linking proposals on confirmed item"))
@@ -35,7 +39,7 @@ object LinkProposal {
 
         ctx.logger.info(s"Starting linking proposals") *>
           MetaProposalType.all
-            .traverse(applyValue(data, proposals, ctx))
+            .traverse(applyValue(data, proposals, ctx, store))
             .map(result => ctx.logger.info(s"Results from proposal processing: $result"))
             .map(_ => data)
       }
@@ -43,7 +47,8 @@ object LinkProposal {
   def applyValue[F[_]: Sync](
       data: ItemData,
       proposalList: MetaProposalList,
-      ctx: Context[F, ProcessItemArgs]
+      ctx: Context[F, ProcessItemArgs],
+      store: Store[F]
   )(mpt: MetaProposalType): F[Result] =
     data.givenMeta.find(mpt).orElse(proposalList.find(mpt)) match {
       case None =>
@@ -51,29 +56,30 @@ object LinkProposal {
           Result.noneFound(mpt).pure[F]
       case Some(a) if a.isSingleValue =>
         ctx.logger.info(s"Found one candidate for ${a.proposalType}") *>
-          setItemMeta(data.item.id, ctx, a.proposalType, a.values.head.ref.id).map(_ =>
+          setItemMeta(data.item.id, ctx, store, a.proposalType, a.values.head.ref.id).map(
-            Result.single(mpt)
+            _ => Result.single(mpt)
           )
       case Some(a) =>
         val ids = a.values.map(_.ref.id.id)
         ctx.logger.info(
           s"Found many (${a.size}, $ids) candidates for ${a.proposalType}. Setting first."
         ) *>
-          setItemMeta(data.item.id, ctx, a.proposalType, a.values.head.ref.id).map(_ =>
+          setItemMeta(data.item.id, ctx, store, a.proposalType, a.values.head.ref.id).map(
-            Result.multiple(mpt)
+            _ => Result.multiple(mpt)
           )
     }
 
   def setItemMeta[F[_]: Sync](
       itemId: Ident,
       ctx: Context[F, ProcessItemArgs],
+      store: Store[F],
       mpt: MetaProposalType,
       value: Ident
   ): F[Int] =
     mpt match {
       case MetaProposalType.CorrOrg =>
         ctx.logger.debug(s"Updating item organization with: ${value.id}") *>
-          ctx.store.transact(
+          store.transact(
             RItem.updateCorrOrg(
               NonEmptyList.of(itemId),
               ctx.args.meta.collective,
@@ -82,7 +88,7 @@ object LinkProposal {
           )
       case MetaProposalType.ConcPerson =>
         ctx.logger.debug(s"Updating item concerning person with: $value") *>
-          ctx.store.transact(
+          store.transact(
             RItem.updateConcPerson(
               NonEmptyList.of(itemId),
               ctx.args.meta.collective,
@@ -91,7 +97,7 @@ object LinkProposal {
           )
       case MetaProposalType.CorrPerson =>
         ctx.logger.debug(s"Updating item correspondent person with: $value") *>
-          ctx.store.transact(
+          store.transact(
             RItem.updateCorrPerson(
               NonEmptyList.of(itemId),
               ctx.args.meta.collective,
@@ -100,7 +106,7 @@ object LinkProposal {
           )
       case MetaProposalType.ConcEquip =>
         ctx.logger.debug(s"Updating item concerning equipment with: $value") *>
-          ctx.store.transact(
+          store.transact(
             RItem.updateConcEquip(
               NonEmptyList.of(itemId),
               ctx.args.meta.collective,
@@ -112,7 +118,7 @@ object LinkProposal {
           case Some(ld) =>
             val ts = Timestamp.from(ld.atStartOfDay(Timestamp.UTC))
             ctx.logger.debug(s"Updating item date ${value.id}") *>
-              ctx.store.transact(
+              store.transact(
                 RItem.updateDate(
                   NonEmptyList.of(itemId),
                   ctx.args.meta.collective,
@@ -128,7 +134,7 @@ object LinkProposal {
           case Some(ld) =>
             val ts = Timestamp.from(ld.atStartOfDay(Timestamp.UTC))
             ctx.logger.debug(s"Updating item due-date suggestion ${value.id}") *>
-              ctx.store.transact(
+              store.transact(
                 RItem.updateDueDate(
                   NonEmptyList.of(itemId),
                   ctx.args.meta.collective,

