Merge pull request #1215 from eikek/dep-updates

Dep updates

.scalafmt.conf

@@ -1,4 +1,4 @@
-version = "3.0.6"
+version = "3.0.8"
 
 preset = default
 align.preset = some

build.sbt

@@ -14,7 +14,7 @@ def inTest(d0: Seq[ModuleID], ds: Seq[ModuleID]*) =
 
 val scalafixSettings = Seq(
   semanticdbEnabled := true, // enable SemanticDB
-  semanticdbVersion := scalafixSemanticdb.revision, //"4.4.0"
+  semanticdbVersion := scalafixSemanticdb.revision, // "4.4.0"
   ThisBuild / scalafixDependencies ++= Dependencies.organizeImports
 )
 
@@ -781,7 +781,7 @@ val restserver = project
     Universal / mappings := {
       val allMappings = (Universal / mappings).value
       allMappings.filter {
-        //scalajs artifacts are not needed at runtime
+        // scalajs artifacts are not needed at runtime
         case (file, name) => !name.contains("_sjs1_")
       }
     }

modules/analysis/src/main/scala/docspell/analysis/nlp/Properties.scala

@@ -53,8 +53,8 @@ object Properties {
       "ner.statisticalOnly" -> "true",
       "ner.rulesOnly" -> "false",
       "ner.applyFineGrained" -> "false",
-      "ner.applyNumericClassifiers" -> "false", //only english supported, not needed currently
+      "ner.applyNumericClassifiers" -> "false", // only english supported, not needed currently
-      "ner.useSUTime" -> "false", //only english, unused in docspell
+      "ner.useSUTime" -> "false", // only english, unused in docspell
       "ner.language" -> "de",
       "ner.model" -> "edu/stanford/nlp/models/ner/german.distsim.crf.ser.gz,edu/stanford/nlp/models/ner/english.conll.4class.distsim.crf.ser.gz"
     ).withRegexNer(regexNerMappingFile).withHighRecall(highRecall)

modules/common/src/main/scala/docspell/common/JobState.scala

@@ -50,7 +50,7 @@ object JobState {
     NonEmptyList.of(Waiting, Scheduled, Running, Stuck, Failed, Cancelled, Success)
   val queued: Set[JobState] = Set(Waiting, Scheduled, Stuck)
   val done: NonEmptyList[JobState] = NonEmptyList.of(Failed, Cancelled, Success)
-  val notDone: NonEmptyList[JobState] = //all - done
+  val notDone: NonEmptyList[JobState] = // all - done
     NonEmptyList.of(Waiting, Scheduled, Running, Stuck)
   val inProgress: Set[JobState] = Set(Scheduled, Running, Stuck)
 

modules/common/src/main/scala/docspell/common/MimeType.scala

@@ -168,7 +168,7 @@ object MimeType {
             left
         }
 
-    //https://datatracker.ietf.org/doc/html/rfc7230#section-3.2.6
+    // https://datatracker.ietf.org/doc/html/rfc7230#section-3.2.6
     private def isToken(s: String): Boolean =
       s.nonEmpty && s.forall(c => c.isLetterOrDigit || tokenExtraChars.contains(c))
 
@@ -186,7 +186,7 @@ object MimeType {
       seq(primary, sub)((p, s) => MimeType(p.toLowerCase, s.toLowerCase, None))
     }
 
-    //https://datatracker.ietf.org/doc/html/rfc2046#section-4.1.2
+    // https://datatracker.ietf.org/doc/html/rfc2046#section-4.1.2
     private val charset: P[Option[Charset]] = in =>
       in.trim.toLowerCase.indexOf("charset=") match {
         case -1 => Right((None, in))

modules/extract/src/main/scala/docspell/extract/PdfExtract.scala

@@ -44,7 +44,7 @@ object PdfExtract {
           s"Using stripped text (not OCR), as it is longer (${strippedRes._1.length} > ${ocrStr.length})"
         ) *> Result(strippedRes).pure[F]
 
