Fix dependencies clash when packaging

Fixes #319

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/internal/diagnosticUtils.kt

@@ -0,0 +1,10 @@
+package org.jetbrains.compose.desktop.application.internal
+
+import java.io.PrintWriter
+import java.io.StringWriter
+import java.lang.Exception
+
+internal fun Exception.stacktraceToString(): String =
+    StringWriter().also { w ->
+        PrintWriter(w).use { pw -> printStackTrace(pw) }
+    }.toString()

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/internal/files/FileCopyingProcessor.kt

@@ -1,4 +1,4 @@
-package org.jetbrains.compose.desktop.application.internal
+package org.jetbrains.compose.desktop.application.internal.files
 
 import java.io.File
 

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/internal/files/MacJarSignFileCopyingProcessor.kt

@@ -1,6 +1,8 @@
-package org.jetbrains.compose.desktop.application.internal
+package org.jetbrains.compose.desktop.application.internal.files
 
 import org.gradle.process.ExecOperations
+import org.jetbrains.compose.desktop.application.internal.MacUtils
+import org.jetbrains.compose.desktop.application.internal.isJarFile
 import org.jetbrains.compose.desktop.application.internal.validation.ValidatedMacOSSigningSettings
 import java.io.*
 import java.util.regex.Pattern

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/internal/files/SimpleFileCopyingProcessor.kt

@@ -1,4 +1,4 @@
-package org.jetbrains.compose.desktop.application.internal
+package org.jetbrains.compose.desktop.application.internal.files
 
 import java.io.File
 

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/internal/files/fileUtils.kt

@@ -0,0 +1,20 @@
+package org.jetbrains.compose.desktop.application.internal.files
+
+import java.io.File
+import java.security.DigestInputStream
+import java.security.MessageDigest
+
+internal fun fileHash(file: File): String {
+    val md5 = MessageDigest.getInstance("MD5")
+    file.inputStream().buffered().use { fis ->
+        DigestInputStream(fis, md5).use { ds ->
+            while (ds.read() != -1) {}
+        }
+    }
+    val digest = md5.digest()
+    return buildString(digest.size * 2) {
+        for (byte in digest) {
+            append(Integer.toHexString(0xFF and byte.toInt()))
+        }
+    }
+}

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/tasks/AbstractJPackageTask.kt

@@ -1,13 +1,11 @@
 package org.jetbrains.compose.desktop.application.tasks
 
-import org.gradle.api.file.ConfigurableFileCollection
-import org.gradle.api.file.Directory
-import org.gradle.api.file.DirectoryProperty
-import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.file.*
 import org.gradle.api.provider.ListProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.provider.Provider
 import org.gradle.api.tasks.*
+import org.gradle.api.tasks.Optional
 import org.gradle.process.ExecResult
 import org.gradle.process.ExecSpec
 import org.gradle.work.ChangeType
@@ -15,10 +13,19 @@ import org.gradle.work.InputChanges
 import org.jetbrains.compose.desktop.application.dsl.MacOSSigningSettings
 import org.jetbrains.compose.desktop.application.dsl.TargetFormat
 import org.jetbrains.compose.desktop.application.internal.*
+import org.jetbrains.compose.desktop.application.internal.files.MacJarSignFileCopyingProcessor
+import org.jetbrains.compose.desktop.application.internal.files.SimpleFileCopyingProcessor
+import org.jetbrains.compose.desktop.application.internal.files.fileHash
 import org.jetbrains.compose.desktop.application.internal.validation.ValidatedMacOSSigningSettings
 import org.jetbrains.compose.desktop.application.internal.validation.validate
 import java.io.File
+import java.io.Serializable
+import java.util.*
 import javax.inject.Inject
+import kotlin.collections.HashMap
+import kotlin.collections.HashSet
+import java.io.ObjectInputStream
+import java.io.ObjectOutputStream
 
 abstract class AbstractJPackageTask @Inject constructor(
     @get:Input
@@ -166,12 +173,28 @@ abstract class AbstractJPackageTask @Inject constructor(
     @get:LocalState
     protected val signDir: Provider<Directory> = project.layout.buildDirectory.dir("compose/tmp/sign")
 
