Merge pull request #299 from eikek/fix-mariadb-text-column

Fix mariadb text column

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

@@ -38,10 +38,20 @@ object ConvertPdf {
       item: ItemData
   ): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
-      def convert(ra: RAttachment) =
-        findMime(ctx)(ra).flatMap(m =>
-          convertSafe(cfg, JsoupSanitizer.clean, ctx, item)(ra, m)
-        )
+      def convert(ra: RAttachment): F[(RAttachment, Option[RAttachmentMeta])] =
+        isConverted(ctx)(ra).flatMap {
+          case true =>
+            ctx.logger.info(
+              s"Conversion to pdf already done for attachment ${ra.name}."
+            ) *>
+              ctx.store
+                .transact(RAttachmentMeta.findById(ra.id))
+                .map(rmOpt => (ra, rmOpt))
+          case false =>
+            findMime(ctx)(ra).flatMap(m =>
+              convertSafe(cfg, JsoupSanitizer.clean, ctx, item)(ra, m)
+            )
+        }
 
       for {
         ras <- item.attachments.traverse(convert)
@@ -51,6 +61,11 @@ object ConvertPdf {
 
     }
 
+  def isConverted[F[_]: Sync](ctx: Context[F, ProcessItemArgs])(
+      ra: RAttachment
+  ): F[Boolean] =
+    ctx.store.transact(RAttachmentSource.isConverted(ra.id))
+
   def findMime[F[_]: Functor](ctx: Context[F, _])(ra: RAttachment): F[Mimetype] =
     OptionT(ctx.store.transact(RFileMeta.findById(ra.fileId)))
       .map(_.mimetype)

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

@@ -1,5 +1,6 @@
 package docspell.joex.process
 
+import cats.data.NonEmptyList
 import cats.data.OptionT
 import cats.effect.Sync
 import cats.implicits._
@@ -125,21 +126,31 @@ object CreateItem {
       for {
         cand <- ctx.store.transact(QItem.findByFileIds(fileMetaIds.toSeq))
         _ <-
-          if (cand.nonEmpty) ctx.logger.warn("Found existing item with these files.")
+          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))
         _ <-
           if (ht.sum > 0)
             ctx.logger.warn(s"Removed ${ht.sum} items with same attachments")
           else ().pure[F]
-        rms <- OptionT(
-          //load attachments but only those mentioned in the task's arguments
-          cand.headOption.traverse(ri =>
-            ctx.store
-              .transact(RAttachment.findByItemAndCollective(ri.id, ri.cid))
-              .map(_.filter(r => fileMetaIds.contains(r.fileId)))
+        rms <- OptionT
+          .fromOption[F](NonEmptyList.fromList(fileMetaIds.toList))
+          .flatMap(fids =>
+            OptionT(
+              //load attachments but only those mentioned in the task's arguments
+              cand.headOption.traverse(ri =>
+                ctx.store
+                  .transact(RAttachment.findByItemCollectiveSource(ri.id, ri.cid, fids))
+                  .flatTap(ats =>
+                    ctx.logger.debug(
+                      s"Found ${ats.size} attachments. Use only those from task args: ${fileMetaIds}"
+                    )
+                  )
+              )
+            )
           )
-        ).getOrElse(Vector.empty)
+          .getOrElse(Vector.empty)
         orig <- rms.traverse(a =>
           ctx.store.transact(RAttachmentSource.findById(a.id)).map(s => (a, s))
         )

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

@@ -7,6 +7,7 @@ import docspell.common._
 import docspell.joex.scheduler.{Context, Task}
 import docspell.store.queries.QItem
 import docspell.store.records.RFileMeta
+import docspell.store.records.RJob
 
 import bitpeace.FileMeta
 import doobie._
@@ -17,7 +18,13 @@ object DuplicateCheck {
   def apply[F[_]: Sync]: Task[F, Args, Args] =
     Task { ctx =>
       if (ctx.args.meta.skipDuplicate)
-        ctx.logger.debug("Checking for duplicate files") *> removeDuplicates(ctx)
+        for {
+          retries <- getRetryCount(ctx)
+          res <-
+            if (retries == 0)
+              ctx.logger.debug("Checking for duplicate files") *> removeDuplicates(ctx)
+            else ctx.args.pure[F]
+        } yield res
       else ctx.logger.debug("Not checking for duplicates") *> ctx.args.pure[F]
     }
 
@@ -30,6 +37,9 @@ object DuplicateCheck {
       ctx.args.files.filterNot(f => ids.contains(f.fileMetaId.id))
     )
 
+  private def getRetryCount[F[_]: Sync](ctx: Context[F, Args]): F[Int] =
+    ctx.store.transact(RJob.getRetries(ctx.jobId)).map(_.getOrElse(0))
+
   private def deleteDuplicate[F[_]: Sync](
       ctx: Context[F, Args]
   )(fd: FileMetaDupes): F[Unit] = {