-    //maybe better: inspect the pdf and decide whether ocr or not
+    // maybe better: inspect the pdf and decide whether ocr or not
     for {
       pdfboxRes <-
         logger.debug("Trying to strip text from pdf using pdfbox.") *>

modules/files/src/test/scala/docspell/files/ImageSizeTest.scala

@@ -16,8 +16,8 @@ import munit._
 
 class ImageSizeTest extends FunSuite {
 
-  //tiff files are not supported on the jdk by default
+  // tiff files are not supported on the jdk by default
-  //requires an external library
+  // requires an external library
   val files = List(
     ExampleFiles.camera_letter_en_jpg -> Dimension(1695, 2378),
     ExampleFiles.camera_letter_en_png -> Dimension(1695, 2378),

modules/files/src/test/scala/docspell/files/Playing.scala

@@ -15,8 +15,8 @@ object Playing extends IOApp {
 
   def run(args: List[String]): IO[ExitCode] =
     IO {
-      //val ods = ExampleFiles.examples_sample_ods.readURL[IO](8192, blocker)
+      // val ods = ExampleFiles.examples_sample_ods.readURL[IO](8192, blocker)
-      //val odt = ExampleFiles.examples_sample_odt.readURL[IO](8192, blocker)
+      // val odt = ExampleFiles.examples_sample_odt.readURL[IO](8192, blocker)
       val rtf = ExampleFiles.examples_sample_rtf.readURL[IO](8192)
 
       val x = for {

modules/joex/src/main/scala/docspell/joex/analysis/RegexNerFile.scala

@@ -46,7 +46,7 @@ object RegexNerFile {
   final private class Impl[F[_]: Async](
       cfg: Config,
       store: Store[F],
-      writer: Semaphore[F] //TODO allow parallelism per collective
+      writer: Semaphore[F] // TODO allow parallelism per collective
   ) extends RegexNerFile[F] {
 
     def makeFile(collective: Ident): F[Option[Path]] =

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

@@ -143,7 +143,7 @@ object CreateItem {
           .fromOption[F](NonEmptyList.fromList(fileMetaIds.toList))
           .flatMap(fids =>
             OptionT(
-              //load attachments but only those mentioned in the task's arguments
+              // 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))
@@ -195,7 +195,7 @@ object CreateItem {
     ctx.logger.error(msg) *> Sync[F].raiseError(new Exception(msg))
   }
 
-  //TODO if no source is present, it must be saved!
+  // TODO if no source is present, it must be saved!
   private def originFileTuple(
       t: (RAttachment, Option[RAttachmentSource])
   ): (Ident, Ident) =

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

@@ -60,7 +60,7 @@ object EvalProposals {
   ): Double =
     mp.proposalType match {
       case MetaProposalType.DueDate =>
-        //for due dates, sort earliest on top
+        // for due dates, sort earliest on top
         MetaProposal
           .parseDate(cand)
           .map { ld =>

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

@@ -108,9 +108,9 @@ object ReProcessItem {
               data.item.cid,
               args.itemId.some,
               lang,
-              None, //direction
+              None, // direction
-              data.item.source, //source-id
+              data.item.source, // source-id
-              None, //folder
+              None, // folder
               Seq.empty,
               false,
               None,

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

@@ -162,7 +162,7 @@ object ScanMailboxTask {
 
     def requireFolder[C](a: Access[F, C])(name: String): MailOp[F, C, MailFolder] =
       if ("INBOX".equalsIgnoreCase(name)) a.getInbox
-      else //TODO resolve sub-folders
+      else // TODO resolve sub-folders
         a.findFolder(None, name)
           .map(_.toRight(new Exception(s"Folder '$name' not found")))
           .mapF(_.rethrow)

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

@@ -227,7 +227,7 @@ final class SchedulerImpl[F[_]: Async](
       job.id,
       config.name,
       store
-    ) //also increments retries if current state=stuck
+    ) // also increments retries if current state=stuck
 
   def wrapTask(
       job: RJob,

modules/joex/src/test/scala/docspell/joex/analysis/NerFileTest.scala

@@ -26,7 +26,7 @@ class NerFileTest extends FunSuite {
 
     for ((name, first) <- names) {
       val ps = Pattern(1)(name).distinct
-      //check if it compiles to a regex pattern
+      // check if it compiles to a regex pattern
       ps.flatMap(_.value.split("\\s+").toList).foreach(_.r)
       ps.foreach(_.value.r)
 

modules/jsonminiq/src/test/scala/docspell/jsonminiq/JsonMiniQueryTest.scala

@@ -59,7 +59,7 @@ class JsonMiniQueryTest extends FunSuite with Fixtures {
     assertEquals(r(sampleEvent), Vector.empty)
   }
 