+    @get:Internal
+    private val libsDir: Provider<Directory> = workingDir.map {
+        it.dir("libs")
+    }
+
+    @get:Internal
+    private val libsMappingFile: Provider<RegularFile> = workingDir.map {
+        it.file("libs-mapping.txt")
+    }
+
+    @get:Internal
+    private val libsMapping = FilesMapping()
+
     override fun makeArgs(tmpDir: File): MutableList<String> = super.makeArgs(tmpDir).apply {
         if (targetFormat == TargetFormat.AppImage || appImage.orNull == null) {
             // Args, that can only be used, when creating an app image or an installer w/o --app-image parameter
             cliArg("--input", tmpDir)
             cliArg("--runtime-image", runtimeImage)
-            cliArg("--main-jar", launcherMainJar.ioFile.name)
+
+            val mappedJar = libsMapping[launcherMainJar.ioFile]
+                ?: error("Main jar was not processed correctly: ${launcherMainJar.ioFile}")
+            cliArg("--main-jar", mappedJar)
             cliArg("--main-class", launcherMainClass)
 
             when (currentOS) {
@@ -241,10 +264,45 @@ abstract class AbstractJPackageTask @Inject constructor(
         }
     }
 
-    override fun prepareWorkingDir(inputChanges: InputChanges) {
-        val workingDir = workingDir.ioFile
+    private fun invalidateMappedLibs(
+        inputChanges: InputChanges
+    ): Set<File> {
+        val outdatedLibs = HashSet<File>()
+        val libsDirFile = libsDir.ioFile
+
+        fun invalidateAllLibs() {
+            outdatedLibs.addAll(files.files)
+            outdatedLibs.add(launcherMainJar.ioFile)
+
+            logger.debug("Clearing all files in working dir: $libsDirFile")
+            fileOperations.delete(libsDirFile)
+            libsDirFile.mkdirs()
+        }
+
+        if (inputChanges.isIncremental) {
+            val allChanges = inputChanges.getFileChanges(files).asSequence() +
+                    inputChanges.getFileChanges(launcherMainJar)
 
-        // todo: parallel processing
+            try {
+                for (change in allChanges) {
+                    libsMapping.remove(change.file)?.let { fileOperations.delete(it) }
+                    if (change.changeType != ChangeType.REMOVED) {
+                        outdatedLibs.add(change.file)
+                    }
+                }
+            } catch (e: Exception) {
+                logger.debug("Could remove outdated libs incrementally: ${e.stacktraceToString()}")
+                invalidateAllLibs()
+            }
+        } else {
+            invalidateAllLibs()
+        }
+
+        return outdatedLibs
+    }
+
+    override fun prepareWorkingDir(inputChanges: InputChanges) {
+        val libsDirFile = libsDir.ioFile
         val fileProcessor =
             withValidatedMacOSSigning { signing ->
                 val tmpDirForSign = signDir.ioFile
@@ -258,35 +316,17 @@ abstract class AbstractJPackageTask @Inject constructor(
                 )
             } ?: SimpleFileCopyingProcessor
 
-        if (inputChanges.isIncremental) {
-            logger.debug("Updating working dir incrementally: $workingDir")
-            val allChanges = inputChanges.getFileChanges(files).asSequence() +
-                    inputChanges.getFileChanges(launcherMainJar)
-            allChanges.forEach { fileChange ->
-                val sourceFile = fileChange.file
-                val targetFile = workingDir.resolve(sourceFile.name)
-
-                if (fileChange.changeType == ChangeType.REMOVED) {
-                    fileOperations.delete(targetFile)
-                    logger.debug("Deleted: $targetFile")
-                } else {
-                    fileProcessor.copy(sourceFile, targetFile)
-                    logger.debug("Updated: $targetFile")
-                }
-            }
-        } else {
-            logger.debug("Updating working dir non-incrementally: $workingDir")
-            fileOperations.delete(workingDir)
-            fileOperations.mkdir(workingDir)
-
-            files.forEach { sourceFile ->
-                val targetFile = workingDir.resolve(sourceFile.name)
-                if (targetFile.exists()) {
-                    // todo: handle possible clashes
-                    logger.warn("w: File already exists: $targetFile")
-                }
-                fileProcessor.copy(sourceFile, targetFile)
-            }
+        val outdatedLibs = invalidateMappedLibs(inputChanges)
+        for (sourceFile in outdatedLibs) {
+            assert(sourceFile.exists()) { "Lib file does not exist: $sourceFile" }
+
+            val targetFileName =
+                if (sourceFile.isJarFile)
+                    "${sourceFile.nameWithoutExtension}-${fileHash(sourceFile)}.jar"
+                else sourceFile.name
+            val targetFile = libsDirFile.resolve(targetFileName)
+            fileProcessor.copy(sourceFile, targetFile)
+            libsMapping[sourceFile] = targetFile
         }
     }
 
