Merge branch 'master' into update/poi-4.1.2

.travis.yml

@@ -23,4 +23,4 @@ before_script:
   - export TZ=Europe/Berlin
 
 script:
-  - sbt ++$TRAVIS_SCALA_VERSION ";project root ;make"
+  - sbt ++$TRAVIS_SCALA_VERSION ";project root ;make ;test"

modules/analysis/src/main/scala/docspell/analysis/contact/Contact.scala

@@ -12,13 +12,13 @@ object Contact {
   def annotate(text: String): Vector[NerLabel] =
     TextSplitter
       .splitToken[Nothing](text, " \t\r\n".toSet)
-      .map({ token =>
+      .map { token =>
         if (isEmailAddress(token.value))
           NerLabel(token.value, NerTag.Email, token.begin, token.end).some
         else if (isWebsite(token.value))
           NerLabel(token.value, NerTag.Website, token.begin, token.end).some
         else None
-      })
+      }
       .flatMap(_.map(Stream.emit).getOrElse(Stream.empty))
       .toVector
 

modules/backend/src/main/scala/docspell/backend/ops/OItem.scala

@@ -11,7 +11,14 @@ import docspell.store.queries.{QAttachment, QItem}
 import OItem.{AttachmentData, AttachmentSourceData, ItemData, ListItem, Query}
 import bitpeace.{FileMeta, RangeDef}
 import docspell.common.{Direction, Ident, ItemState, MetaProposalList, Timestamp}
-import docspell.store.records.{RAttachment, RAttachmentMeta, RAttachmentSource, RItem, RSource, RTagItem}
+import docspell.store.records.{
+  RAttachment,
+  RAttachmentMeta,
+  RAttachmentSource,
+  RItem,
+  RSource,
+  RTagItem
+}
 
 trait OItem[F[_]] {
 
@@ -80,8 +87,11 @@ object OItem {
     val fileId = ra.fileId
   }
 
-  case class AttachmentSourceData[F[_]](rs: RAttachmentSource, meta: FileMeta, data: Stream[F, Byte])
+  case class AttachmentSourceData[F[_]](
-  extends BinaryData[F] {
+      rs: RAttachmentSource,
+      meta: FileMeta,
+      data: Stream[F, Byte]
+  ) extends BinaryData[F] {
     val name   = rs.name
     val fileId = rs.fileId
   }
@@ -131,7 +141,11 @@ object OItem {
 
       private def makeBinaryData[A](fileId: Ident)(f: FileMeta => A): F[Option[A]] =
         store.bitpeace
-        .get(fileId.id).unNoneTerminate.compile.last.map(
+          .get(fileId.id)
+          .unNoneTerminate
+          .compile
+          .last
+          .map(
             _.map(m => f(m))
           )
 

modules/backend/src/main/scala/docspell/backend/signup/OSignup.scala

@@ -51,7 +51,8 @@ object OSignup {
                   res <- if (ok) addUser(data).map(SignupResult.fromAddResult)
                   else SignupResult.invalidInvitationKey.pure[F]
                   _ <- if (retryInvite(res))
-                        logger.fdebug(s"Adding account failed ($res). Allow retry with invite.") *> store
+                    logger
+                      .fdebug(s"Adding account failed ($res). Allow retry with invite.") *> store
                       .transact(
                         RInvitation.insert(RInvitation(inv, now))
                       )

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

@@ -26,9 +26,7 @@ object AccountId {
           invalid
       }
 
-    val separated = sepearatorChars.foldRight(invalid) { (c, v) =>
+    val separated = sepearatorChars.foldRight(invalid)((c, v) => v.orElse(parse0(c)))
-      v.orElse(parse0(c))
-    }
 
     separated.orElse(Ident.fromString(str).map(id => AccountId(id, id)))
   }

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

@@ -1,8 +1,6 @@
 package docspell.common
 
-sealed trait DataType {
+sealed trait DataType {}
-
-}
 
 object DataType {
 
@@ -10,7 +8,6 @@ object DataType {
 
   case class Hint(hint: MimeTypeHint) extends DataType
 
-
   def apply(mt: MimeType): DataType =
     Exact(mt)
 

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

@@ -65,11 +65,13 @@ object File {
     javaList.asScala.toList.sortBy(_.getFileName.toString)
   }
 
-  def readAll[F[_]: Sync: ContextShift](file: Path, blocker: Blocker, chunkSize: Int): Stream[F, Byte] =
+  def readAll[F[_]: Sync: ContextShift](
+      file: Path,
+      blocker: Blocker,
+      chunkSize: Int
+  ): Stream[F, Byte] =
     fs2.io.file.readAll(file, blocker, chunkSize)
 
   def readText[F[_]: Sync: ContextShift](file: Path, blocker: Blocker): F[String] =
-    readAll[F](file, blocker, 8192).
+    readAll[F](file, blocker, 8192).through(fs2.text.utf8Decode).compile.foldMonoid
-      through(fs2.text.utf8Decode).
-      compile.foldMonoid
 }

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

@@ -66,9 +66,7 @@ case class LenientUri(
       )
 
   def readText[F[_]: Sync: ContextShift](chunkSize: Int, blocker: Blocker): F[String] =
-    readURL[F](chunkSize, blocker).
+    readURL[F](chunkSize, blocker).through(fs2.text.utf8Decode).compile.foldMonoid
-      through(fs2.text.utf8Decode).
-      compile.foldMonoid
 
   def host: Option[String] =
     authority.map(a =>

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

@@ -17,7 +17,6 @@ trait Logger[F[_]] {
 
 object Logger {
 
-
   def log4s[F[_]: Sync](log: Log4sLogger): Logger[F] = new Logger[F] {
     def trace(msg: => String): F[Unit] =
       log.ftrace(msg)

