Feature/ybrowse integration

app/actions/AuthenticatedAction.scala

@@ -47,7 +47,7 @@ class AuthenticatedAction @Inject()(
  * Allows requiring specific roles on top of authentication.
  */
 class RoleAction @Inject()(authService: AuthService)(implicit ec: ExecutionContext) {
-  
+
   def apply(requiredRoles: String*): ActionFilter[AuthenticatedRequest] = new ActionFilter[AuthenticatedRequest] {
     override protected def executionContext: ExecutionContext = ec
 
@@ -59,3 +59,21 @@ class RoleAction @Inject()(authService: AuthService)(implicit ec: ExecutionConte
     }
   }
 }
+
+/**
+ * PermissionAction builder factory.
+ * Allows requiring specific permissions on top of authentication.
+ */
+class PermissionAction @Inject()(authService: AuthService)(implicit ec: ExecutionContext) {
+
+  def apply(permission: String): ActionFilter[AuthenticatedRequest] = new ActionFilter[AuthenticatedRequest] {
+    override protected def executionContext: ExecutionContext = ec
+
+    override protected def filter[A](request: AuthenticatedRequest[A]): Future[Option[Result]] = {
+      authService.hasPermission(request.user.id.get, permission).map { hasPermission =>
+        if (hasPermission) None
+        else Some(Results.Forbidden(s"Missing required permission: $permission"))
+      }
+    }
+  }
+}

app/actors/YBrowseVariantUpdateActor.scala

@@ -0,0 +1,122 @@
+package actors
+
+import config.GenomicsConfig
+import org.apache.pekko.actor.Actor
+import play.api.Logging
+import services.genomics.YBrowseVariantIngestionService
+
+import java.io.{BufferedInputStream, FileOutputStream}
+import java.net.{HttpURLConnection, URI}
+import java.nio.file.Files
+import scala.concurrent.{ExecutionContext, Future}
+import scala.util.{Failure, Success, Try}
+
+object YBrowseVariantUpdateActor {
+  case object RunUpdate
+  case class UpdateResult(success: Boolean, variantsIngested: Int, message: String)
+}
+
+/**
+ * Actor responsible for downloading and ingesting Y-DNA SNP data from YBrowse.
+ *
+ * This actor:
+ * 1. Downloads the VCF file from ybrowse.org
+ * 2. Stores it at the configured local path
+ * 3. Triggers variant ingestion via YBrowseVariantIngestionService
+ */
+class YBrowseVariantUpdateActor @javax.inject.Inject()(
+  genomicsConfig: GenomicsConfig,
+  ingestionService: YBrowseVariantIngestionService
+)(implicit ec: ExecutionContext) extends Actor with Logging {
+
+  import YBrowseVariantUpdateActor.*
+
+  override def receive: Receive = {
+    case RunUpdate =>
+      logger.info("YBrowseVariantUpdateActor: Starting YBrowse variant update")
+      val senderRef = sender()
+
+      runUpdate().onComplete {
+        case Success(result) =>
+          logger.info(s"YBrowseVariantUpdateActor: Update completed - ${result.message}")
+          senderRef ! result
+        case Failure(ex) =>
+          logger.error(s"YBrowseVariantUpdateActor: Update failed - ${ex.getMessage}", ex)
+          senderRef ! UpdateResult(success = false, variantsIngested = 0, s"Update failed: ${ex.getMessage}")
+      }
+  }
+
+  private def runUpdate(): Future[UpdateResult] = {
+    Future {
+      downloadVcfFile()
+    }.flatMap {
+      case Success(_) =>
+        logger.info("VCF file downloaded successfully, starting ingestion")
+        ingestionService.ingestVcf(genomicsConfig.ybrowseVcfStoragePath).map { count =>
+          UpdateResult(success = true, variantsIngested = count, s"Successfully ingested $count variants")
+        }
+      case Failure(ex) =>
+        Future.successful(UpdateResult(success = false, variantsIngested = 0, s"Download failed: ${ex.getMessage}"))
+    }
+  }
+
+  private def downloadVcfFile(): Try[Unit] = Try {
+    val url = URI.create(genomicsConfig.ybrowseVcfUrl).toURL
+    val targetFile = genomicsConfig.ybrowseVcfStoragePath
+
+    // Ensure parent directory exists
+    val parentDir = targetFile.getParentFile
+    if (parentDir != null && !parentDir.exists()) {
+      Files.createDirectories(parentDir.toPath)
+      logger.info(s"Created directory: ${parentDir.getAbsolutePath}")
+    }
+
+    // Download to a temp file first, then rename (atomic operation)
+    val tempFile = new java.io.File(targetFile.getAbsolutePath + ".tmp")
+
+    logger.info(s"Downloading VCF from ${genomicsConfig.ybrowseVcfUrl} to ${tempFile.getAbsolutePath}")
+
+    val connection = url.openConnection().asInstanceOf[HttpURLConnection]
+    connection.setRequestMethod("GET")
+    connection.setConnectTimeout(30000) // 30 seconds
+    connection.setReadTimeout(300000)   // 5 minutes for large file
+
+    try {
+      val responseCode = connection.getResponseCode
+      if (responseCode != HttpURLConnection.HTTP_OK) {
+        throw new RuntimeException(s"HTTP request failed with status $responseCode")
+      }
+
+      val inputStream = new BufferedInputStream(connection.getInputStream)
+      val outputStream = new FileOutputStream(tempFile)
+
+      try {
+        val buffer = new Array[Byte](8192)
+        var bytesRead = 0
+        var totalBytes = 0L
+
+        while ({ bytesRead = inputStream.read(buffer); bytesRead != -1 }) {
+          outputStream.write(buffer, 0, bytesRead)
+          totalBytes += bytesRead
+        }
+
+        logger.info(s"Downloaded $totalBytes bytes")
+      } finally {
+        inputStream.close()
+        outputStream.close()
+      }
+
+      // Atomic rename
+      if (targetFile.exists()) {
+        targetFile.delete()
+      }
+      if (!tempFile.renameTo(targetFile)) {
+        throw new RuntimeException(s"Failed to rename temp file to ${targetFile.getAbsolutePath}")
+      }
+
+      logger.info(s"VCF file saved to ${targetFile.getAbsolutePath}")
+    } finally {
+      connection.disconnect()
+    }
+  }
+}