-  //content.[added,removed].(category=expense & name=grocery)
+  // content.[added,removed].(category=expense & name=grocery)
   test("combine fields and filter") {
     val andOk = JQ.at("content").at("added", "removed") >>
       (JQ.at("name").is("grocery") && JQ.at("category").is("expense"))
@@ -156,6 +156,6 @@ class JsonMiniQueryTest extends FunSuite with Fixtures {
     val json4 = parseJson(
       """[{"name":"max", "count":4}, {"name":"me", "count": 3}, {"name":"max", "count": 3}]"""
     )
-    println(q4(json4))
+    assertEquals(q4(json4), values("max", "max"))
   }
 }

modules/pubsub/naive/src/main/scala/docspell/pubsub/naive/NaivePubSub.scala

@@ -80,7 +80,7 @@ final class NaivePubSub[F[_]: Async](
     } yield head
 
   def publish(topic: Topic): Pipe[F, Json, MessageHead] =
-    ms => //TODO Do some optimization by grouping messages to the same topic
+    ms => // TODO Do some optimization by grouping messages to the same topic
       ms.evalMap(publish0(topic, _))
 
   def subscribe(topics: NonEmptyList[Topic]): Stream[F, Message[Json]] =

modules/pubsub/naive/src/test/scala/docspell/pubsub/naive/NaivePubSubTest.scala

@@ -58,7 +58,7 @@ class NaivePubSubTest extends CatsEffectSuite with Fixtures {
       res <- subscribe(ps, Topics.jobSubmitted)
       (received, halt, subFiber) = res
       _ <- ps.publish1(otherTopic, JobSubmittedMsg("hello".id))
-      _ <- IO.sleep(100.millis) //allow some time for receiving
+      _ <- IO.sleep(100.millis) // allow some time for receiving
       _ <- halt.set(true)
       outcome <- subFiber.join
       _ = assert(outcome.isSuccess)

modules/query/shared/src/main/scala/docspell/query/internal/ExprString.scala

@@ -113,7 +113,7 @@ object ExprString {
       case Expr.NamesMacro(name) =>
         s"${C.names}:${quote(name)}"
       case Expr.YearMacro(_, year) =>
-        s"${C.year}:$year" //currently, only for Attr.Date
+        s"${C.year}:$year" // currently, only for Attr.Date
       case Expr.ConcMacro(term) =>
         s"${C.conc}:${quote(term)}"
       case Expr.CorrMacro(term) =>

modules/restserver/src/main/scala/docspell/restserver/conv/Conversions.scala

@@ -236,9 +236,9 @@ trait Conversions {
       i.concPerson.map(mkIdName),
       i.concEquip.map(mkIdName),
       i.folder.map(mkIdName),
-      Nil, //attachments
+      Nil, // attachments
-      Nil, //tags
+      Nil, // tags
-      Nil, //customfields
+      Nil, // customfields
       i.notes,
       Nil // highlight
     )

modules/restserver/src/main/scala/docspell/restserver/http4s/ContentDisposition.scala

@@ -141,7 +141,7 @@ object ContentDisposition {
   }
 
   private val parser = makeParser(mimeValue)
-  //private val origParser = makeParser(Rfc7230.token | Rfc7230.quotedString)
+  // private val origParser = makeParser(Rfc7230.token | Rfc7230.quotedString)
 
   implicit val headerInstance: Header[ContentDisposition, Header.Single] = {
     val oh = `Content-Disposition`.headerInstance

modules/restserver/src/main/scala/docspell/restserver/routes/IntegrationEndpointRoutes.scala