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

@@ -66,9 +66,7 @@ object MetaProposalList {
         case None      => map.updated(mp.proposalType, mp)
       }
 
-    val merged = ml.foldLeft(init) { (map, el) =>
+    val merged = ml.foldLeft(init)((map, el) => el.proposals.foldLeft(map)(updateMap))
-      el.proposals.foldLeft(map)(updateMap)
-    }
 
     fromMap(merged)
   }

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

@@ -23,7 +23,8 @@ object SystemCommand {
         repl.foldLeft(s) {
           case (res, (k, v)) =>
             res.replace(k, v)
-        })
+        }
+      )
 
     def toCmd: List[String] =
       program :: args.toList
@@ -75,12 +76,18 @@ object SystemCommand {
       else Stream.emit(r)
     }
 
-  private def startProcess[F[_]: Sync, A](cmd: Config, wd: Option[Path], logger: Logger[F], stdin: Stream[F, Byte])(
+  private def startProcess[F[_]: Sync, A](
+      cmd: Config,
+      wd: Option[Path],
+      logger: Logger[F],
+      stdin: Stream[F, Byte]
+  )(
       f: Process => Stream[F, A]
   ): Stream[F, A] = {
     val log      = logger.debug(s"Running external command: ${cmd.cmdString}")
     val hasStdin = stdin.take(1).compile.last.map(_.isDefined)
-    val proc = log *> hasStdin.flatMap(flag => Sync[F].delay {
+    val proc = log *> hasStdin.flatMap(flag =>
+      Sync[F].delay {
         val pb = new ProcessBuilder(cmd.toCmd.asJava)
           .redirectInput(if (flag) Redirect.PIPE else Redirect.INHERIT)
           .redirectError(Redirect.PIPE)
@@ -88,12 +95,11 @@ object SystemCommand {
 
         wd.map(_.toFile).foreach(pb.directory)
         pb.start()
-    })
+      }
+    )
     Stream
       .bracket(proc)(p =>
-        logger.debug(s"Closing process: `${cmd.cmdString}`").map { _ =>
+        logger.debug(s"Closing process: `${cmd.cmdString}`").map(_ => p.destroy())
-          p.destroy()
-        }
       )
       .flatMap(f)
   }

modules/convert/src/main/scala/docspell/convert/Conversion.scala

@@ -13,7 +13,9 @@ import docspell.files.{ImageSize, TikaMimetype}
 
 trait Conversion[F[_]] {
 
-  def toPDF[A](dataType: DataType, lang: Language, handler: Handler[F, A])(in: Stream[F, Byte]): F[A]
+  def toPDF[A](dataType: DataType, lang: Language, handler: Handler[F, A])(
+      in: Stream[F, Byte]
+  ): F[A]
 
 }
 
@@ -26,7 +28,9 @@ object Conversion {
   ): Resource[F, Conversion[F]] =
     Resource.pure(new Conversion[F] {
 
-      def toPDF[A](dataType: DataType, lang: Language, handler: Handler[F, A])(in: Stream[F, Byte]): F[A] =
+      def toPDF[A](dataType: DataType, lang: Language, handler: Handler[F, A])(
+          in: Stream[F, Byte]
+      ): F[A] =
         TikaMimetype.resolve(dataType, in).flatMap {
           case MimeType.pdf =>
             handler.run(ConversionResult.successPdf(in))

modules/convert/src/main/scala/docspell/convert/ConvertConfig.scala

@@ -3,9 +3,11 @@ package docspell.convert
 import docspell.convert.extern.{TesseractConfig, UnoconvConfig, WkHtmlPdfConfig}
 import docspell.convert.flexmark.MarkdownConfig
 
-case class ConvertConfig(chunkSize: Int,
+case class ConvertConfig(
+    chunkSize: Int,
     maxImageSize: Int,
     markdown: MarkdownConfig,
     wkhtmlpdf: WkHtmlPdfConfig,
     tesseract: TesseractConfig,
-                         unoconv: UnoconvConfig)
+    unoconv: UnoconvConfig
+)

modules/convert/src/main/scala/docspell/convert/extern/ExternConv.scala

@@ -20,7 +20,9 @@ private[extern] object ExternConv {
       logger: Logger[F],
       reader: (Path, SystemCommand.Result) => F[ConversionResult[F]]
   )(in: Stream[F, Byte], handler: Handler[F, A]): F[A] =
-    Stream.resource(File.withTempDir[F](wd, s"docspell-$name")).flatMap { dir =>
+    Stream
+      .resource(File.withTempDir[F](wd, s"docspell-$name"))
+      .flatMap { dir =>
         val inFile = dir.resolve("infile").toAbsolutePath.normalize
         val out    = dir.resolve("out.pdf").toAbsolutePath.normalize
         val sysCfg =
@@ -40,12 +42,12 @@ private[extern] object ExternConv {
           SystemCommand
             .execSuccess[F](sysCfg, blocker, logger, Some(dir), if (useStdin) in else Stream.empty)
             .evalMap(result =>
-              logResult(name, result, logger).
+              logResult(name, result, logger).flatMap(_ => reader(out, result)).flatMap(handler.run)
-                flatMap(_ => reader(out, result)).
-                flatMap(handler.run)
             )
         }
-      }.compile.lastOrError
+      }
+      .compile
+      .lastOrError
 
   def readResult[F[_]: Sync: ContextShift](
       blocker: Blocker,
@@ -60,9 +62,11 @@ private[extern] object ExternConv {
             successPdf(File.readAll(out, blocker, chunkSize)).pure[F]
 
