Stricter Checks on Paths in DataSources

conf/messages

@@ -127,6 +127,8 @@ dataVault.setup.failed=Failed to set up remote file system
 dataVault.getPath.failed=Failed to get remote path
 
 dataSource.notFound=Datasource not found on datastore server. Might still be initializing.
+dataSource.add.pathsNotAllowed=Cannot directly add a datasource with local paths that leave the dataset, or with paths that match the WEBKNOSSOS reserved paths.
+dataSource.update.newExplicitPaths=Cannot update a dataset with new explicit paths. To add mags or layers, please use the compose functionality.
 
 dataStore.list.failed=Failed to retrieve list of data stores.
 dataStore.notFound=DataStore not found.

test/e2e/End2EndSpec.scala

@@ -10,7 +10,7 @@ import play.api.libs.ws.{WSClient, WSResponse}
 import play.api.test.WithServer
 
 import java.io.File
-import java.nio.file.Paths
+import java.nio.file.Path
 import scala.concurrent.Await
 import scala.concurrent.duration._
 import scala.sys.process._
@@ -64,7 +64,7 @@ class End2EndSpec(arguments: Arguments) extends Specification with GuiceFakeAppl
     if (!dataDirectory.listFiles().exists(_.getName == "test-dataset"))
       ZipIO.unzipToDirectory(
         testDatasetZip,
-        Paths.get(dataDirectory.toPath.toString, "test-dataset"),
+        Path.of(dataDirectory.toPath.toString, "test-dataset"),
         includeHiddenFiles = true,
         hiddenFilesWhitelist = List(),
         truncateCommonPrefix = true,

util/src/main/scala/com/scalableminds/util/io/PathUtils.scala

@@ -1,7 +1,7 @@
 package com.scalableminds.util.io
 
 import java.io.File
-import java.nio.file.{Path, _}
+import java.nio.file._
 import com.typesafe.scalalogging.LazyLogging
 import com.scalableminds.util.tools.Box.tryo
 import com.scalableminds.util.tools.{Box, Failure, Full}
@@ -42,7 +42,7 @@ trait PathUtils extends LazyLogging {
     val elements = p1.iterator.asScala.zip(p2.iterator.asScala).takeWhile(Function.tupled(_ == _)).map(_._1)
     val joined = elements.mkString("/")
     val absoluteIfNeeded = if (p1.startsWith("/")) f"/$joined" else joined
-    Paths.get(absoluteIfNeeded)
+    Path.of(absoluteIfNeeded)
   }
 
   def commonPrefix(ps: List[Path]): Path =
@@ -162,14 +162,14 @@ trait PathUtils extends LazyLogging {
     lastCutOffIndex match {
       case -1 => path
       // subpath(0, 0) is forbidden, therefore we handle this special case ourselves
-      case 0 => Paths.get("")
+      case 0 => Path.of("")
       case i => path.subpath(0, i)
     }
   }
 
   // Remove a single file name from previously computed common prefix
   def removeSingleFileNameFromPrefix(prefix: Path, fileNames: List[String]): Path = {
-    def isFileNameInPrefix(prefix: Path, fileName: String) = prefix.endsWith(Paths.get(fileName).getFileName)
+    def isFileNameInPrefix(prefix: Path, fileName: String) = prefix.endsWith(Path.of(fileName).getFileName)
 
     fileNames match {
       case head :: tail if tail.isEmpty && isFileNameInPrefix(prefix, head) =>
@@ -180,7 +180,7 @@ trait PathUtils extends LazyLogging {
 
   private def removeOneName(path: Path): Path =
     if (path.getNameCount == 1) {
-      Paths.get("")
+      Path.of("")
     } else path.getParent
 
   def deleteDirectoryRecursively(path: Path): Box[Unit] = {

util/src/main/scala/com/scalableminds/util/io/ZipIO.scala

@@ -1,7 +1,7 @@
 package com.scalableminds.util.io
 
 import java.io._
-import java.nio.file.{Files, Path, Paths}
+import java.nio.file.{Files, Path}
 import java.util.zip.{GZIPOutputStream => DefaultGZIPOutputStream, _}
 import com.scalableminds.util.tools.{Fox, FoxImplicits, TextUtils}
 import com.typesafe.scalalogging.LazyLogging
@@ -178,23 +178,23 @@ object ZipIO extends LazyLogging with FoxImplicits {
 