@@ -309,4 +349,69 @@ abstract class AbstractJPackageTask @Inject constructor(
         val outputFile = findOutputFileOrDir(destinationDir.ioFile, targetFormat)
         logger.lifecycle("The distribution is written to ${outputFile.canonicalPath}")
     }
+
+    override fun initState() {
+        val mappingFile = libsMappingFile.ioFile
+        if (mappingFile.exists()) {
+            try {
+                libsMapping.loadFrom(mappingFile)
+            } catch (e: Exception) {
+                fileOperations.delete(mappingFile)
+                throw e
+            }
+            logger.debug("Loaded libs mapping from $mappingFile")
+        }
+    }
+
+    override fun saveStateAfterFinish() {
+        val mappingFile = libsMappingFile.ioFile
+        libsMapping.saveTo(mappingFile)
+        logger.debug("Saved libs mapping to $mappingFile")
+    }
+}
+
+// Serializable is only needed to avoid breaking configuration cache:
+// https://docs.gradle.org/current/userguide/configuration_cache.html#config_cache:requirements
+private class FilesMapping : Serializable {
+    private var mapping = HashMap<File, File>()
+
+    operator fun get(key: File): File? =
+        mapping[key]
+
+    operator fun set(key: File, value: File) {
+        mapping[key] = value
+    }
+
+    fun remove(key: File): File? =
+        mapping.remove(key)
+
+    fun loadFrom(mappingFile: File) {
+        mappingFile.readLines().forEach { line ->
+            if (line.isNotBlank()) {
+                val (k, v) = line.split(File.pathSeparatorChar)
+                mapping[File(k)] = File(v)
+            }
+        }
+    }
+
+    fun saveTo(mappingFile: File) {
+        mappingFile.parentFile.mkdirs()
+        mappingFile.bufferedWriter().use { writer ->
+            mapping.entries
+                .sortedBy { (k, _) -> k.absolutePath }
+                .forEach { (k, v) ->
+                    writer.append(k.absolutePath)
+                    writer.append(File.pathSeparatorChar)
+                    writer.appendln(v.absolutePath)
+                }
+        }
+    }
+
+    private fun writeObject(stream: ObjectOutputStream) {
+        stream.writeObject(mapping)
+    }
+
+    private fun readObject(stream: ObjectInputStream) {
+        mapping = stream.readObject() as HashMap<File, File>
+    }
 }

gradle-plugins/compose/src/main/kotlin/org/jetbrains/compose/desktop/application/tasks/AbstractJvmToolOperationTask.kt

@@ -16,8 +16,6 @@ import org.gradle.process.ExecSpec
 import org.gradle.work.InputChanges
 import org.jetbrains.compose.desktop.application.internal.*
 import org.jetbrains.compose.desktop.application.internal.ComposeProperties
-import org.jetbrains.compose.desktop.application.internal.OS
-import org.jetbrains.compose.desktop.application.internal.currentOS
 import org.jetbrains.compose.desktop.application.internal.notNullProperty
 import java.io.File
 import javax.inject.Inject
@@ -68,6 +66,7 @@ abstract class AbstractJvmToolOperationTask(private val toolName: String) : Defa
 
     @TaskAction
     fun run(inputChanges: InputChanges) {
+        initState()
         val javaHomePath = javaHome.get()
 
         val jtool = File(javaHomePath).resolve("bin/${executableName(toolName)}")
@@ -96,5 +95,9 @@ abstract class AbstractJvmToolOperationTask(private val toolName: String) : Defa
                 fileOperations.delete(workingDir)
             }
         }
+        saveStateAfterFinish()
     }
+
+    protected open fun initState() {}
+    protected open fun saveStateAfterFinish() {}
 }

gradle-plugins/compose/src/test/kotlin/org/jetbrains/compose/DesktopApplicationTest.kt