       case false =>
-        ConversionResult.failure[F](
+        ConversionResult
+          .failure[F](
             new Exception(s"Command result=${result.rc}. No output file found.")
-        ).pure[F]
+          )
+          .pure[F]
     }
 
   def readResultTesseract[F[_]: Sync: ContextShift](
@@ -75,7 +79,7 @@ private[extern] object ExternConv {
     File.existsNonEmpty[F](outPdf).flatMap {
       case true =>
         val outTxt = out.resolveSibling(s"$outPrefix.txt")
-        File.exists(outTxt).flatMap(txtExists => {
+        File.exists(outTxt).flatMap { txtExists =>
           val pdfData = File.readAll(out, blocker, chunkSize)
           if (result.rc == 0) {
             if (txtExists) successPdfTxt(pdfData, File.readText(outTxt, blocker)).pure[F]
@@ -84,12 +88,14 @@ private[extern] object ExternConv {
             logger.warn(s"Command not successful (rc=${result.rc}), but file exists.") *>
               successPdf(pdfData).pure[F]
           }
-        })
+        }
 
       case false =>
-        ConversionResult.failure[F](
+        ConversionResult
+          .failure[F](
             new Exception(s"Command result=${result.rc}. No output file found.")
-        ).pure[F]
+          )
+          .pure[F]
     }
   }
 

modules/convert/src/main/scala/docspell/convert/extern/Tesseract.scala

@@ -21,7 +21,15 @@ object Tesseract {
     val reader: (Path, SystemCommand.Result) => F[ConversionResult[F]] =
       ExternConv.readResultTesseract[F](outBase, blocker, chunkSize, logger)
 
-    ExternConv.toPDF[F, A]("tesseract", cfg.command.replace(Map("{{lang}}" -> lang.iso3)), cfg.workingDir, false, blocker, logger, reader)(in, handler)
+    ExternConv.toPDF[F, A](
+      "tesseract",
+      cfg.command.replace(Map("{{lang}}" -> lang.iso3)),
+      cfg.workingDir,
+      false,
+      blocker,
+      logger,
+      reader
+    )(in, handler)
   }
 
 }

modules/convert/src/main/scala/docspell/convert/extern/Unoconv.scala

@@ -19,7 +19,10 @@ object Unoconv {
     val reader: (Path, SystemCommand.Result) => F[ConversionResult[F]] =
       ExternConv.readResult[F](blocker, chunkSize, logger)
 
-    ExternConv.toPDF[F, A]("unoconv", cfg.command, cfg.workingDir, false, blocker, logger, reader)(in, handler)
+    ExternConv.toPDF[F, A]("unoconv", cfg.command, cfg.workingDir, false, blocker, logger, reader)(
+      in,
+      handler
+    )
   }
 
 }

modules/convert/src/main/scala/docspell/convert/extern/WkHtmlPdf.scala

@@ -14,12 +14,16 @@ object WkHtmlPdf {
       cfg: WkHtmlPdfConfig,
       chunkSize: Int,
       blocker: Blocker,
-      logger: Logger[F],
+      logger: Logger[F]
   )(in: Stream[F, Byte], handler: Handler[F, A]): F[A] = {
     val reader: (Path, SystemCommand.Result) => F[ConversionResult[F]] =
       ExternConv.readResult[F](blocker, chunkSize, logger)
 
-    ExternConv.toPDF[F, A]("wkhtmltopdf", cfg.command, cfg.workingDir, true, blocker, logger, reader)(in, handler)
+    ExternConv
+      .toPDF[F, A]("wkhtmltopdf", cfg.command, cfg.workingDir, true, blocker, logger, reader)(
+        in,
+        handler
+      )
   }
 
 }

modules/convert/src/main/scala/docspell/convert/flexmark/Markdown.scala

@@ -27,7 +27,6 @@ object Markdown {
     }.toEither
   }
 
-
   def toHtml(md: String, cfg: MarkdownConfig): String = {
     val p   = createParser()
     val r   = createRenderer()
@@ -36,10 +35,9 @@ object Markdown {
   }
 
   def toHtml[F[_]: Sync](data: Stream[F, Byte], cfg: MarkdownConfig): F[String] =
-    data.through(fs2.text.utf8Decode).compile.foldMonoid.
+    data.through(fs2.text.utf8Decode).compile.foldMonoid.map(str => toHtml(str, cfg))
-      map(str => toHtml(str, cfg))
 
-  private def wrapHtml(body: String, cfg: MarkdownConfig): String = {
+  private def wrapHtml(body: String, cfg: MarkdownConfig): String =
     s"""<!DOCTYPE html>
        |<html>
        |<head>
@@ -53,13 +51,13 @@ object Markdown {
        |</body>
        |</html>
        |""".stripMargin
-  }
 
   private def createParser(): Parser = {
     val opts = new MutableDataSet()
-    opts.set(Parser.EXTENSIONS.asInstanceOf[DataKey[util.Collection[_]]],
+    opts.set(
-      util.Arrays.asList(TablesExtension.create(),
+      Parser.EXTENSIONS.asInstanceOf[DataKey[util.Collection[_]]],
-        StrikethroughExtension.create()));
+      util.Arrays.asList(TablesExtension.create(), StrikethroughExtension.create())
+    );
 
     Parser.builder(opts).build()
   }

modules/convert/src/test/scala/docspell/convert/FileChecks.scala

@@ -55,5 +55,4 @@ trait FileChecks {
   def commandExists(cmd: String): Boolean =
     Runtime.getRuntime.exec(Array("which", cmd)).waitFor() == 0
 
