Prepared for include into zip implementation

build.sbt

@@ -10,7 +10,8 @@ resolvers += Resolver.sonatypeRepo("releases")
 libraryDependencies ++= Seq(
   "net.lingala.zip4j" % "zip4j" % "1.3.2",
   "org.openjdk.jmh" % "jmh-core" % "1.21",
-  "org.openjdk.jmh" % "jmh-generator-annprocess" % "1.21"
+  "org.openjdk.jmh" % "jmh-generator-annprocess" % "1.21",
+  "org.scala-sbt" %% "io" % "1.2.1"
 )
 
 enablePlugins(JmhPlugin)

src/main/java/org/virtuslab/zipops/ZipMetadata.java

@@ -461,6 +461,10 @@ public static class Entry extends IndexNode {
 
         Entry() {}
 
+        public long getLastModifiedTime() {
+            return mtime;
+        }
+
         public long getEntryOffset() {
             return locoff;
         }

src/main/scala/org/virtuslab/zipops/IndexBasedZipOps.scala

@@ -4,8 +4,12 @@ import java.nio.channels.{ FileChannel, Channels, ReadableByteChannel }
 import java.io._
 import java.nio.file.{ Files, Path }
 
+import org.virtuslab.zipops.ZipOps.InZipPath
+
 trait IndexBasedZipOps extends ZipOps {
 
+  override def includeFiles(zip: File, files: Seq[(File, InZipPath)]): Unit = () // noop for now
+
   override def readPaths(jar: File): Seq[String] = {
     val metadata = readMetadata(jar.toPath)
     val headers = getHeaders(metadata)

src/main/scala/org/virtuslab/zipops/ZipOps.scala

@@ -2,14 +2,23 @@ package org.virtuslab.zipops
 
 import java.io.File
 
+import org.virtuslab.zipops.ZipOps.{ InZipPath, Timestamp }
+
+object ZipOps {
+  type InZipPath = String
+  type Timestamp = Long
+}
+
 trait ZipOps {
-  def readPaths(jar: File): Seq[String]
+  def readPaths(jar: File): Seq[InZipPath]
   def createStamper(jar: File): Stamper
   def readCentralDirectory(jar: File): Unit = ()
-  def removeEntries(jarFile: File, classes: Iterable[String]): Unit
+  def removeEntries(jarFile: File, classes: Iterable[InZipPath]): Unit
   def mergeArchives(into: File, from: File): Unit
+  def includeFiles(zip: File, files: Seq[(File, InZipPath)])
 }
 
 trait Stamper {
-  def readStamp(jar: File, cls: String): Long
+
+  def readStamp(jar: File, cls: InZipPath): Timestamp
 }

src/main/scala/org/virtuslab/zipops/bench/BenchUtil.scala

@@ -14,7 +14,13 @@ trait BenchUtil {
     tempFile.toFile
   }
 
-  def extract(zip: File, targetDir: Path): Unit = {
+  def extractSomewhere(file: File): Path = {
+    val tempDir = Files.createTempDirectory("lols")
+    extract(file, tempDir)
+    tempDir
+  }
+
+  private def extract(zip: File, targetDir: Path): Unit = {
     new ZipFile(zip).extractAll(targetDir.toString)
   }
 

src/main/scala/org/virtuslab/zipops/bench/CentralDirBenchmark.scala

@@ -3,8 +3,9 @@ package org.virtuslab.zipops.bench
 import org.virtuslab.zipops.ZipOps
 import org.openjdk.jmh.annotations._
 import java.io.File
+import ZipOpsBench._
 
-class BigCentralDirBench extends CentralDirBenchmark("scala-library-2.12.6.jar")
+class BigCentralDirBench extends CentralDirBenchmark(BigJar)
 
 @State(Scope.Thread)
 abstract class CentralDirBenchmark(jar: String) extends ZipOpsBench with BenchUtil {

src/main/scala/org/virtuslab/zipops/bench/DeleteBenchmarks.scala

@@ -4,8 +4,9 @@ import java.io.File
 
 import org.openjdk.jmh.annotations._
 import org.virtuslab.zipops.ZipOps
+import ZipOpsBench._
 
-class DeleteFromBigJarBench extends DeleteBenchmark("scala-library-2.12.6.jar") {
+class DeleteFromBigJarBench extends DeleteBenchmark(BigJar) {
 
   val toDelete = Set(
     "scala/util/matching/Regex$MatchIterator$$anon$1.class",
@@ -33,7 +34,7 @@ class DeleteFromBigJarBench extends DeleteBenchmark("scala-library-2.12.6.jar")
 
 }
 
-class SmallJarDeleteBench extends DeleteBenchmark("scala-xml_2.12-1.0.6.jar") {
+class SmallJarDeleteBench extends DeleteBenchmark(MediumJar) {
 