modules/joex/src/main/scala/docspell/joex/process/ProcessItem.scala

@@ -8,7 +8,6 @@ package docspell.joex.process
 
 import cats.effect._
 import cats.implicits._
-
 import docspell.analysis.TextAnalyser
 import docspell.backend.ops.OItem
 import docspell.common.ProcessItemArgs
@@ -16,6 +15,7 @@ import docspell.ftsclient.FtsClient
 import docspell.joex.Config
 import docspell.joex.analysis.RegexNerFile
 import docspell.scheduler.Task
+import docspell.store.Store
 
 object ProcessItem {
 
@@ -24,12 +24,13 @@ object ProcessItem {
       itemOps: OItem[F],
       fts: FtsClient[F],
       analyser: TextAnalyser[F],
-      regexNer: RegexNerFile[F]
+      regexNer: RegexNerFile[F],
+      store: Store[F]
   )(item: ItemData): Task[F, ProcessItemArgs, ItemData] =
-    ExtractArchive(item)
+    ExtractArchive(store)(item)
       .flatMap(Task.setProgress(20))
-      .flatMap(processAttachments0(cfg, fts, analyser, regexNer, (40, 60, 80)))
+      .flatMap(processAttachments0(cfg, fts, analyser, regexNer, store, (40, 60, 80)))
-      .flatMap(LinkProposal.onlyNew[F])
+      .flatMap(LinkProposal.onlyNew[F](store))
       .flatMap(SetGivenData.onlyNew[F](itemOps))
       .flatMap(Task.setProgress(99))
       .flatMap(RemoveEmptyItem(itemOps))
@@ -38,34 +39,37 @@ object ProcessItem {
       cfg: Config,
       fts: FtsClient[F],
       analyser: TextAnalyser[F],
-      regexNer: RegexNerFile[F]
+      regexNer: RegexNerFile[F],
+      store: Store[F]
   )(item: ItemData): Task[F, ProcessItemArgs, ItemData] =
-    processAttachments0[F](cfg, fts, analyser, regexNer, (30, 60, 90))(item)
+    processAttachments0[F](cfg, fts, analyser, regexNer, store, (30, 60, 90))(item)
 
   def analysisOnly[F[_]: Async](
       cfg: Config,
       analyser: TextAnalyser[F],
-      regexNer: RegexNerFile[F]
+      regexNer: RegexNerFile[F],
+      store: Store[F]
   )(item: ItemData): Task[F, ProcessItemArgs, ItemData] =
-    TextAnalysis[F](cfg.textAnalysis, analyser, regexNer)(item)
+    TextAnalysis[F](cfg.textAnalysis, analyser, regexNer, store)(item)
-      .flatMap(FindProposal[F](cfg.textAnalysis))
+      .flatMap(FindProposal[F](cfg.textAnalysis, store))
-      .flatMap(EvalProposals[F])
+      .flatMap(EvalProposals[F](store))
-      .flatMap(CrossCheckProposals[F])
+      .flatMap(CrossCheckProposals[F](store))
-      .flatMap(SaveProposals[F])
+      .flatMap(SaveProposals[F](store))
 
   private def processAttachments0[F[_]: Async](
       cfg: Config,
       fts: FtsClient[F],
       analyser: TextAnalyser[F],
       regexNer: RegexNerFile[F],
+      store: Store[F],
       progress: (Int, Int, Int)
   )(item: ItemData): Task[F, ProcessItemArgs, ItemData] =
-    ConvertPdf(cfg.convert, item)
+    ConvertPdf(cfg.convert, store, item)
       .flatMap(Task.setProgress(progress._1))
-      .flatMap(TextExtraction(cfg.extraction, fts))
+      .flatMap(TextExtraction(cfg.extraction, fts, store))
-      .flatMap(AttachmentPreview(cfg.extraction.preview))
+      .flatMap(AttachmentPreview(cfg.extraction.preview, store))
-      .flatMap(AttachmentPageCount())
+      .flatMap(AttachmentPageCount(store))
       .flatMap(Task.setProgress(progress._2))
-      .flatMap(analysisOnly[F](cfg, analyser, regexNer))
+      .flatMap(analysisOnly[F](cfg, analyser, regexNer, store))
       .flatMap(Task.setProgress(progress._3))
 }

modules/joex/src/main/scala/docspell/joex/process/ReProcessItem.scala

@@ -9,7 +9,6 @@ package docspell.joex.process
 import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
-
 import docspell.analysis.TextAnalyser
 import docspell.backend.ops.OItem
 import docspell.common._
@@ -18,6 +17,7 @@ import docspell.joex.Config
 import docspell.joex.analysis.RegexNerFile
 import docspell.scheduler.Context
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.queries.QItem
 import docspell.store.records.RAttachment
 import docspell.store.records.RAttachmentSource
@@ -32,13 +32,14 @@ object ReProcessItem {
       fts: FtsClient[F],
       itemOps: OItem[F],
       analyser: TextAnalyser[F],
-      regexNer: RegexNerFile[F]
+      regexNer: RegexNerFile[F],
+      store: Store[F]
   ): Task[F, Args, Unit] =
     Task
       .log[F, Args](_.info("===== Start reprocessing ======"))
       .flatMap(_ =>
-        loadItem[F]
+        loadItem[F](store)
-          .flatMap(safeProcess[F](cfg, fts, itemOps, analyser, regexNer))
+          .flatMap(safeProcess[F](cfg, fts, itemOps, analyser, regexNer, store))
           .map(_ => ())
       )
 