-
 }

modules/convert/src/test/scala/docspell/convert/extern/ExternConvTest.scala

@@ -103,5 +103,4 @@ object ExternConvTest extends SimpleTestSuite with FileChecks {
     }
   }
 
-
 }

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

@@ -29,7 +29,7 @@ object Extraction {
           data: Stream[F, Byte],
           dataType: DataType,
           lang: Language
-      ): F[ExtractResult] = {
+      ): F[ExtractResult] =
         TikaMimetype.resolve(dataType, data).flatMap {
           case MimeType.pdf =>
             PdfExtract
@@ -50,16 +50,23 @@ object Extraction {
               .extractOCR(data, blocker, logger, lang.iso3, cfg.ocr)
               .compile
               .lastOrError
+              .map(_.trim)
               .attempt
               .map(ExtractResult.fromEither)
 
             ImageSize.get(data).flatMap {
               case Some(dim) =>
                 if (dim.product > cfg.ocr.maxImageSize) {
-                  logger.info(s"Image size (${dim.product}) is too large (max ${cfg.ocr.maxImageSize}).") *>
+                  logger.info(
-                  ExtractResult.failure(new Exception(
+                    s"Image size (${dim.product}) is too large (max ${cfg.ocr.maxImageSize})."
-                    s"Image size (${dim.width}x${dim.height}) is too large (max ${cfg.ocr.maxImageSize}).")
+                  ) *>
-                  ).pure[F]
+                    ExtractResult
+                      .failure(
+                        new Exception(
+                          s"Image size (${dim.width}x${dim.height}) is too large (max ${cfg.ocr.maxImageSize})."
+                        )
+                      )
+                      .pure[F]
                 } else {
                   doExtract
                 }
@@ -69,7 +76,8 @@ object Extraction {
             }
 
           case OdfType.container =>
-            logger.info(s"File detected as ${OdfType.container}. Try to read as OpenDocument file.") *>
+            logger
+              .info(s"File detected as ${OdfType.container}. Try to read as OpenDocument file.") *>
               OdfExtract.get(data).map(ExtractResult.fromEither)
 
           case mt @ MimeType("text", sub) if !sub.contains("html") =>
@@ -83,6 +91,5 @@ object Extraction {
 
         }
     }
-    }
 
 }

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

@@ -33,7 +33,8 @@ object PdfExtract {
 
     //maybe better: inspect the pdf and decide whether ocr or not
     for {
-      pdfboxRes <- logger.debug("Trying to strip text from pdf using pdfbox.") *> PdfboxExtract.get[F](in)
+      pdfboxRes <- logger.debug("Trying to strip text from pdf using pdfbox.") *> PdfboxExtract
+        .get[F](in)
       res <- pdfboxRes.fold(
         ex =>
           logger.info(

modules/extract/src/main/scala/docspell/extract/ocr/OcrConfig.scala

@@ -10,8 +10,7 @@ case class OcrConfig(
     pageRange: OcrConfig.PageRange,
     unpaper: OcrConfig.Unpaper,
     tesseract: OcrConfig.Tesseract
-) {
+) {}
-}
 
 object OcrConfig {
 

modules/extract/src/main/scala/docspell/extract/odf/OdfExtract.scala

@@ -17,8 +17,8 @@ object OdfExtract {
   def get[F[_]: Sync](data: Stream[F, Byte]): F[Either[Throwable, String]] =
     data.compile.to(Array).map(new ByteArrayInputStream(_)).map(get)
 
-
+  def get(is: InputStream) =
-  def get(is: InputStream) = Try {
+    Try {
       val handler  = new BodyContentHandler()
       val pctx     = new ParseContext()
       val meta     = new Metadata()

modules/extract/src/main/scala/docspell/extract/pdfbox/PdfboxExtract.scala

@@ -14,9 +14,7 @@ import fs2.Stream
 object PdfboxExtract {
 
   def get[F[_]: Sync](data: Stream[F, Byte]): F[Either[Throwable, String]] =
-    data.compile.to(Array).map { bytes =>
+    data.compile.to(Array).map(bytes => Using(PDDocument.load(bytes))(readText).toEither.flatten)
-      Using(PDDocument.load(bytes))(readText).toEither.flatten
-    }
 
   def get(is: InputStream): Either[Throwable, String] =
     Using(PDDocument.load(is))(readText).toEither.flatten

modules/extract/src/main/scala/docspell/extract/poi/PoiExtract.scala

@@ -52,25 +52,25 @@ object PoiExtract {
   def getDocx(is: InputStream): Either[Throwable, String] =
     Try {
       val xt = new XWPFWordExtractor(new XWPFDocument(is))
-      xt.getText.trim
+      Option(xt.getText).map(_.trim).getOrElse("")
     }.toEither
 
   def getDoc(is: InputStream): Either[Throwable, String] =
     Try {
       val xt = new WordExtractor(is)
-      xt.getText.trim
+      Option(xt.getText).map(_.trim).getOrElse("")
     }.toEither
 
   def getXlsx(is: InputStream): Either[Throwable, String] =
     Try {
       val xt = new XSSFExcelExtractor(new XSSFWorkbook(is))
-      xt.getText.trim
+      Option(xt.getText).map(_.trim).getOrElse("")
     }.toEither
 
   def getXls(is: InputStream): Either[Throwable, String] =
     Try {
       val xt = new ExcelExtractor(new HSSFWorkbook(is))
-      xt.getText.trim
+      Option(xt.getText).map(_.trim).getOrElse("")
     }.toEither
 
   def getDocx[F[_]: Sync](data: Stream[F, Byte]): F[Either[Throwable, String]] =

modules/extract/src/test/scala/docspell/extract/odf/OdfExtractTest.scala

@@ -14,7 +14,8 @@ object OdfExtractTest extends SimpleTestSuite {
   )
 
