script to list all groups and dataset within n5 container

n5-tree.kts

#!/usr/bin/env kscript

@file:MavenRepository("imagej.public", "https://maven.imagej.net/content/groups/public")
@file:DependsOn("org.janelia.saalfeldlab:n5:2.1.0")
@file:DependsOn("info.picocli:picocli:4.2.0")
@file:DependsOn("ch.qos.logback:logback-classic:1.3.0-alpha5")

import java.util.concurrent.Callable

import org.janelia.saalfeldlab.n5.N5FSReader

import picocli.CommandLine
import picocli.CommandLine.Command
import picocli.CommandLine.Option
import picocli.CommandLine.Parameters

import org.slf4j.Logger
import org.slf4j.LoggerFactory

@Command(name = "n5-tree", showDefaultValues = true)
class N5TreeArgs : Callable<Int> {

    private val logger = LoggerFactory.getLogger("n5-tree")

    @Parameters(index = "0", paramLabel = "CONTAINER", arity = "1")
    lateinit var container: String

    @Option(names = ["--from", "-f"], paramLabel = "FROM", required = false, description = ["Start from this group or dataset. Defaults to root group `/' if not specified."], defaultValue = "/")
    lateinit var from: String

    @Option(names = ["--breadth-first"], description = ["Traverse breadth-first (depth first by default)"], defaultValue = "false")
    var breadthFirst: Boolean = false

    @Option(names = ["--ignore-multiscale-group-children"], description = ["Treat multi-scale groups like datasets (leaves of the tree) and stop traversal. multi-scale groups are groups with an attribute `\"multiScale\": true'"])
    var ignoreMultiscaleGroupChildren: Boolean = false

    @kotlin.ExperimentalStdlibApi
    override fun call(): Int {

        val container = N5FSReader(this.container)

        if (!container.exists("/")) {
            logger.error("Container ${this.container} does not exist!")
            return 1
        }

        val queue = ArrayDeque<String>()
        val tree = ArrayList<String>()

        queue += from

        while (queue.isNotEmpty()) {
            val current = if (breadthFirst) queue.removeFirst() else queue.removeLast()
            if (container.exists(current)) {
                tree += current
                val isDataset = container.datasetExists(current)
                val ignoreChildren = isDataset || ignoreMultiscaleGroupChildren && container.getAttribute<Boolean?>(current, "multiScale", Boolean::class.java as Class<Boolean?>) == true
                if (ignoreChildren)
                    continue
                val children = container.list(current)
                children
                        .sorted()
                        .let { if (breadthFirst) it else it.reversed() }
                        .forEach { queue += "${current.trimEnd('/')}/$it" }
            }
        }

        println(tree.joinToString("\n"))
        
        return 0
    }
}

val exitCode = CommandLine(N5TreeArgs()).execute(*args)
kotlin.system.exitProcess(exitCode)