Support Fiji update processing

src/main/scala/ij_plugins/imagej_launcher/Launcher.scala

@@ -17,7 +17,7 @@ class Launcher(logger: Logger):
   private val jarsDirName = "jars"
 
   def run(config: Config): Unit =
-    createCommandLine(config) match
+    prepareLaunch(config) match
       case Right(commandLine) =>
         if config.dryRun then
           logger.debug("dry-run")
@@ -27,9 +27,10 @@ class Launcher(logger: Logger):
       case Left(errorMessage) =>
         logger.error(errorMessage)
 
-  private def createCommandLine(config: Config): Either[String, Seq[String]] =
+  private def prepareLaunch(config: Config): Either[String, Seq[String]] =
     for
       ijDir       <- locateIJDir(config)
+      _           <- Updater.update(Path(ijDir), config.dryRun, logger)
       launcherJar <- findImageJLauncherJar(ijDir)
       javaExe     <- locateJavaExecutable(config, ijDir)
       systemType  <- determineSystemType()

src/main/scala/ij_plugins/imagej_launcher/Main.scala

@@ -58,10 +58,6 @@ object Main:
           .action((path, c) => c.copy(javaHome = Option(path)))
           .text("specify JAVA_HOME explicitly"),
         //
-        opt[Unit]("print-java-home")
-          .action((_, c) => c.copy(dryRun = true))
-          .text("print ImageJ's idea of JAVA_HOME"),
-        //
         opt[File]("ij-dir")
           .valueName("<path>")
           .action((path, c) => c.copy(ijDir = Option(path)))

src/main/scala/ij_plugins/imagej_launcher/Updater.scala

@@ -0,0 +1,60 @@
+package ij_plugins.imagej_launcher
+
+import os.Path
+
+import scala.util.control.NonFatal
+
+object Updater:
+
+  /**
+   * Perform update using files in `update` subdirectory, if it exists.
+   * @param ijDir imagej
+   * @param dryRun locate files to process but do not make any changes, but count the files that would be processed
+   * @param logger configured logger
+   * @return Number of files processed or an error message.
+   */
+  def update(ijDir: Path, dryRun: Boolean, logger: Logger): Either[String, Long] =
+    try
+      val updateDir = ijDir / "update"
+      // Count used only for debug info
+      var count     = 0
+      if os.exists(updateDir) then
+        logger.info("Performing update..")
+        os.walk(updateDir)
+          .filter(os.isFile)
+          .foreach { src =>
+            val dst = ijDir / src.relativeTo(updateDir)
+            if os.size(src) == 0 then
+              logger.debug(s"remove: $dst")
+              if !dryRun then os.remove(dst)
+              logger.debug(s"remove: $src")
+              if !dryRun then os.remove(src)
+            else
+              logger.debug(s"move  : $src -> $dst")
+              if !dryRun then os.move(src, dst, replaceExisting = true, createFolders = true)
+            count += 1
+          }
+        logger.debug(s"Delete update directory: $updateDir")
+        if !dryRun then deleteEmptyDirs(updateDir, logger)
+        Right(count)
+      else
+        logger.info("No update found")
+        Right(count)
+    catch
+      case NonFatal(ex) =>
+        ex.printStackTrace()
+        Left(s"Failed to perform update: ${ex.getMessage} - ${ex.getClass.getSimpleName}")
+
+  private def deleteEmptyDirs(dir: Path, logger: Logger): Unit =
+    logger.debug(s"Cleaning directory: $dir")
+    os.list(dir)
+      .filter(os.isDir)
+      .foreach(p => deleteEmptyDirs(p, logger))
+
+    if os.list(dir).isEmpty then
+      logger.debug(s"Removing empty dir: $dir")
+      os.remove(dir)
+    else
+      logger.debug(s"Cannot delete directory, not empty: $dir")
+
+end Updater

src/test/scala/ij_plugins/imagej_launcher/UpdaterDemo.scala

@@ -0,0 +1,9 @@
+package ij_plugins.imagej_launcher
+
+import os.Path
+
+@main
+def updaterDemo(ijDir: String): Unit =
+  Updater.update(Path(ijDir), dryRun = false, new Logger(Logger.Level.Debug)) match
+    case Right(count) => println(s"Processed $count files")
+    case Left(error)  => println(s"Failed with error: $error")