   test("test extract from odt") {
-    files.foreach { case (file, len) =>
+    files.foreach {
+      case (file, len) =>
         val is   = file.toJavaUrl.map(_.openStream()).fold(sys.error, identity)
         val str1 = OdfExtract.get(is).fold(throw _, identity)
         assertEquals(str1.length, len)

modules/files/src/main/scala/docspell/files/ImageSize.scala

@@ -29,12 +29,11 @@ object ImageSize {
   /** Return the image size from its header without reading
     * the whole image into memory.
     */
-  def get[F[_]: Sync](data: Stream[F, Byte]): F[Option[Dimension]] = {
+  def get[F[_]: Sync](data: Stream[F, Byte]): F[Option[Dimension]] =
-    data.take(768).compile.to(Array).map(ar => {
+    data.take(768).compile.to(Array).map { ar =>
       val iis = ImageIO.createImageInputStream(new ByteArrayInputStream(ar))
       if (iis == null) sys.error("no reader given for the array")
       else getDimension(iis)
-    })
     }
 
   private def getDimension(in: ImageInputStream): Option[Dimension] =

modules/files/src/main/scala/docspell/files/TikaMimetype.scala

@@ -52,8 +52,8 @@ object TikaMimetype {
   def detect[F[_]: Sync](file: Path): F[MimeType] =
     Sync[F].delay {
       val hint = MimeTypeHint.filename(file.getFileName.toString)
-      Using(new BufferedInputStream(Files.newInputStream(file), 64))({ in =>
+      Using(new BufferedInputStream(Files.newInputStream(file), 64)) { in =>
         convert(tika.detect(in, makeMetadata(hint)))
-      }).toEither
+      }.toEither
     }.rethrow
 }

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

@@ -10,5 +10,4 @@ trait ExampleFilesSupport {
       case None    => sys.error(s"Resource '$resource' not found")
     }
 
-
 }

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

@@ -8,15 +8,14 @@ import scala.concurrent.ExecutionContext
 object Playing extends IOApp {
   val blocker = Blocker.liftExecutionContext(ExecutionContext.global)
 
-
   def run(args: List[String]): IO[ExitCode] = IO {
     //val ods = ExampleFiles.examples_sample_ods.readURL[IO](8192, blocker)
     //val odt = ExampleFiles.examples_sample_odt.readURL[IO](8192, blocker)
     val rtf = ExampleFiles.examples_sample_rtf.readURL[IO](8192, blocker)
 
     val x = for {
-      odsm1 <- TikaMimetype.detect(rtf,
+      odsm1 <- TikaMimetype
-        MimeTypeHint.filename(ExampleFiles.examples_sample_rtf.path.segments.last))
+        .detect(rtf, MimeTypeHint.filename(ExampleFiles.examples_sample_rtf.path.segments.last))
       odsm2 <- TikaMimetype.detect(rtf, MimeTypeHint.none)
     } yield (odsm1, odsm2)
     println(x.unsafeRunSync())

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

@@ -68,7 +68,9 @@ object ConvertPdf {
             .through(ctx.store.bitpeace.fetchData2(RangeDef.all))
           val handler = conversionHandler[F](ctx, cfg, ra, item)
           ctx.logger.info(s"Converting file ${ra.name} (${mime.asString}) into a PDF") *>
-            conv.toPDF(DataType(MimeType(mime.primary, mime.sub)), ctx.args.meta.language, handler)(data)
+            conv.toPDF(DataType(MimeType(mime.primary, mime.sub)), ctx.args.meta.language, handler)(
+              data
+            )
       }
     }
 
@@ -119,7 +121,9 @@ object ConvertPdf {
       .compile
       .lastOrError
       .map(fm => Ident.unsafe(fm.id))
-      .flatMap(fmId => ctx.store.transact(RAttachment.updateFileIdAndName(ra.id, fmId, newName)).map(_ => fmId))
+      .flatMap(fmId =>
+        ctx.store.transact(RAttachment.updateFileIdAndName(ra.id, fmId, newName)).map(_ => fmId)
+      )
       .map(fmId => ra.copy(fileId = fmId, name = newName))
   }
 }

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

@@ -95,10 +95,10 @@ object FindProposal {
       labels => self.find(labels).map(f)
 
     def next(f: Finder[F])(implicit F: FlatMap[F], F3: Applicative[F]): Finder[F] =
-      flatMap({ ml0 =>
+      flatMap { ml0 =>
         if (ml0.hasResultsAll) Finder.unit[F](ml0)
         else f.map(ml1 => ml0.fillEmptyFrom(ml1))
-      })
+      }
 
     def nextWhenEmpty(f: Finder[F], mt0: MetaProposalType, mts: MetaProposalType*)(
         implicit F: FlatMap[F],