@@ -140,9 +140,9 @@ object IntegrationEndpointRoutes {
         cfg: Config.IntegrationEndpoint.AllowedIps
     ): HttpRoutes[F] =
       HttpRoutes { req =>
-        //The `req.from' take the X-Forwarded-For header into account,
+        // The `req.from' take the X-Forwarded-For header into account,
-        //which is not desirable here. The `http-header' auth config
+        // which is not desirable here. The `http-header' auth config
-        //can be used to authenticate based on headers.
+        // can be used to authenticate based on headers.
         val from = req.remote.map(_.host)
         if (from.exists(cfg.containsAddress)) OptionT.none[F, Response[F]]
         else OptionT.pure(Responses.forbidden[F])

modules/store/src/main/scala/db/migration/MigrationTasks.scala

@@ -81,7 +81,7 @@ trait MigrationTasks {
 
   def mkTransactor(ctx: Context): Transactor[IO] = {
     val xa = Transactor.fromConnection[IO](ctx.getConnection())
-    Transactor.strategy.set(xa, Strategy.void) //transactions are handled by flyway
+    Transactor.strategy.set(xa, Strategy.void) // transactions are handled by flyway
   }
 
 }

modules/store/src/main/scala/docspell/store/queries/QJob.scala

@@ -61,7 +61,7 @@ object QJob {
       retryPause: Duration,
       currentTry: Int
   ): F[Either[Unit, Option[RJob]]] = {
-    //if this fails, we have to restart takeNextJob
+    // if this fails, we have to restart takeNextJob
     def markJob(job: RJob): F[Either[Unit, RJob]] =
       store.transact(for {
         n <- RJob.setScheduled(job.id, worker)
@@ -236,7 +236,7 @@ object QJob {
     val JC = RJob.T
     val waiting = NonEmptyList.of(JobState.Waiting, JobState.Stuck, JobState.Scheduled)
     val running = NonEmptyList.of(JobState.Running)
-    //val done                   = JobState.all.filterNot(js => ).diff(waiting).diff(running)
+    // val done                   = JobState.all.filterNot(js => ).diff(waiting).diff(running)
 
     def selectJobs(now: Timestamp): Stream[ConnectionIO, RJob] = {
       val refDate = now.minusHours(24)

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

@@ -20,7 +20,7 @@ import doobie.implicits._
   * a 0..1-1 relationship.
   */
 case class RAttachmentArchive(
-    id: Ident, //same as RAttachment.id
+    id: Ident, // same as RAttachment.id
     fileId: Ident,
     name: Option[String],
     messageId: Option[String],

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

@@ -17,7 +17,7 @@ import doobie._
 import doobie.implicits._
 
 case class RAttachmentMeta(
-    id: Ident, //same as RAttachment.id
+    id: Ident, // same as RAttachment.id
     content: Option[String],
     nerlabels: List[NerLabel],
     proposals: MetaProposalList,

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

@@ -19,7 +19,7 @@ import doobie.implicits._
   * 1-1 (or 0..1-1) relationship.
   */
 case class RAttachmentPreview(
-    id: Ident, //same as RAttachment.id
+    id: Ident, // same as RAttachment.id
     fileId: Ident,
     name: Option[String],
     created: Timestamp

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

@@ -19,7 +19,7 @@ import doobie.implicits._
   * 1-1 (or 0..1-1) relationship.
   */
 case class RAttachmentSource(
-    id: Ident, //same as RAttachment.id
+    id: Ident, // same as RAttachment.id
     fileId: Ident,
     name: Option[String],
     created: Timestamp

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

@@ -120,7 +120,7 @@ object RCollective {
         cs.listType.s,
         es.schedule.s,
         es.minAge.s,
-        const(0) //dummy value to load Nil as list of passwords
+        const(0) // dummy value to load Nil as list of passwords
       ),
       from(c).leftJoin(cs, cs.cid === c.id).leftJoin(es, es.cid === c.id),
       c.id === coll

project/Dependencies.scala

@@ -15,7 +15,7 @@ object Dependencies {
   val DoobieVersion = "1.0.0-RC1"
   val EmilVersion = "0.10.0-M3"
   val FlexmarkVersion = "0.62.2"
-  val FlywayVersion = "8.2.0"
+  val FlywayVersion = "8.2.1"
   val Fs2Version = "3.2.3"
   val Fs2CronVersion = "0.7.1"
   val H2Version = "1.4.200"
@@ -288,7 +288,8 @@ object Dependencies {
   // https://github.com/flyway/flyway
   // ASL 2.0
   val flyway = Seq(
-    "org.flywaydb" % "flyway-core" % FlywayVersion
+    "org.flywaydb" % "flyway-core" % FlywayVersion,
+    "org.flywaydb" % "flyway-mysql" % FlywayVersion
   )
 
   val yamusca = Seq(