app/config/FeatureFlags.scala

@@ -0,0 +1,20 @@
+package config
+
+import jakarta.inject.{Inject, Singleton}
+import play.api.Configuration
+
+/**
+ * Configuration wrapper for feature flags.
+ * Allows features to be enabled/disabled via application.conf.
+ */
+@Singleton
+class FeatureFlags @Inject()(config: Configuration) {
+
+  private val featuresConfig = config.getOptional[Configuration]("features").getOrElse(Configuration.empty)
+
+  /**
+   * Show branch age estimates (Formed/TMRCA dates) on tree nodes.
+   * Disabled by default until age data is populated.
+   */
+  val showBranchAgeEstimates: Boolean = featuresConfig.getOptional[Boolean]("tree.showBranchAgeEstimates").getOrElse(false)
+}

app/config/GenomicsConfig.scala

@@ -0,0 +1,49 @@
+package config
+
+import jakarta.inject.{Inject, Singleton}
+import play.api.Configuration
+
+import java.io.File
+
+/**
+ * Configuration wrapper for genomics-related settings.
+ */
+@Singleton
+class GenomicsConfig @Inject()(config: Configuration) {
+
+  private val genomicsConfig = config.get[Configuration]("genomics")
+
+  val supportedReferences: Seq[String] = genomicsConfig.get[Seq[String]]("references.supported")
+
+  val referenceAliases: Map[String, String] = genomicsConfig.getOptional[Map[String, String]]("references.aliases").getOrElse(Map.empty)
+
+  val fastaPaths: Map[String, File] = genomicsConfig.get[Map[String, String]]("references.fasta_paths").map {
+    case (genome, path) => genome -> new File(path)
+  }
+
+  // YBrowse configuration
+  val ybrowseVcfUrl: String = genomicsConfig.get[String]("ybrowse.vcf_url")
+  val ybrowseVcfStoragePath: File = new File(genomicsConfig.get[String]("ybrowse.vcf_storage_path"))
+
+  /**
+   * Retrieves the path to a liftover chain file for a given source and target genome.
+   *
+   * @param source The source reference genome (e.g., "GRCh38").
+   * @param target The target reference genome (e.g., "GRCh37").
+   * @return An Option containing the File if the chain is configured and exists, otherwise None.
+   */
+  def getLiftoverChainFile(source: String, target: String): Option[File] = {
+    val key = s"$source->$target"
+    genomicsConfig.getOptional[String](s"liftover.chains.\"$key\"").map(new File(_))
+  }
+
+  /**
+   * Resolves a genome name to its canonical form using the aliases configuration.
+   *
+   * @param name The input genome name.
+   * @return The canonical name if an alias exists, otherwise the input name.
+   */
+  def resolveReferenceName(name: String): String = {
+    referenceAliases.getOrElse(name, name)
+  }
+}