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

@@ -19,9 +19,7 @@ object ItemHandler {
       .map(_ => ())
 
   def itemStateTask[F[_]: Sync, A](state: ItemState)(data: ItemData): Task[F, A, ItemData] =
-    Task { ctx =>
+    Task(ctx => ctx.store.transact(RItem.updateState(data.item.id, state)).map(_ => data))
-      ctx.store.transact(RItem.updateState(data.item.id, state)).map(_ => data)
-    }
 
   def isLastRetry[F[_]: Sync, A](ctx: Context[F, A]): F[Boolean] =
     for {

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

@@ -11,9 +11,7 @@ object TestTasks {
   private[this] val logger = getLogger
 
   def success[F[_]]: Task[F, ProcessItemArgs, Unit] =
-    Task { ctx =>
+    Task(ctx => ctx.logger.info(s"Running task now: ${ctx.args}"))
-      ctx.logger.info(s"Running task now: ${ctx.args}")
-    }
 
   def failing[F[_]: Sync]: Task[F, ProcessItemArgs, Unit] =
     Task { ctx =>

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

@@ -76,16 +76,15 @@ object TextExtraction {
         .getOrElse(Mimetype.`application/octet-stream`)
 
     findMime
-        .flatMap(mt =>
+      .flatMap(mt => extr.extractText(data, DataType(MimeType(mt.primary, mt.sub)), lang))
-          extr.extractText(data, DataType(MimeType(mt.primary, mt.sub)), lang))
   }
 
   private def extractTextFallback[F[_]: Sync: ContextShift](
       ctx: Context[F, _],
       cfg: ExtractConfig,
       ra: RAttachment,
-                                                             lang: Language,
+      lang: Language
-  )(fileIds: List[Ident]): F[Option[String]] = {
+  )(fileIds: List[Ident]): F[Option[String]] =
     fileIds match {
       case Nil =>
         ctx.logger.error(s"Cannot extract text").map(_ => None)
@@ -99,15 +98,18 @@ object TextExtraction {
               txt.some.pure[F]
 
             case ExtractResult.UnsupportedFormat(mt) =>
-              ctx.logger.warn(s"Cannot extract text from file ${stripAttachmentName(ra)}: unsupported format ${mt.asString}. Try with converted file.").
+              ctx.logger
-                flatMap(_ => extractTextFallback[F](ctx, cfg, ra, lang)(rest))
+                .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))
 
             case ExtractResult.Failure(ex) =>
-              ctx.logger.warn(s"Cannot extract text: ${ex.getMessage}. Try with converted file").
+              ctx.logger
-                flatMap(_ => extractTextFallback[F](ctx, cfg, ra, lang)(rest))
+                .warn(s"Cannot extract text: ${ex.getMessage}. Try with converted file")
+                .flatMap(_ => extractTextFallback[F](ctx, cfg, ra, lang)(rest))
           })
     }
-  }
 
   /** Returns the fileIds to extract text from. First, the source file
     * is tried. If that fails, the converted file is tried.

modules/microsite/docs/doc/nix.md

@@ -128,6 +128,9 @@ Please see the `nix/module-server.nix` and `nix/module-joex.nix` files
 for the set of options. The nixos options are modelled after the
 default configuration file.
 
+The modules files are only applicable to the newest version of
+Docspell. If you really need an older version, checkout the
+appropriate commit.
 
 ## NixOs Example
 

modules/microsite/docs/features.md

@@ -9,7 +9,8 @@ title: Features and Limitations
 - Multiple users per account
 - Handle multiple documents as one unit
 - OCR using [tesseract](https://github.com/tesseract-ocr/tesseract)
-- Conversion to PDF: all files are converted into a PDF file
+- Conversion to PDF: all files are converted into a PDF file, while
+  the original file is preserved
 - Text is analysed to find and attach meta data automatically
 - Manage document processing (cancel jobs, set priorities)
 - Everything available via a documented [REST Api](api)

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

@@ -204,7 +204,8 @@ trait Conversions {
 
     val files = mp.parts
       .filter(p => p.name.forall(s => !s.equalsIgnoreCase("meta")))
-      .map(p => OUpload.File(p.filename, p.headers.get(`Content-Type`).map(fromContentType), p.body)
+      .map(p =>
+        OUpload.File(p.filename, p.headers.get(`Content-Type`).map(fromContentType), p.body)
       )
     for {
       metaData <- meta

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

@@ -55,10 +55,10 @@ object AttachmentRoutes {
           inm     = req.headers.get(`If-None-Match`).flatMap(_.tags)
           matches = matchETag(fileData.map(_.meta), inm)
           resp <- fileData
-                   .map({ data =>
+            .map { data =>
               if (matches) withResponseHeaders(NotModified())(data)
               else makeByteResp(data)
-                   })
+            }
             .getOrElse(NotFound(BasicResult(false, "Not found")))
         } yield resp
 
@@ -76,10 +76,10 @@ object AttachmentRoutes {
           inm     = req.headers.get(`If-None-Match`).flatMap(_.tags)
           matches = matchETag(fileData.map(_.meta), inm)
           resp <- fileData
-            .map({ data =>
+            .map { data =>
               if (matches) withResponseHeaders(NotModified())(data)
               else makeByteResp(data)
-            })
+            }
             .getOrElse(NotFound(BasicResult(false, "Not found")))
         } yield resp
 

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

@@ -14,10 +14,15 @@ object QAttachment {
 
   def deleteById[F[_]: Sync](store: Store[F])(attachId: Ident, coll: Ident): F[Int] =
     for {
-      raFile <- store.transact(RAttachment.findByIdAndCollective(attachId, coll)).map(_.map(_.fileId))
+      raFile <- store
-      rsFile <- store.transact(RAttachmentSource.findByIdAndCollective(attachId, coll)).map(_.map(_.fileId))
+        .transact(RAttachment.findByIdAndCollective(attachId, coll))
+        .map(_.map(_.fileId))
+      rsFile <- store
+        .transact(RAttachmentSource.findByIdAndCollective(attachId, coll))
+        .map(_.map(_.fileId))
       n <- store.transact(RAttachment.delete(attachId))
-      f <- Stream.emits(raFile.toSeq ++ rsFile.toSeq)
+      f <- Stream
+        .emits(raFile.toSeq ++ rsFile.toSeq)
         .map(_.id)
         .flatMap(store.bitpeace.delete)
         .map(flag => if (flag) 1 else 0)
@@ -29,10 +34,12 @@ object QAttachment {
     for {
       s <- store.transact(RAttachmentSource.findById(ra.id))
       n <- store.transact(RAttachment.delete(ra.id))
-      f <- Stream.emits(ra.fileId.id +: s.map(_.fileId.id).toSeq).
+      f <- Stream
-        flatMap(store.bitpeace.delete).
+        .emits(ra.fileId.id +: s.map(_.fileId.id).toSeq)
-        map(flag => if (flag) 1 else 0).
+        .flatMap(store.bitpeace.delete)
-        compile.foldMonoid
+        .map(flag => if (flag) 1 else 0)
+        .compile
+        .foldMonoid
     } yield n + f
 
