re-add tar handler

src/main/kotlin/org/veupathdb/vdi/lib/common/compression/Tar.kt

@@ -0,0 +1,57 @@
+package org.veupathdb.vdi.lib.common.compression
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream
+import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream
+import java.nio.file.Path
+import java.util.zip.GZIPInputStream
+import java.util.zip.GZIPOutputStream
+import kotlin.io.path.*
+
+object Tar {
+  fun compressWithGZip(output: Path, inputs: Collection<Path>) {
+    if (output.exists())
+      throw IllegalStateException("target output path already exists!")
+
+    TarArchiveOutputStream(GZIPOutputStream(output.outputStream().buffered())).use { tar ->
+      inputs.forEach { file ->
+        tar.putArchiveEntry(TarArchiveEntry(file, file.name))
+        file.inputStream().use { inp -> inp.transferTo(tar) }
+        tar.closeArchiveEntry()
+      }
+    }
+  }
+
+  fun decompressWithGZip(inputFile: Path, outputDir: Path) {
+    if (!outputDir.exists())
+      outputDir.createDirectories()
+    if (!outputDir.isDirectory())
+      throw IllegalStateException("target output path does not point to a directory")
+
+    TarArchiveInputStream(GZIPInputStream(inputFile.inputStream().buffered())).use { tar ->
+      tar.forEach { entry ->
+        val target = outputDir.resolve(entry.name)
+
+        if (entry.isDirectory) {
+          target.createDirectories()
+        } else if (entry.isFile) {
+          if (target.exists()) {
+            if (target.isDirectory())
+              throw IllegalStateException("unable to unpack the file $target due to a directory already existing at that path")
+            else
+              throw IllegalStateException("unable to unpack the file $target due to a conflicting file already existing at that path")
+          }
+
+          target.parent.createDirectories()
+          target.createFile()
+          target.outputStream().use { os -> tar.transferTo(os) }
+        }
+      }
+    }
+  }
+
+  private inline fun TarArchiveInputStream.forEach(fn: (entry: TarArchiveEntry) -> Unit) {
+    while (true)
+      fn(nextEntry ?: break)
+  }
+}