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

@@ -20,7 +20,9 @@ object TextExtraction {
   ): Task[F, ProcessItemArgs, ItemData] =
     Task { ctx =>
       for {
-        _     <- ctx.logger.info("Starting text extraction")
+        _ <- ctx.logger.info(
+          s"Starting text extraction for ${item.attachments.size} files"
+        )
         start <- Duration.stopTime[F]
         txt <- item.attachments.traverse(
           extractTextIfEmpty(
@@ -31,9 +33,10 @@ object TextExtraction {
             item
           )
         )
-        _ <- ctx.logger.debug("Storing extracted texts")
+        _ <- ctx.logger.debug("Storing extracted texts …")
         _ <-
           txt.toList.traverse(res => ctx.store.transact(RAttachmentMeta.upsert(res.am)))
+        _ <- ctx.logger.debug(s"Extracted text stored.")
         idxItem = TextData.item(
           item.item.id,
           ctx.args.meta.collective,

modules/store/src/main/resources/db/migration/mariadb/V1.9.2__fix_text_length.sql

@@ -0,0 +1,14 @@
+ALTER TABLE `attachmentmeta`
+MODIFY COLUMN `content` longtext;
+
+ALTER TABLE `attachmentmeta`
+MODIFY COLUMN `nerlabels` longtext;
+
+ALTER TABLE `attachmentmeta`
+MODIFY COLUMN `itemproposals` longtext;
+
+ALTER TABLE `job`
+MODIFY COLUMN `args` mediumtext;
+
+ALTER TABLE `joblog`
+MODIFY COLUMN `message` mediumtext;

modules/store/src/main/scala/docspell/store/impl/Column.scala

@@ -44,6 +44,9 @@ case class Column(name: String, ns: String = "", alias: String = "") {
   def isNot[A: Put](value: A): Fragment =
     f ++ fr"<> $value"
 
+  def isNot(c: Column): Fragment =
+    f ++ fr"<>" ++ c.f
+
   def isNull: Fragment =
     f ++ fr"is null"
 

modules/store/src/main/scala/docspell/store/records/RAttachment.scala

@@ -1,5 +1,6 @@
 package docspell.store.records
 
+import cats.data.NonEmptyList
 import cats.implicits._
 import fs2.Stream
 
@@ -158,6 +159,36 @@ object RAttachment {
     q.query[RAttachment].to[Vector]
   }
 
+  def findByItemCollectiveSource(
+      id: Ident,
+      coll: Ident,
+      fileIds: NonEmptyList[Ident]
+  ): ConnectionIO[Vector[RAttachment]] = {
+
+    val iId   = RItem.Columns.id.prefix("i")
+    val iColl = RItem.Columns.cid.prefix("i")
+    val aItem = Columns.itemId.prefix("a")
+    val aId   = Columns.id.prefix("a")
+    val aFile = Columns.fileId.prefix("a")
+    val sId   = RAttachmentSource.Columns.id.prefix("s")
+    val sFile = RAttachmentSource.Columns.fileId.prefix("s")
+    val rId   = RAttachmentArchive.Columns.id.prefix("r")
+    val rFile = RAttachmentArchive.Columns.fileId.prefix("r")
+
+    val from = table ++ fr"a INNER JOIN" ++
+      RItem.table ++ fr"i ON" ++ iId.is(aItem) ++ fr"LEFT JOIN" ++
+      RAttachmentSource.table ++ fr"s ON" ++ sId.is(aId) ++ fr"LEFT JOIN" ++
+      RAttachmentArchive.table ++ fr"r ON" ++ rId.is(aId)
+
+    val cond = and(
+      iId.is(id),
+      iColl.is(coll),
+      or(aFile.isIn(fileIds), sFile.isIn(fileIds), rFile.isIn(fileIds))
+    )
+
+    selectSimple(all.map(_.prefix("a")), from, cond).query[RAttachment].to[Vector]
+  }
+
   def findByItemAndCollectiveWithMeta(
       id: Ident,
       coll: Ident

modules/store/src/main/scala/docspell/store/records/RAttachmentMeta.scala

@@ -46,6 +46,9 @@ object RAttachmentMeta {
   def exists(attachId: Ident): ConnectionIO[Boolean] =
     selectCount(id, table, id.is(attachId)).query[Int].unique.map(_ > 0)
 
+  def findById(attachId: Ident): ConnectionIO[Option[RAttachmentMeta]] =
+    selectSimple(all, table, id.is(attachId)).query[RAttachmentMeta].option
+
   def upsert(v: RAttachmentMeta): ConnectionIO[Int] =
     for {
       n0 <- update(v)

modules/store/src/main/scala/docspell/store/records/RAttachmentSource.scala

@@ -48,6 +48,21 @@ object RAttachmentSource {
       .unique
       .map(_ > 0)
 
+  def isConverted(attachId: Ident): ConnectionIO[Boolean] = {
+    val sId   = Columns.id.prefix("s")
+    val sFile = Columns.fileId.prefix("s")
+    val aId   = RAttachment.Columns.id.prefix("a")
+    val aFile = RAttachment.Columns.fileId.prefix("a")
+
+    val from = table ++ fr"s INNER JOIN" ++
+      RAttachment.table ++ fr"a ON" ++ aId.is(sId)
+
+    selectCount(aId, from, and(aId.is(attachId), aFile.isNot(sFile)))
+      .query[Int]
+      .unique
+      .map(_ > 0)
+  }
+
   def delete(attachId: Ident): ConnectionIO[Int] =
     deleteFrom(table, id.is(attachId)).update.run