   def deleteItemAttachments[F[_]: Sync](store: Store[F])(itemId: Ident, coll: Ident): F[Int] =

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

@@ -27,7 +27,6 @@ object QCollective {
       and(IC.cid.is(coll), IC.incoming.is(Direction.outgoing))
     ).query[Int].unique
 
-
     val fileSize = sql"""
       select sum(length) from (
       with attachs as
@@ -42,7 +41,6 @@ object QCollective {
          inner join filemeta m on m.id = a.file_id where a.id in (select aid from attachs)
       ) as t""".query[Option[Long]].unique
 
-
     val q3 = fr"SELECT" ++ commas(
       TC.name.prefix("t").f,
       fr"count(" ++ RC.itemId.prefix("r").f ++ fr")"

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

@@ -39,7 +39,8 @@ object QItem {
     val EC  = REquipment.Columns.all.map(_.prefix("e"))
     val ICC = List(RItem.Columns.id, RItem.Columns.name).map(_.prefix("ref"))
 
-    val cq = selectSimple(IC ++ OC ++ P0C ++ P1C ++ EC ++ ICC, RItem.table ++ fr"i", Fragment.empty) ++
+    val cq =
+      selectSimple(IC ++ OC ++ P0C ++ P1C ++ EC ++ ICC, RItem.table ++ fr"i", Fragment.empty) ++
         fr"LEFT JOIN" ++ ROrganization.table ++ fr"o ON" ++ RItem.Columns.corrOrg
         .prefix("i")
         .is(ROrganization.Columns.oid.prefix("o")) ++
@@ -235,7 +236,8 @@ object QItem {
   def findByFileIds(fileMetaIds: List[Ident]): ConnectionIO[Vector[RItem]] = {
     val IC = RItem.Columns
     val AC = RAttachment.Columns
-    val q = fr"SELECT DISTINCT" ++ commas(IC.all.map(_.prefix("i").f)) ++ fr"FROM" ++ RItem.table ++ fr"i" ++
+    val q =
+      fr"SELECT DISTINCT" ++ commas(IC.all.map(_.prefix("i").f)) ++ fr"FROM" ++ RItem.table ++ fr"i" ++
         fr"INNER JOIN" ++ RAttachment.table ++ fr"a ON" ++ AC.itemId
         .prefix("a")
         .is(IC.id.prefix("i")) ++

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

@@ -21,11 +21,11 @@ object QJob {
     Stream
       .range(0, 10)
       .evalMap(n => takeNextJob1(store)(priority, worker, retryPause, n))
-      .evalTap({ x =>
+      .evalTap { x =>
         if (x.isLeft)
           logger.fdebug[F]("Cannot mark job, probably due to concurrent updates. Will retry.")
         else ().pure[F]
-      })
+      }
       .find(_.isRight)
       .flatMap({
         case Right(job) =>
@@ -97,7 +97,8 @@ object QJob {
     val sql2 = fr"SELECT min(" ++ jgroup.f ++ fr") as g FROM" ++ RJob.table ++ fr"a" ++
       fr"WHERE" ++ stateCond
 
-    val union = sql"SELECT g FROM ((" ++ sql1 ++ sql") UNION ALL (" ++ sql2 ++ sql")) as t0 WHERE g is not null"
+    val union =
+      sql"SELECT g FROM ((" ++ sql1 ++ sql") UNION ALL (" ++ sql2 ++ sql")) as t0 WHERE g is not null"
 
     union
       .query[Ident]

modules/store/src/main/scala/docspell/store/queue/JobQueue.scala

@@ -34,11 +34,11 @@ object JobQueue {
       def insert(job: RJob): F[Unit] =
         store
           .transact(RJob.insert(job))
-          .flatMap({ n =>
+          .flatMap { n =>
             if (n != 1)
               Effect[F].raiseError(new Exception(s"Inserting job failed. Update count: $n"))
             else ().pure[F]
-          })
+          }
 
       def insertAll(jobs: Seq[RJob]): F[Unit] =
         jobs.toList

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

@@ -104,7 +104,8 @@ object RAttachment {
   def findByItemWithMeta(id: Ident): ConnectionIO[Vector[(RAttachment, FileMeta)]] = {
     import bitpeace.sql._
 
-    val q = fr"SELECT a.*,m.* FROM" ++ table ++ fr"a, filemeta m WHERE a.filemetaid = m.id AND a.itemid = $id ORDER BY a.position ASC"
+    val q =
+      fr"SELECT a.*,m.* FROM" ++ table ++ fr"a, filemeta m WHERE a.filemetaid = m.id AND a.itemid = $id ORDER BY a.position ASC"
     q.query[(RAttachment, FileMeta)].to[Vector]
   }
 

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

@@ -38,14 +38,16 @@ object RAttachmentSource {
   def insert(v: RAttachmentSource): ConnectionIO[Int] =
     insertRow(table, all, fr"${v.id},${v.fileId},${v.name},${v.created}").update.run
 