@@ -53,13 +54,13 @@ object ReProcessItem {
     else ra => selection.contains(ra.id)
   }
 
-  def loadItem[F[_]: Sync]: Task[F, Args, ItemData] =
+  def loadItem[F[_]: Sync](store: Store[F]): Task[F, Args, ItemData] =
     Task { ctx =>
       (for {
-        item <- OptionT(ctx.store.transact(RItem.findById(ctx.args.itemId)))
+        item <- OptionT(store.transact(RItem.findById(ctx.args.itemId)))
-        attach <- OptionT.liftF(ctx.store.transact(RAttachment.findByItem(item.id)))
+        attach <- OptionT.liftF(store.transact(RAttachment.findByItem(item.id)))
         asrc <-
-          OptionT.liftF(ctx.store.transact(RAttachmentSource.findByItem(ctx.args.itemId)))
+          OptionT.liftF(store.transact(RAttachmentSource.findByItem(ctx.args.itemId)))
         asrcMap = asrc.map(s => s.id -> s).toMap
         // copy the original files over to attachments to run the default processing task
         // the processing doesn't touch the original files, only RAttachments
@@ -97,6 +98,7 @@ object ReProcessItem {
       itemOps: OItem[F],
       analyser: TextAnalyser[F],
       regexNer: RegexNerFile[F],
+      store: Store[F],
       data: ItemData
   ): Task[F, Args, ItemData] = {
 
@@ -121,21 +123,21 @@ object ReProcessItem {
             Nil
           ).pure[F]
 
-    getLanguage[F].flatMap { lang =>
+    getLanguage[F](store).flatMap { lang =>
       ProcessItem
-        .processAttachments[F](cfg, fts, analyser, regexNer)(data)
+        .processAttachments[F](cfg, fts, analyser, regexNer, store)(data)
-        .flatMap(LinkProposal[F])
+        .flatMap(LinkProposal[F](store))
         .flatMap(SetGivenData[F](itemOps))
         .contramap[Args](convertArgs(lang))
     }
   }
 
-  def getLanguage[F[_]: Sync]: Task[F, Args, Language] =
+  def getLanguage[F[_]: Sync](store: Store[F]): Task[F, Args, Language] =
     Task { ctx =>
       val lang1 = OptionT(
-        ctx.store.transact(QItem.getItemLanguage(ctx.args.itemId)).map(_.headOption)
+        store.transact(QItem.getItemLanguage(ctx.args.itemId)).map(_.headOption)
       )
-      val lang2 = OptionT(ctx.store.transact(RCollective.findByItem(ctx.args.itemId)))
+      val lang2 = OptionT(store.transact(RCollective.findByItem(ctx.args.itemId)))
         .map(_.language)
 
       lang1.orElse(lang2).getOrElse(Language.German)
@@ -149,11 +151,12 @@ object ReProcessItem {
       fts: FtsClient[F],
       itemOps: OItem[F],
       analyser: TextAnalyser[F],
-      regexNer: RegexNerFile[F]
+      regexNer: RegexNerFile[F],
+      store: Store[F]
   )(data: ItemData): Task[F, Args, ItemData] =
     isLastRetry[F].flatMap {
       case true =>
-        processFiles[F](cfg, fts, itemOps, analyser, regexNer, data).attempt
+        processFiles[F](cfg, fts, itemOps, analyser, regexNer, store, data).attempt
           .flatMap {
             case Right(d) =>
               Task.pure(d)
@@ -163,7 +166,7 @@ object ReProcessItem {
               ).andThen(_ => Sync[F].raiseError(ex))
           }
       case false =>
-        processFiles[F](cfg, fts, itemOps, analyser, regexNer, data)
+        processFiles[F](cfg, fts, itemOps, analyser, regexNer, store, data)
     }
 
   private def logWarn[F[_]](msg: => String): Task[F, Args, Unit] =

modules/joex/src/main/scala/docspell/joex/process/SaveProposals.scala

@@ -8,17 +8,16 @@ package docspell.joex.process
 
 import cats.effect.Sync
 import cats.implicits._
-
 import docspell.common._
 import docspell.scheduler.{Context, Task}
-import docspell.store.AddResult
+import docspell.store.{AddResult, Store}
 import docspell.store.records._
 