@@ -5,7 +5,6 @@ import org.jetbrains.compose.desktop.application.internal.OS
 import org.jetbrains.compose.desktop.application.internal.currentOS
 import org.jetbrains.compose.desktop.application.internal.currentTarget
 import org.jetbrains.compose.test.*
-import org.junit.jupiter.api.Assertions.assertArrayEquals
 import org.junit.jupiter.api.Assertions.assertEquals
 import org.junit.jupiter.api.Test
 import java.util.jar.JarFile
@@ -93,4 +92,14 @@ class DesktopApplicationTest : GradlePluginTestBase() {
             }
         }
     }
+
+    @Test
+    fun testModuleClash() = with(testProject(TestProjects.moduleClashCli)) {
+        gradle(":app:runDistributable").build().checks { check ->
+            check.taskOutcome(":app:createDistributable", TaskOutcome.SUCCESS)
+            check.taskOutcome(":app:runDistributable", TaskOutcome.SUCCESS)
+            check.logContains("Called lib1#util()")
+            check.logContains("Called lib2#util()")
+        }
+    }
 }

gradle-plugins/compose/src/test/kotlin/org/jetbrains/compose/FileHashTest.kt

@@ -0,0 +1,78 @@
+package org.jetbrains.compose
+
+import org.gradle.internal.impldep.org.testng.Assert
+import org.jetbrains.compose.desktop.application.internal.OS
+import org.jetbrains.compose.desktop.application.internal.currentOS
+import org.jetbrains.compose.desktop.application.internal.files.fileHash
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+import java.io.File
+import java.util.concurrent.TimeUnit
+
+class FileHashTest {
+    @TempDir
+    lateinit var workingDir: File
+
+    private val inputDir: File
+        get() = workingDir.resolve("inputs").apply { mkdirs() }
+
+    private fun inputFile(name: String, content: String): File {
+        return inputDir.resolve(name).apply { writeText(content) }
+    }
+
+    private fun outputFile(name: String) =
+        workingDir.resolve("outputs/$name").apply {
+            parentFile.mkdirs()
+        }
+
+    @Test
+    fun testFileHashIsAffectedByContent() {
+        val input1 = inputFile("input1.txt", "1")
+
+        val initJar =  createJar("init", input1)
+        input1.writeText("2")
+        val modifiedJar = createJar("modified", input1)
+
+        val initHash = fileHash(initJar)
+        val modifiedHash = fileHash(modifiedJar)
+        Assert.assertNotEquals(modifiedHash, initHash)
+    }
+
+    private fun createJar(outputFileName: String, vararg files: File): File {
+        val outputFile = outputFile(outputFileName)
+
+        val cmd = arrayListOf(jarUtilFile.absolutePath, "cvf", outputFile.absolutePath)
+        for (file in files) {
+            cmd.add(file.relativeTo(inputDir).path)
+        }
+        val outFile = workingDir.resolve("jar-stdout.txt").apply { delete() }
+        val errFile = workingDir.resolve("jar-error.txt").apply { delete() }
+        val process = ProcessBuilder(cmd).run {
+            redirectOutput(outFile)
+            redirectError(errFile)
+            directory(inputDir)
+            start()
+        }
+        if (!process.waitFor(30, TimeUnit.SECONDS)) {
+            error("Process hang up: [${cmd.joinToString(" ")}]")
+        }
+        val exitCode = process.exitValue()
+        check(exitCode == 0) {
+            """
+                Stdout log: $outFile
+                Error log: $errFile
+                Process exited with error: $exitCode
+            """
+        }
+        outFile.delete()
+        errFile.delete()
+
+        return outputFile
+    }
+}
+
+private val jarUtilFile = run {
+    val javaHome = File(System.getProperty("java.home"))
+    val executableName = if (currentOS == OS.Windows) "jar.exe" else "jar"
+    javaHome.resolve("bin/$executableName")
+}

gradle-plugins/compose/src/test/kotlin/org/jetbrains/compose/test/TestProject.kt

@@ -36,6 +36,7 @@ data class TestProject(
             withGradleVersion(TestProperties.gradleVersionForTests)
             withProjectDir(workingDir)
             withArguments(args.toList() + additionalArgs)
+            forwardOutput()
         }
 
     @Suppress("DeprecatedCallableAddReplaceWith")

gradle-plugins/compose/src/test/kotlin/org/jetbrains/compose/test/TestProjects.kt