     val zipEntries = zip.entries.asScala.filter { e: ZipEntry =>
       !e.isDirectory && (includeHiddenFiles || !isFileHidden(e) || hiddenFilesWhitelist.contains(
-        Paths.get(e.getName).getFileName.toString))
+        Path.of(e.getName).getFileName.toString))
     }.toList
 
     val commonPrefix = if (truncateCommonPrefix) {
-      val commonPrefixNotFixed = PathUtils.commonPrefix(zipEntries.map(e => Paths.get(e.getName)))
+      val commonPrefixNotFixed = PathUtils.commonPrefix(zipEntries.map(e => Path.of(e.getName)))
       val strippedPrefix =
         PathUtils.cutOffPathAtLastOccurrenceOf(commonPrefixNotFixed, excludeFromPrefix.getOrElse(List.empty))
       PathUtils.removeSingleFileNameFromPrefix(strippedPrefix, zipEntries.map(_.getName))
     } else {
-      Paths.get("")
+      Path.of("")
     }
 
     val resultFox = zipEntries.foldLeft[Fox[List[A]]](Fox.successful(List.empty)) { (results, entry) =>
       results.shiftBox.map {
         case Full(rs) =>
           val input: InputStream = zip.getInputStream(entry)
-          val path = commonPrefix.relativize(Paths.get(entry.getName))
+          val path = commonPrefix.relativize(Path.of(entry.getName))
           val innerResultFox: Fox[List[A]] = Fox.fromFutureBox(f(path, input).futureBox.map {
             case Full(result) =>
               input.close()
@@ -230,16 +230,16 @@ object ZipIO extends LazyLogging with FoxImplicits {
 
     val zipEntries = zip.entries.asScala.filter { e: ZipEntry =>
       !e.isDirectory && (includeHiddenFiles || !isFileHidden(e) || hiddenFilesWhitelist.contains(
-        Paths.get(e.getName).getFileName.toString))
+        Path.of(e.getName).getFileName.toString))
     }.toList
 
     val commonPrefix = if (truncateCommonPrefix) {
-      val commonPrefixNotFixed = PathUtils.commonPrefix(zipEntries.map(e => Paths.get(e.getName)))
+      val commonPrefixNotFixed = PathUtils.commonPrefix(zipEntries.map(e => Path.of(e.getName)))
       val strippedPrefix =
         PathUtils.cutOffPathAtLastOccurrenceOf(commonPrefixNotFixed, excludeFromPrefix.getOrElse(List.empty))
       PathUtils.removeSingleFileNameFromPrefix(strippedPrefix, zipEntries.map(_.getName))
     } else {
-      Paths.get("")
+      Path.of("")
     }
 
     val result = zipEntries.foldLeft[Box[List[A]]](Full(Nil)) { (results, entry) =>
@@ -248,7 +248,7 @@ object ZipIO extends LazyLogging with FoxImplicits {
           var input: InputStream = null
           try {
             input = zip.getInputStream(entry)
-            val path = commonPrefix.relativize(Paths.get(entry.getName))
+            val path = commonPrefix.relativize(Path.of(entry.getName))
             val r = f(path, input) match {
               case Full(result) =>
                 Full(rs :+ result)

webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala

@@ -22,7 +22,7 @@ import com.scalableminds.webknossos.datastore.services._
 import com.scalableminds.webknossos.datastore.services.mesh.{MeshFileService, MeshMappingHelper}
 import com.scalableminds.webknossos.datastore.services.segmentindex.SegmentIndexFileService
 import com.scalableminds.webknossos.datastore.services.uploading._
-import com.scalableminds.webknossos.datastore.storage.DataVaultService
+import com.scalableminds.webknossos.datastore.storage.{DataVaultService, RemoteSourceDescriptorService}
 import com.scalableminds.util.tools.Box.tryo
 import com.scalableminds.util.tools.{Box, Empty, Failure, Full}
 import com.scalableminds.webknossos.datastore.services.connectome.{
@@ -56,6 +56,7 @@ class DataSourceController @Inject()(
     agglomerateService: AgglomerateService,
     storageUsageService: DSUsedStorageService,
     datasetErrorLoggingService: DSDatasetErrorLoggingService,
+    remoteSourceDescriptorService: RemoteSourceDescriptorService,
     exploreRemoteLayerService: ExploreRemoteLayerService,
     uploadService: UploadService,
     composeService: ComposeService,
@@ -385,7 +386,9 @@ class DataSourceController @Inject()(
         for {
           dataSource <- dataSourceRepository.get(DataSourceId(datasetDirectoryName, organizationId)).toFox ?~> Messages(
             "dataSource.notFound") ~> NOT_FOUND
-          _ <- dataSourceService.updateDataSource(request.body.copy(id = dataSource.id), expectExisting = true)
+          _ <- dataSourceService.updateDataSource(request.body.copy(id = dataSource.id),
+                                                  expectExisting = true,
+                                                  preventNewPaths = true)
         } yield Ok
       }
     }
@@ -395,6 +398,9 @@ class DataSourceController @Inject()(
     Action.async(validateJson[DataSource]) { implicit request =>
       accessTokenService.validateAccessFromTokenContext(UserAccessRequest.administrateDataSources) {
         for {
+          _ <- Fox.fromBool(
+            request.body.allExplicitPaths
+              .forall(remoteSourceDescriptorService.pathIsAllowedToAddDirectly)) ?~> "dataSource.add.pathsNotAllowed"
           reservedAdditionalInfo <- dsRemoteWebknossosClient.reserveDataSourceUpload(
             ReserveUploadInformation(
               uploadId = "", // Set by core backend
@@ -410,7 +416,9 @@ class DataSourceController @Inject()(
             )
           ) ?~> "dataset.upload.validation.failed"
           datasourceId = DataSourceId(reservedAdditionalInfo.directoryName, organizationId)
-          _ <- dataSourceService.updateDataSource(request.body.copy(id = datasourceId), expectExisting = false)
+          _ <- dataSourceService.updateDataSource(request.body.copy(id = datasourceId),
+                                                  expectExisting = false,
+                                                  preventNewPaths = false)
           uploadedDatasetId <- dsRemoteWebknossosClient.reportUpload(datasourceId,
                                                                      0L,
                                                                      needsConversion = false,

webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/ExportsController.scala

@@ -1,6 +1,6 @@
 package com.scalableminds.webknossos.datastore.controllers
 
-import java.nio.file.{Files, Path, Paths}
+import java.nio.file.{Files, Path}
 import com.google.inject.Inject
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.scalableminds.webknossos.datastore.DataStoreConfig
@@ -30,7 +30,7 @@ class ExportsController @Inject()(webknossosClient: DSRemoteWebknossosClient,
     extends Controller
     with FoxImplicits {
 
-  private val dataBaseDir: Path = Paths.get(config.Datastore.baseDirectory)
+  private val dataBaseDir: Path = Path.of(config.Datastore.baseDirectory)
 
   override def allowRemoteOrigin: Boolean = true
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/datavault/FileSystemDataVault.scala

@@ -8,7 +8,7 @@ import org.apache.commons.lang3.builder.HashCodeBuilder
 
 import java.nio.ByteBuffer
 import java.nio.channels.{AsynchronousFileChannel, CompletionHandler}
-import java.nio.file.{Files, Path, Paths, StandardOpenOption}
+import java.nio.file.{Files, Path, StandardOpenOption}
 import java.util.stream.Collectors
 import scala.concurrent.{ExecutionContext, Promise}
 import scala.jdk.CollectionConverters._
@@ -96,7 +96,7 @@ class FileSystemDataVault extends DataVault {
     for {
       _ <- Fox.fromBool(uri.getScheme == null || uri.getScheme == DataVaultService.schemeFile) ?~> "trying to read from FileSystemDataVault, but uri scheme is not file or null"
       _ <- Fox.fromBool(uri.getHost == null || uri.getHost.isEmpty) ?~> s"trying to read from FileSystemDataVault, but hostname ${uri.getHost} is non-empty"
-      localPath = Paths.get(uri.getPath)
+      localPath = Path.of(uri.getPath)
       _ <- Fox.fromBool(localPath.isAbsolute) ?~> "trying to read from FileSystemDataVault, but hostname is non-empty"
     } yield localPath
   }

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataLayer.scala

@@ -275,6 +275,9 @@ trait DataLayerLike {
     case _                                => None
   }
 
+  def allExplicitPaths: Seq[String] =
+    magsOpt.map(_.flatMap(_.path)).orElse(wkwResolutionsOpt.map(_.flatMap(_.path))).getOrElse(Seq.empty) ++
+      attachments.map(_.allAttachments.map(_.path.toString)).getOrElse(Seq.empty)
 }
 
 object DataLayerLike {

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/datasource/DataSource.scala

@@ -65,6 +65,7 @@ package object datasource {
 
     def withUpdatedId(newId: DataSourceId): GenericDataSource[T] = copy(id = newId)
 