 /** Saves the proposals in the database */
 object SaveProposals {
   type Args = ProcessItemArgs
 
-  def apply[F[_]: Sync](data: ItemData): Task[F, Args, ItemData] =
+  def apply[F[_]: Sync](store: Store[F])(data: ItemData): Task[F, Args, ItemData] =
     Task { ctx =>
       for {
         _ <- ctx.logger.info("Storing proposals")
@@ -26,20 +25,24 @@ object SaveProposals {
           .traverse(rm =>
             ctx.logger.debug(
               s"Storing attachment proposals: ${rm.proposals}"
-            ) *> ctx.store.transact(RAttachmentMeta.updateProposals(rm.id, rm.proposals))
+            ) *> store.transact(RAttachmentMeta.updateProposals(rm.id, rm.proposals))
           )
         _ <-
           if (data.classifyProposals.isEmpty && data.classifyTags.isEmpty) 0.pure[F]
-          else saveItemProposal(ctx, data)
+          else saveItemProposal(ctx, store, data)
       } yield data
     }
 
-  def saveItemProposal[F[_]: Sync](ctx: Context[F, Args], data: ItemData): F[Unit] = {
+  def saveItemProposal[F[_]: Sync](
+      ctx: Context[F, Args],
+      store: Store[F],
+      data: ItemData
+  ): F[Unit] = {
     def upsert(v: RItemProposal): F[Int] =
-      ctx.store.add(RItemProposal.insert(v), RItemProposal.exists(v.itemId)).flatMap {
+      store.add(RItemProposal.insert(v), RItemProposal.exists(v.itemId)).flatMap {
         case AddResult.Success => 1.pure[F]
         case AddResult.EntityExists(_) =>
-          ctx.store.transact(RItemProposal.update(v))
+          store.transact(RItemProposal.update(v))
         case AddResult.Failure(ex) =>
           ctx.logger.warn(s"Could not store item proposals: ${ex.getMessage}") *> 0
             .pure[F]
@@ -47,7 +50,7 @@ object SaveProposals {
 
     for {
       _ <- ctx.logger.debug(s"Storing classifier proposals: ${data.classifyProposals}")
-      tags <- ctx.store.transact(
+      tags <- store.transact(
         RTag.findAllByNameOrId(data.classifyTags, ctx.args.meta.collective)
       )
       tagRefs = tags.map(t => IdRef(t.tagId, t.name))

modules/joex/src/main/scala/docspell/joex/process/TextAnalysis.scala

@@ -9,7 +9,6 @@ package docspell.joex.process
 import cats.Traverse
 import cats.effect._
 import cats.implicits._
-
 import docspell.analysis.classifier.TextClassifier
 import docspell.analysis.{NlpSettings, TextAnalyser}
 import docspell.common.MetaProposal.Candidate
@@ -20,6 +19,7 @@ import docspell.joex.learn.{ClassifierName, Classify, LearnClassifierTask}
 import docspell.joex.process.ItemData.AttachmentDates
 import docspell.scheduler.Context
 import docspell.scheduler.Task
+import docspell.store.Store
 import docspell.store.records.{RAttachmentMeta, RClassifierSetting}
 
 object TextAnalysis {
@@ -28,7 +28,8 @@ object TextAnalysis {
   def apply[F[_]: Async](
       cfg: Config.TextAnalysis,
       analyser: TextAnalyser[F],
-      nerFile: RegexNerFile[F]
+      nerFile: RegexNerFile[F],
+      store: Store[F]
   )(item: ItemData): Task[F, Args, ItemData] =
     Task { ctx =>
       for {
@@ -41,18 +42,19 @@ object TextAnalysis {
             )
         _ <- ctx.logger.debug(s"Storing tags: ${t.map(_._1.copy(content = None))}")
         _ <- t.traverse(m =>
-          ctx.store.transact(RAttachmentMeta.updateLabels(m._1.id, m._1.nerlabels))
+          store.transact(RAttachmentMeta.updateLabels(m._1.id, m._1.nerlabels))
         )
 
         v = t.toVector
-        autoTagEnabled <- getActiveAutoTag(ctx, cfg)
+        autoTagEnabled <- getActiveAutoTag(ctx, store, cfg)
         tag <-
-          if (autoTagEnabled) predictTags(ctx, cfg, item.metas, analyser.classifier)
+          if (autoTagEnabled)
+            predictTags(ctx, store, cfg, item.metas, analyser.classifier)
           else List.empty[String].pure[F]
 