-
   def findById(attachId: Ident): ConnectionIO[Option[RAttachmentSource]] =
     selectSimple(all, table, id.is(attachId)).query[RAttachmentSource].option
 
   def delete(attachId: Ident): ConnectionIO[Int] =
     deleteFrom(table, id.is(attachId)).update.run
 
-  def findByIdAndCollective(attachId: Ident, collective: Ident): ConnectionIO[Option[RAttachmentSource]] = {
+  def findByIdAndCollective(
+      attachId: Ident,
+      collective: Ident
+  ): ConnectionIO[Option[RAttachmentSource]] = {
     val bId   = RAttachment.Columns.id.prefix("b")
     val aId   = Columns.id.prefix("a")
     val bItem = RAttachment.Columns.itemId.prefix("b")
@@ -77,8 +79,9 @@ object RAttachmentSource {
       RAttachment.table ++ fr"b ON" ++ aId.is(bId)
     val where = bItem.is(id)
 
-    (selectSimple(cols, from, where) ++ orderBy(bPos.asc)).
+    (selectSimple(cols, from, where) ++ orderBy(bPos.asc))
-      query[(RAttachmentSource, FileMeta)].to[Vector]
+      .query[(RAttachmentSource, FileMeta)]
+      .to[Vector]
   }
 
 }

modules/webapp/src/main/elm/Comp/ItemDetail.elm

@@ -407,6 +407,20 @@ update key flags next msg model =
                         )
                         m4
 
+                ( m6, c6 ) =
+                    update key
+                        flags
+                        next
+                        (ConcEquipMsg
+                            (Comp.Dropdown.SetSelection
+                                (item.concEquipment
+                                    |> Maybe.map List.singleton
+                                    |> Maybe.withDefault []
+                                )
+                            )
+                        )
+                        m5
+
                 proposalCmd =
                     if item.state == "created" then
                         Api.getItemProposals flags item.id GetProposalResp
@@ -414,7 +428,7 @@ update key flags next msg model =
                     else
                         Cmd.none
             in
-            ( { m5
+            ( { m6
                 | item = item
                 , nameModel = item.name
                 , notesModel = item.notes
@@ -428,6 +442,7 @@ update key flags next msg model =
                 , c3
                 , c4
                 , c5
+                , c6
                 , getOptions flags
                 , proposalCmd
                 , Api.getSentMails flags item.id SentMailsResp

project/Dependencies.scala

@@ -21,8 +21,8 @@ object Dependencies {
   val LogbackVersion = "1.2.3"
   val MariaDbVersion = "2.5.4"
   val MiniTestVersion = "2.7.0"
-  val PdfboxVersion = "2.0.18"
+  val PdfboxVersion = "2.0.19"
-  val PoiVersion = "4.1.2"
+  val PoiVersion = "4.1.1"
   val PostgresVersion = "42.2.10"
   val PureConfigVersion = "0.12.2"
   val Slf4jVersion = "1.7.30"

tools/ds.sh

@@ -15,6 +15,9 @@
 #   url.2=...
 #
 # Lines starting with a `#' are ignored.
+#
+# The `-e|--exists' option allows to skip uploading and only check
+# whether a given file exists in docspell.
 
 # saner programming env: these switches turn some bugs into errors
 set -o errexit -o pipefail -o noclobber -o nounset
@@ -30,8 +33,8 @@ if [[ ${PIPESTATUS[0]} -ne 4 ]]; then
     exit 1
 fi
 
-OPTIONS=c:hsd
+OPTIONS=c:hsde
-LONGOPTS=config:,help,skip,delete
+LONGOPTS=config:,help,skip,delete,exists
 
 ! PARSED=$(getopt --options=$OPTIONS --longoptions=$LONGOPTS --name "$0" -- "$@")
 if [[ ${PIPESTATUS[0]} -ne 0 ]]; then
@@ -43,7 +46,7 @@ fi
 # read getopt’s output this way to handle the quoting right:
 eval set -- "$PARSED"
 
-delete=n help=n config="${XDG_CONFIG_HOME:-$HOME/.config}/docspell/ds.conf"
+exists=n delete=n help=n config="${XDG_CONFIG_HOME:-$HOME/.config}/docspell/ds.conf"
 while true; do
     case "$1" in
         -h|--help)
@@ -58,6 +61,10 @@ while true; do
             delete="y"
             shift
             ;;
+        -e|--exists)
+            exists=y
+            shift
+            ;;
         --)
             shift
             break
@@ -121,9 +128,10 @@ showUsage() {
     info "  -c | --config        Provide a config file. (value: $config)"
     info "  -d | --delete        Delete the files when successfully uploaded (value: $delete)"
     info "  -h | --help          Prints this help text. (value: $help)"
+    info "  -e | --exists        Checks for the existence of a file instead of uploading (value: $exists)"
     info ""
     info "Arguments:"
-    info "  One or more PDF files to upload."
+    info "  One or more files to check for existence or upload."
     info ""
 }
 
@@ -153,6 +161,13 @@ done <<< $($GREP_CMD -v '^#.*' "$config")
 IFS=$'\n'
 for file in $*; do
     for url in "${urls[@]}"; do
+        if [ "$exists" = "y" ]; then
+            if checkFile "$url" "$file"; then
+                info "$url $file: true"
+            else
+                info "$url $file: false"
+            fi
+        else
             info "Uploading '$file' to '$url'"
             set +e
             upload "$file" "$url"
@@ -161,5 +176,6 @@ for file in $*; do
                 info "Deleting file: $file"
                 rm -f "$file"
             fi
+        fi
     done
 done