@@ -4,4 +4,5 @@ object TestProjects {
     const val jvm = "application/jvm"
     const val mpp = "application/mpp"
     const val jvmKotlinDsl = "application/jvmKotlinDsl"
+    const val moduleClashCli = "application/moduleClashCli"
 }

gradle-plugins/compose/src/test/kotlin/org/jetbrains/compose/test/assertUtils.kt

@@ -1,9 +1,45 @@
 package org.jetbrains.compose.test
 
+import org.gradle.testkit.runner.BuildResult
+import org.gradle.testkit.runner.TaskOutcome
+
 internal fun <T> Collection<T>.checkContains(vararg elements: T) {
     val expectedElements = elements.toMutableSet()
     forEach { expectedElements.remove(it) }
     if (expectedElements.isNotEmpty()) {
         error("Expected elements are missing from the collection: [${expectedElements.joinToString(", ")}]")
     }
+}
+
+internal fun BuildResult.checks(fn: (BuildResultChecks) -> Unit) {
+    fn(BuildResultChecks(this))
+}
+
+internal class BuildResultChecks(private val result: BuildResult) {
+    fun logContains(substring: String) {
+        if (!result.output.contains(substring)) {
+            throw AssertionError("Test output does not contain the expected string: '$substring'")
+        }
+    }
+
+    fun taskOutcome(task: String, expectedOutcome: TaskOutcome) {
+        val actualOutcome = result.task(task)?.outcome
+        if (actualOutcome != expectedOutcome) {
+            throw AssertionError(
+                """|Unexpected outcome for task '$task'
+                   |Expected: $expectedOutcome
+                   |Actual: $actualOutcome
+            """.trimMargin())
+        }
+    }
+}
+
+internal fun BuildResult.checkOutputLogContains(substring: String) {
+    if (output.contains(substring)) return
+
+    println("Test output:")
+    output.lineSequence().forEach {
+        println("  > $it")
+    }
+    throw AssertionError("Test output does not contain the expected string: '$substring'")
 }

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/app/build.gradle

@@ -0,0 +1,23 @@
+import org.jetbrains.compose.desktop.application.dsl.TargetFormat
+
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+    id "org.jetbrains.compose"
+}
+
+dependencies {
+    implementation "org.jetbrains.kotlin:kotlin-stdlib"
+    implementation compose.desktop.currentOs
+
+    implementation project(":lib1:utils")
+    implementation project(":lib2:utils")
+}
+
+compose.desktop {
+    application {
+        mainClass = "MainKt"
+        nativeDistributions {
+            targetFormats(TargetFormat.Dmg, TargetFormat.Msi, TargetFormat.Deb)
+        }
+    }
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/app/src/main/kotlin/main.kt

@@ -0,0 +1,7 @@
+import lib1.*
+import lib2.*
+
+fun main() {
+    lib1.util()
+    lib2.util()
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/build.gradle

@@ -0,0 +1,15 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm" apply false
+    id "org.jetbrains.compose" apply false
+}
+
+subprojects {
+    repositories {
+        google()
+        mavenCentral()
+        jcenter()
+        maven {
+            url "https://maven.pkg.jetbrains.space/public/p/compose/dev"
+        }
+    }
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/lib1/utils/build.gradle

@@ -0,0 +1,7 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+}
+
+dependencies {
+    implementation "org.jetbrains.kotlin:kotlin-stdlib"
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/lib1/utils/src/main/kotlin/lib1/utils.kt

@@ -0,0 +1,5 @@
+package lib1
+
+fun util() {
+    println("Called lib1#util()")
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/lib2/utils/build.gradle

@@ -0,0 +1,7 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+}
+
+dependencies {
+    implementation "org.jetbrains.kotlin:kotlin-stdlib"
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/lib2/utils/src/main/kotlin/lib2/utils.kt

@@ -0,0 +1,5 @@
+package lib2
+
+fun util() {
+    println("Called lib2#util()")
+}

gradle-plugins/compose/src/test/test-projects/application/moduleClashCli/settings.gradle

@@ -0,0 +1,11 @@
+pluginManagement {
+    plugins {
+        id 'org.jetbrains.kotlin.jvm' version 'KOTLIN_VERSION_PLACEHOLDER'
+        id 'org.jetbrains.compose' version 'COMPOSE_VERSION_PLACEHOLDER'
+    }
+    repositories {
+        mavenLocal()
+        gradlePluginPortal()
+    }
+}
+include ':lib1:utils', ':lib2:utils', ':app'