         classProposals <-
           if (cfg.classification.enabled)
-            predictItemEntities(ctx, cfg, item.metas, analyser.classifier)
+            predictItemEntities(ctx, store, cfg, item.metas, analyser.classifier)
           else MetaProposalList.empty.pure[F]
 
         e <- s
@@ -86,16 +88,17 @@ object TextAnalysis {
 
   def predictTags[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: Config.TextAnalysis,
       metas: Vector[RAttachmentMeta],
       classifier: TextClassifier[F]
   ): F[List[String]] = {
     val text = metas.flatMap(_.content).mkString(LearnClassifierTask.pageSep)
     val classifyWith: ClassifierName => F[Option[String]] =
-      makeClassify(ctx, cfg, classifier)(text)
+      makeClassify(ctx, store, cfg, classifier)(text)
 
     for {
-      names <- ctx.store.transact(
+      names <- store.transact(
         ClassifierName.findTagClassifiers(ctx.args.meta.collective)
       )
       _ <- ctx.logger.debug(s"Guessing tags for ${names.size} categories")
@@ -105,6 +108,7 @@ object TextAnalysis {
 
   def predictItemEntities[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: Config.TextAnalysis,
       metas: Vector[RAttachmentMeta],
       classifier: TextClassifier[F]
@@ -116,7 +120,7 @@ object TextAnalysis {
         mtype: MetaProposalType
     ): F[Option[MetaProposal]] =
       for {
-        label <- makeClassify(ctx, cfg, classifier)(text).apply(cname)
+        label <- makeClassify(ctx, store, cfg, classifier)(text).apply(cname)
       } yield label.map(str =>
         MetaProposal(mtype, Candidate(IdRef(Ident.unsafe(""), str), Set.empty))
       )
@@ -136,13 +140,14 @@ object TextAnalysis {
 
   private def makeClassify[F[_]: Async](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: Config.TextAnalysis,
       classifier: TextClassifier[F]
   )(text: String): ClassifierName => F[Option[String]] =
     Classify[F](
       ctx.logger,
       cfg.workingDir,
-      ctx.store,
+      store,
       classifier,
       ctx.args.meta.collective,
       text
@@ -150,10 +155,11 @@ object TextAnalysis {
 
   private def getActiveAutoTag[F[_]: Sync](
       ctx: Context[F, Args],
+      store: Store[F],
       cfg: Config.TextAnalysis
   ): F[Boolean] =
     if (cfg.classification.enabled)
-      ctx.store
+      store
         .transact(RClassifierSetting.findById(ctx.args.meta.collective))
         .map(_.exists(_.autoTagEnabled))
         .flatTap(enabled =>

modules/joex/src/main/scala/docspell/joex/process/TextExtraction.scala

@@ -9,16 +9,16 @@ package docspell.joex.process
 import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
-
 import docspell.common._
 import docspell.extract.{ExtractConfig, ExtractResult, Extraction}
 import docspell.ftsclient.{FtsClient, TextData}
 import docspell.scheduler.{Context, Task}
+import docspell.store.Store
 import docspell.store.records.{RAttachment, RAttachmentMeta, RFileMeta}
 
 object TextExtraction {
 
-  def apply[F[_]: Async](cfg: ExtractConfig, fts: FtsClient[F])(
+  def apply[F[_]: Async](cfg: ExtractConfig, fts: FtsClient[F], store: Store[F])(
       item: ItemData
   ): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
@@ -30,6 +30,7 @@ object TextExtraction {
         txt <- item.attachments.traverse(
           extractTextIfEmpty(
             ctx,
+            store,
             cfg,
             ctx.args.meta.language,
             ctx.args.meta.collective,
@@ -38,7 +39,7 @@ object TextExtraction {
         )
         _ <- ctx.logger.debug("Storing extracted texts …")
         _ <-
-          txt.toList.traverse(res => ctx.store.transact(RAttachmentMeta.upsert(res.am)))
+          txt.toList.traverse(res => store.transact(RAttachmentMeta.upsert(res.am)))
         _ <- ctx.logger.debug(s"Extracted text stored.")
         idxItem = TextData.item(
           item.item.id,
@@ -65,6 +66,7 @@ object TextExtraction {
 