+    def allExplicitPaths: Seq[String] = dataLayers.flatMap(_.allExplicitPaths)
   }
 
   object GenericDataSource {

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataServiceHolder.scala

@@ -1,6 +1,6 @@
 package com.scalableminds.webknossos.datastore.services
 
-import java.nio.file.Paths
+import java.nio.file.Path
 import com.scalableminds.webknossos.datastore.DataStoreConfig
 import com.scalableminds.webknossos.datastore.services.mapping.AgglomerateService
 import com.scalableminds.webknossos.datastore.storage.RemoteSourceDescriptorService
@@ -23,7 +23,7 @@ class BinaryDataServiceHolder @Inject()(config: DataStoreConfig,
                                         agglomerateService: AgglomerateService)(implicit ec: ExecutionContext) {
 
   val binaryDataService: BinaryDataService = new BinaryDataService(
-    Paths.get(config.Datastore.baseDirectory),
+    Path.of(config.Datastore.baseDirectory),
     Some(agglomerateService),
     Some(remoteSourceDescriptorService),
     Some(chunkCacheService.sharedChunkContentsCache),

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DSUsedStorageService.scala

@@ -10,7 +10,7 @@ import com.scalableminds.util.tools.Box.tryo
 import org.apache.commons.io.FileUtils
 import play.api.libs.json.{Json, OFormat}
 
-import java.nio.file.{Files, Path, Paths}
+import java.nio.file.{Files, Path}
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 
@@ -30,7 +30,7 @@ class DSUsedStorageService @Inject()(config: DataStoreConfig)(implicit ec: Execu
     extends FoxImplicits
     with LazyLogging {
 
-  private val baseDir: Path = Paths.get(config.Datastore.baseDirectory)
+  private val baseDir: Path = Path.of(config.Datastore.baseDirectory)
 
   private def noSymlinksFilter(p: Path) = !Files.isSymbolicLink(p)
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataSourceService.scala

@@ -22,7 +22,7 @@ import play.api.libs.json.Json
 
 import java.io.{File, FileWriter}
 import java.net.URI
-import java.nio.file.{Files, Path, Paths}
+import java.nio.file.{Files, Path}
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 import scala.io.Source
@@ -46,10 +46,10 @@ class DataSourceService @Inject()(
 
   override protected def tickerInitialDelay: FiniteDuration = config.Datastore.WatchFileSystem.initialDelay
 
-  val dataBaseDir: Path = Paths.get(config.Datastore.baseDirectory)
+  val dataBaseDir: Path = Path.of(config.Datastore.baseDirectory)
 
-  private val propertiesFileName = Paths.get(GenericDataSource.FILENAME_DATASOURCE_PROPERTIES_JSON)
-  private val logFileName = Paths.get("datasource-properties-backups.log")
+  private val propertiesFileName = Path.of(GenericDataSource.FILENAME_DATASOURCE_PROPERTIES_JSON)
+  private val logFileName = Path.of("datasource-properties-backups.log")
 
   private var inboxCheckVerboseCounter = 0
 
@@ -138,7 +138,7 @@ class DataSourceService @Inject()(
     if (isRemote) {
       MagPathInfo(dataLayer.name, mag.mag, magURI.toString, magURI.toString, hasLocalData = false)
     } else {
-      val magPath = Paths.get(magURI)
+      val magPath = Path.of(magURI)
       val realPath = magPath.toRealPath()
       // Does this dataset have local data, i.e. the data that is referenced by the mag path is within the dataset directory
       val isLocal = realPath.startsWith(datasetPath.toAbsolutePath)
@@ -269,20 +269,38 @@ class DataSourceService @Inject()(
     }
   }
 
-  def updateDataSource(dataSource: DataSource, expectExisting: Boolean): Fox[Unit] = {
+  def updateDataSource(dataSource: DataSource, expectExisting: Boolean, preventNewPaths: Boolean): Fox[Unit] = {
     val organizationDir = dataBaseDir.resolve(dataSource.id.organizationId)
     val dataSourcePath = organizationDir.resolve(dataSource.id.directoryName)
     for {
       _ <- validateDataSource(dataSource, organizationDir).toFox
       propertiesFile = dataSourcePath.resolve(propertiesFileName)
       _ <- Fox.runIf(!expectExisting)(ensureDirectoryBox(dataSourcePath).toFox)
       _ <- Fox.runIf(!expectExisting)(Fox.fromBool(!Files.exists(propertiesFile))) ?~> "dataSource.alreadyPresent"
+      _ <- Fox.runIf(expectExisting && preventNewPaths)(assertNoNewPaths(dataSourcePath, dataSource)) ?~> "dataSource.update.newExplicitPaths"
       _ <- Fox.runIf(expectExisting)(backupPreviousProperties(dataSourcePath).toFox) ?~> "Could not update datasource-properties.json"
       _ <- JsonHelper.writeToFile(propertiesFile, dataSource).toFox ?~> "Could not update datasource-properties.json"
       _ <- dataSourceRepository.updateDataSource(dataSource)
     } yield ()
   }
 