   val toDelete = Set(
     "scala/xml/pull/EvText.class",

src/main/scala/org/virtuslab/zipops/bench/IncludeFilesBenchmark.scala

@@ -0,0 +1,51 @@
+package org.virtuslab.zipops.bench
+
+import org.virtuslab.zipops.ZipOps
+import java.io.File
+
+import ZipOpsBench._
+
+import org.openjdk.jmh.annotations._
+import sbt.io.{ IO, DirectoryFilter }
+
+class IncludeSomeFilesBench extends IncludeFilesBenchmark(zip = BigJar, zipToExtractAndInclude = SmallJar)
+
+@State(Scope.Thread)
+abstract class IncludeFilesBenchmark(
+  zip: String,
+  zipToExtractAndInclude: String
+) extends ZipOpsBench with BenchUtil {
+
+  var zipFile: File = _
+  var extractDir: File = _
+  var extractedFiles: Seq[(File, String)] = _
+
+  @Setup(Level.Invocation)
+  def setup(): Unit = {
+    zipFile = copyResource(zip)
+
+    val zipToExtract = copyResource(zipToExtractAndInclude)
+    extractDir = extractSomewhere(zipToExtract).toFile
+    extractedFiles = dirContent(extractDir)
+  }
+
+  private def dirContent(dir: File): Seq[(File, String)] = {
+    import sbt.io.syntax._
+    (dir ** -DirectoryFilter).get.flatMap { extractedFile =>
+      IO.relativize(dir, extractedFile) match {
+        case Some(relPath) =>
+          List((extractedFile, relPath))
+        case _ => Nil
+      }
+    }
+  }
+
+  @TearDown(Level.Invocation)
+  def teardown(): Unit = {
+    zipFile.delete()
+    IO.delete(extractDir)
+  }
+
+  override def run(ops: ZipOps): Unit = ops.includeFiles(zipFile, extractedFiles)
+
+}

src/main/scala/org/virtuslab/zipops/bench/MergeBenchmarks.scala

@@ -4,12 +4,13 @@ import java.io.File
 
 import org.virtuslab.zipops.ZipOps
 import org.openjdk.jmh.annotations._
+import ZipOpsBench._
 
-class MergeToSmallBench extends MergeBench("scala-xml_2.12-1.0.6.jar", "zip-ops_2.12-0.1.jar")
+class MergeToSmallBench extends MergeBench(MediumJar, SmallJar)
 
-class MergeToBigBench extends MergeBench("scala-library-2.12.6.jar", "zip-ops_2.12-0.1.jar")
+class MergeToBigBench extends MergeBench(BigJar, SmallJar)
 
-class MergeBigToSmallBench extends MergeBench("zip-ops_2.12-0.1.jar", "scala-library-2.12.6.jar")
+class MergeBigToSmallBench extends MergeBench(SmallJar, BigJar)
 
 @State(Scope.Thread)
 abstract class MergeBench(target: String, source: String) extends ZipOpsBench with BenchUtil {

src/main/scala/org/virtuslab/zipops/bench/StamperBenchmark.scala

@@ -9,9 +9,10 @@ import java.util.concurrent.TimeUnit.{ SECONDS, MILLISECONDS }
 import ZipOpsBench._
 import org.openjdk.jmh.infra.Blackhole
 import org.virtuslab.zipops.impl.MyZipFsOps
+import sbt.io.IO
 
-class BigJarStamperBenchmark extends StamperBenchmark("scala-library-2.12.6.jar")
-class SmallJarStamperBenchmark extends StamperBenchmark("zip-ops_2.12-0.1.jar")
+class BigJarStamperBenchmark extends StamperBenchmark(BigJar)
+class SmallJarStamperBenchmark extends StamperBenchmark(SmallJar)
 
 @State(Scope.Thread)
 abstract class StamperBenchmark(jar: String) extends ZipOpsBench with BenchUtil {
@@ -24,16 +25,15 @@ abstract class StamperBenchmark(jar: String) extends ZipOpsBench with BenchUtil
   @Setup(Level.Trial)
   def setup(): Unit = {
     jarFile = copyResource(jar)
-    extractDir = Files.createTempDirectory("lols")
-    extract(jarFile, extractDir)
+    extractDir = extractSomewhere(jarFile)
     inJarPaths = MyZipFsOps.readPaths(jarFile)
     absExtractedPaths = inJarPaths.map(extractDir.resolve).map(_.toAbsolutePath)
   }
 
   @TearDown(Level.Trial)
   def teardown(): Unit = {
     jarFile.delete()
-    // TODO rm extract dir
+    IO.delete(extractDir.toFile)
   }
 
   @Benchmark

src/main/scala/org/virtuslab/zipops/bench/ZipOpsBench.scala

@@ -12,6 +12,10 @@ object ZipOpsBench {
   final val WarmupIterationTime = 20
   final val Iterations = 10
   final val IterationTime = 20
+
+  val BigJar = "scala-library-2.12.6.jar" // 2542 files
+  val MediumJar = "scala-xml_2.12-1.0.6.jar" // 249 files
+  val SmallJar = "zip-ops_2.12-0.1.jar" // 9 files, 3 dirs
 }
 
 trait ZipOpsBench {

src/main/scala/org/virtuslab/zipops/impl/MyZipFsOps.scala

@@ -45,7 +45,7 @@ trait MyZipFsOpsBase extends IndexBasedZipOps {
   }
 
   protected def getLastModifiedTime(header: Header): Long = {
-    header.mtime
+    header.getLastModifiedTime
   }
 
   protected def dumpMetadata(metadata: Metadata, outputStream: OutputStream): Unit = {

src/main/scala/org/virtuslab/zipops/impl/ZipFsOps.scala

@@ -7,10 +7,26 @@ import java.util.function.Consumer
 import java.io.File
 import java.nio.file._
 
+import org.virtuslab.zipops.ZipOps.InZipPath
 import org.virtuslab.zipops.{ Stamper, ZipOps }
 
 object ZipFsOps extends ZipOps {
 
+  override def includeFiles(zip: File, files: Seq[(File, InZipPath)]): Unit = {
+    withZipFs(zip, create = true) { fs =>
+      files.foreach {
+        case (file, target) =>
+          val targetPath = fs.getPath(target)
+          Option(targetPath.getParent).foreach(Files.createDirectories(_))
+          Files.copy(
+            file.toPath,
+            targetPath,
+            StandardCopyOption.REPLACE_EXISTING,
+            StandardCopyOption.COPY_ATTRIBUTES)
+      }
+    }
+  }
+
   override def readPaths(jar: File): Seq[String] = {
     if (jar.exists()) {
       withZipFs(jar) { fs =>