   def extractTextIfEmpty[F[_]: Async](
       ctx: Context[F, ProcessItemArgs],
+      store: Store[F],
       cfg: ExtractConfig,
       lang: Language,
       collective: Ident,
@@ -91,13 +93,14 @@ object TextExtraction {
         ctx.logger.info("TextExtraction skipped, since text is already available.") *>
           makeTextData((rm, Nil)).pure[F]
       case _ =>
-        extractTextToMeta[F](ctx, cfg, lang, item)(ra)
+        extractTextToMeta[F](ctx, store, cfg, lang, item)(ra)
           .map(makeTextData)
     }
   }
 
   def extractTextToMeta[F[_]: Async](
       ctx: Context[F, _],
+      store: Store[F],
       cfg: ExtractConfig,
       lang: Language,
       item: ItemData
@@ -105,8 +108,8 @@ object TextExtraction {
     for {
       _ <- ctx.logger.debug(s"Extracting text for attachment ${stripAttachmentName(ra)}")
       dst <- Duration.stopTime[F]
-      fids <- filesToExtract(ctx)(item, ra)
+      fids <- filesToExtract(store)(item, ra)
-      res <- extractTextFallback(ctx, cfg, ra, lang)(fids)
+      res <- extractTextFallback(ctx, store, cfg, ra, lang)(fids)
       meta = item.changeMeta(
         ra.id,
         lang,
@@ -123,14 +126,14 @@ object TextExtraction {
     } yield (meta, tags)
 
   def extractText[F[_]: Sync](
-      ctx: Context[F, _],
+      store: Store[F],
       extr: Extraction[F],
       lang: Language
   )(fileId: FileKey): F[ExtractResult] = {
-    val data = ctx.store.fileRepo.getBytes(fileId)
+    val data = store.fileRepo.getBytes(fileId)
 
     def findMime: F[MimeType] =
-      OptionT(ctx.store.fileRepo.findMeta(fileId))
+      OptionT(store.fileRepo.findMeta(fileId))
         .map(_.mimetype)
         .getOrElse(MimeType.octetStream)
 
@@ -140,6 +143,7 @@ object TextExtraction {
 
   private def extractTextFallback[F[_]: Async](
       ctx: Context[F, _],
+      store: Store[F],
       cfg: ExtractConfig,
       ra: RAttachment,
       lang: Language
@@ -151,7 +155,7 @@ object TextExtraction {
       case id :: rest =>
         val extr = Extraction.create[F](ctx.logger, cfg)
 
-        extractText[F](ctx, extr, lang)(id)
+        extractText[F](store, extr, lang)(id)
           .flatMap {
             case res @ ExtractResult.Success(_, _) =>
               res.some.pure[F]
@@ -161,12 +165,12 @@ object TextExtraction {
                 .warn(
                   s"Cannot extract text from file ${stripAttachmentName(ra)}: unsupported format ${mt.asString}. Try with converted file."
                 )
-                .flatMap(_ => extractTextFallback[F](ctx, cfg, ra, lang)(rest))
+                .flatMap(_ => extractTextFallback[F](ctx, store, cfg, ra, lang)(rest))
 
             case ExtractResult.Failure(ex) =>
               ctx.logger
                 .warn(s"Cannot extract text: ${ex.getMessage}. Try with converted file")
-                .flatMap(_ => extractTextFallback[F](ctx, cfg, ra, lang)(rest))
+                .flatMap(_ => extractTextFallback[F](ctx, store, cfg, ra, lang)(rest))
           }
     }
 
@@ -176,13 +180,13 @@ object TextExtraction {
     * If the source file is a PDF, then use the converted file. This may then already
     * contain the text if ocrmypdf is enabled. If it is disabled, both files are the same.
     */
-  private def filesToExtract[F[_]: Sync](ctx: Context[F, _])(
+  private def filesToExtract[F[_]: Sync](store: Store[F])(
       item: ItemData,
       ra: RAttachment
   ): F[List[FileKey]] =
     item.originFile.get(ra.id) match {
       case Some(sid) =>
-        ctx.store.transact(RFileMeta.findMime(sid)).map {
+        store.transact(RFileMeta.findMime(sid)).map {
           case Some(MimeType.PdfMatch(_)) =>
             List(ra.fileId)
           case _ =>

modules/joex/src/main/scala/docspell/joex/routes/JoexRoutes.scala

@@ -12,7 +12,7 @@ import cats.implicits._
 import docspell.common.{Duration, Ident, Timestamp}
 import docspell.joex.JoexApp
 import docspell.joexapi.model._
-import docspell.store.records.{RJob, RJobLog}
+import docspell.store.records.RJobLog
 
 import org.http4s.HttpRoutes
 import org.http4s.circe.CirceEntityEncoder._
@@ -67,17 +67,19 @@ object JoexRoutes {
     }
   }
 