+  private def assertNoNewPaths(dataSourcePath: Path, newDataSource: DataSource): Fox[Unit] = {
+    val propertiesPath = dataSourcePath.resolve(propertiesFileName)
+    if (Files.exists(propertiesPath)) {
+      Fox
+        .runOptional(newDataSource.toUsable) { newUsableDataSource =>
+          Fox.runOptional(dataSourceFromDir(dataSourcePath, newDataSource.id.organizationId).toUsable) {
+            oldUsableDataSource =>
+              val oldPaths = oldUsableDataSource.allExplicitPaths.toSet
+              Fox.fromBool(newUsableDataSource.allExplicitPaths.forall(oldPaths.contains))
+          }
+        }
+        .map(_ => ())
+    } else {
+      Fox.successful(())
+    }
+  }
+
   private def backupPreviousProperties(dataSourcePath: Path): Box[Unit] = {
     val propertiesFile = dataSourcePath.resolve(propertiesFileName)
     val previousContentOrEmpty = if (Files.exists(propertiesFile)) {

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/connectome/ConnectomeFileService.scala

@@ -19,7 +19,7 @@ import org.apache.commons.io.FilenameUtils
 import play.api.i18n.{Messages, MessagesProvider}
 import play.api.libs.json.{Json, OFormat}
 
-import java.nio.file.Paths
+import java.nio.file.Path
 import javax.inject.Inject
 import scala.collection.mutable.ListBuffer
 import scala.concurrent.ExecutionContext
@@ -89,7 +89,7 @@ class ConnectomeFileService @Inject()(config: DataStoreConfig,
     extends FoxImplicits
     with LazyLogging {
 
-  private val dataBaseDir = Paths.get(config.Datastore.baseDirectory)
+  private val dataBaseDir = Path.of(config.Datastore.baseDirectory)
   private val localConnectomesDir = "connectomes"
   private val hdf5ConnectomeFileExtension = "hdf5"
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/connectome/Hdf5ConnectomeFileService.scala

@@ -8,13 +8,13 @@ import com.scalableminds.webknossos.datastore.services.connectome.SynapticPartne
 import com.scalableminds.webknossos.datastore.storage.{CachedHdf5File, Hdf5FileCache}
 import com.scalableminds.webknossos.datastore.DataStoreConfig
 
-import java.nio.file.Paths
+import java.nio.file.Path
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 
 class Hdf5ConnectomeFileService @Inject()(config: DataStoreConfig) extends FoxImplicits with ConnectomeFileUtils {
 
-  private val dataBaseDir = Paths.get(config.Datastore.baseDirectory)
+  private val dataBaseDir = Path.of(config.Datastore.baseDirectory)
 
   private lazy val fileHandleCache = new Hdf5FileCache(30)
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/mapping/AgglomerateService.scala

@@ -21,7 +21,7 @@ import com.scalableminds.webknossos.datastore.storage.{AgglomerateFileKey, Remot
 import com.typesafe.scalalogging.LazyLogging
 import org.apache.commons.io.FilenameUtils
 
-import java.nio.file.Paths
+import java.nio.file.Path
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration.DurationInt
@@ -34,7 +34,7 @@ class AgglomerateService @Inject()(config: DataStoreConfig,
     with FoxImplicits {
   private val localAgglomeratesDir = "agglomerates"
   private val hdf5AgglomerateFileExtension = "hdf5"
-  private val dataBaseDir = Paths.get(config.Datastore.baseDirectory)
+  private val dataBaseDir = Path.of(config.Datastore.baseDirectory)
 
   private val agglomerateFileKeyCache
     : AlfuCache[(DataSourceId, String, String), AgglomerateFileKey] = AlfuCache() // dataSourceId, layerName, mappingName → AgglomerateFileKey