-  def mkJob(j: RJob): Job =
+  // TODO !!
+
+  def mkJob(j: docspell.scheduler.Job[String]): Job =
     Job(
       j.id,
       j.subject,
-      j.submitted,
+      Timestamp.Epoch,
       j.priority,
-      j.retries,
+      -1,
-      j.progress,
+      -1,
-      j.started.getOrElse(Timestamp.Epoch)
+      Timestamp.Epoch
     )
 
-  def mkJobLog(j: RJob, jl: Vector[RJobLog]): JobAndLog =
+  def mkJobLog(j: docspell.scheduler.Job[String], jl: Vector[RJobLog]): JobAndLog =
     JobAndLog(mkJob(j), jl.map(r => JobLogEvent(r.created, r.level, r.message)).toList)
 }

modules/joex/src/main/scala/docspell/joex/scanmailbox/ScanMailboxTask.scala

@@ -12,7 +12,6 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import fs2._
-
 import docspell.backend.ops.{OJoex, OUpload}
 import docspell.common._
 import docspell.joex.Config
@@ -20,8 +19,8 @@ import docspell.scheduler.{Context, Task}
 import docspell.logging.Logger
 import docspell.store.queries.QOrganization
 import docspell.store.records._
-
 import _root_.io.circe.syntax._
+import docspell.store.Store
 import emil.SearchQuery.{All, ReceivedDate}
 import emil.javamail.syntax._
 import emil.{MimeType => _, _}
@@ -32,6 +31,7 @@ object ScanMailboxTask {
 
   def apply[F[_]: Sync](
       cfg: Config.ScanMailbox,
+      store: Store[F],
       emil: Emil[F],
       upload: OUpload[F],
       joex: OJoex[F]
@@ -42,22 +42,22 @@ object ScanMailboxTask {
           s"=== Start importing mails for user ${ctx.args.account.user.id}"
         )
         _ <- ctx.logger.debug(s"Settings: ${ctx.args.asJson.noSpaces}")
-        mailCfg <- getMailSettings(ctx)
+        mailCfg <- getMailSettings(ctx, store)
         folders = ctx.args.folders.mkString(", ")
         userId = ctx.args.account.user
         imapConn = ctx.args.imapConnection
         _ <- ctx.logger.info(
           s"Reading mails for user ${userId.id} from ${imapConn.id}/$folders"
         )
-        _ <- importMails(cfg, mailCfg, emil, upload, joex, ctx)
+        _ <- importMails(cfg, mailCfg, emil, upload, joex, ctx, store)
       } yield ()
     }
 
   def onCancel[F[_]]: Task[F, ScanMailboxArgs, Unit] =
     Task.log(_.warn("Cancelling scan-mailbox task"))
 
-  def getMailSettings[F[_]: Sync](ctx: Context[F, Args]): F[RUserImap] =
+  def getMailSettings[F[_]: Sync](ctx: Context[F, Args], store: Store[F]): F[RUserImap] =
-    ctx.store
+    store
       .transact(RUserImap.getByName(ctx.args.account, ctx.args.imapConnection))
       .flatMap {
         case Some(c) => c.pure[F]
@@ -75,10 +75,11 @@ object ScanMailboxTask {
       theEmil: Emil[F],
       upload: OUpload[F],
       joex: OJoex[F],
-      ctx: Context[F, Args]
+      ctx: Context[F, Args],
+      store: Store[F]
   ): F[Unit] = {
     val mailer = theEmil(mailCfg.toMailConfig)
-    val impl = new Impl[F](cfg, ctx)
+    val impl = new Impl[F](cfg, ctx, store)
     val inFolders = ctx.args.folders.take(cfg.maxFolders)
 
     val getInitialInput =
@@ -142,7 +143,11 @@ object ScanMailboxTask {
       ScanResult(List(folder -> left), processed)
   }
 
-  final private class Impl[F[_]: Sync](cfg: Config.ScanMailbox, ctx: Context[F, Args]) {
+  final private class Impl[F[_]: Sync](
+      cfg: Config.ScanMailbox,
+      ctx: Context[F, Args],
+      store: Store[F]
+  ) {
 
     private def logOp[C](f: Logger[F] => F[Unit]): MailOp[F, C, Unit] =
       MailOp(_ => f(ctx.logger))
@@ -213,7 +218,7 @@ object ScanMailboxTask {
       NonEmptyList.fromFoldable(headers.flatMap(_.mh.messageId)) match {
         case Some(nl) =>
           for {
-            archives <- ctx.store.transact(
+            archives <- store.transact(
               RAttachmentArchive
                 .findByMessageIdAndCollective(nl, ctx.args.account.collective)
             )
@@ -237,7 +242,7 @@ object ScanMailboxTask {
         for {
           from <- OptionT.fromOption[F](mh.from)
           _ <- OptionT(
-            ctx.store.transact(
+            store.transact(
               QOrganization
                 .findPersonByContact(
                   ctx.args.account.collective,

modules/joex/src/main/scala/docspell/joex/updatecheck/UpdateCheckTask.scala

@@ -10,9 +10,9 @@ import cats.data.OptionT
 import cats.effect._
 import cats.implicits._
 import docspell.common._
-import docspell.scheduler.Context
 import docspell.scheduler.Task
 import docspell.scheduler.usertask.UserTask
+import docspell.store.Store
 import docspell.store.records.RUserEmail
 import emil._
 
@@ -37,6 +37,7 @@ object UpdateCheckTask {
   def apply[F[_]: Async](
       cfg: UpdateCheckConfig,
       sendCfg: MailSendConfig,
+      store: Store[F],
       emil: Emil[F],
       updateCheck: UpdateCheck[F],
       thisVersion: ThisVersion
@@ -50,7 +51,7 @@ object UpdateCheckTask {
           _ <- ctx.logger.debug(
             s"Get SMTP connection for ${cfg.senderAccount.asString} and ${cfg.smtpId}"
           )
-          smtpCfg <- findConnection(ctx, cfg)
+          smtpCfg <- findConnection(store, cfg)
           _ <- ctx.logger.debug("Checking for latest release at GitHub")
           latest <- updateCheck.latestRelease
           _ <- ctx.logger.debug(s"Got latest release: $latest.")
@@ -77,10 +78,10 @@ object UpdateCheckTask {
       Task.pure(())
 
   def findConnection[F[_]: Sync](
-      ctx: Context[F, _],
+      store: Store[F],
       cfg: UpdateCheckConfig
   ): F[RUserEmail] =
-    OptionT(ctx.store.transact(RUserEmail.getByName(cfg.senderAccount, cfg.smtpId)))
+    OptionT(store.transact(RUserEmail.getByName(cfg.senderAccount, cfg.smtpId)))
       .getOrElseF(
         Sync[F].raiseError(
           new Exception(

modules/scheduler/api/src/main/scala/docspell/scheduler/Context.scala

@@ -8,7 +8,6 @@ package docspell.scheduler
 
 import docspell.common._
 import docspell.logging.Logger
-import docspell.store.Store
 
 trait Context[F[_], A] { self =>
 
@@ -22,8 +21,6 @@ trait Context[F[_], A] { self =>
 
   def setProgress(percent: Int): F[Unit]
 
-  def store: Store[F]
-
   def isLastRetry: F[Boolean]
 
   def map[C](f: A => C): Context[F, C]

modules/scheduler/api/src/main/scala/docspell/scheduler/Scheduler.scala

@@ -10,13 +10,12 @@ import cats.effect._
 import fs2.Stream
 
 import docspell.common.Ident
-import docspell.store.records.RJob
 
 trait Scheduler[F[_]] {
 
   def config: SchedulerConfig
 
-  def getRunning: F[Vector[RJob]]
+  def getRunning: F[Vector[Job[String]]]
 
   def requestCancel(jobId: Ident): F[Boolean]
 

modules/scheduler/impl/src/main/scala/docspell/scheduler/impl/ContextImpl.scala

@@ -13,7 +13,7 @@ import docspell.store.records.RJob
 class ContextImpl[F[_]: Functor, A](
     val args: A,
     val logger: Logger[F],
-    val store: Store[F],
+    store: Store[F],
     val config: SchedulerConfig,
     val jobId: Ident
 ) extends Context[F, A] {

modules/scheduler/impl/src/main/scala/docspell/scheduler/impl/SchedulerImpl.scala

@@ -64,8 +64,23 @@ final class SchedulerImpl[F[_]: Async](
         .drain
     )
 
-  def getRunning: F[Vector[RJob]] =
+  def getRunning: F[Vector[Job[String]]] =
-    state.get.flatMap(s => QJob.findAll(s.getRunning, store))
+    state.get
+      .flatMap(s => QJob.findAll(s.getRunning, store))
+      .map(
+        _.map(rj =>
+          Job(
+            rj.id,
+            rj.task,
+            rj.group,
+            rj.args,
+            rj.subject,
+            rj.submitter,
+            rj.priority,
+            rj.tracker
+          )
+        )
+      )
 
   def requestCancel(jobId: Ident): F[Boolean] =
     logger.info(s"Scheduler requested to cancel job: ${jobId.id}") *>