Move copy functions to IoUtils

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -5,10 +5,9 @@ import java.net.URL
 
 import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.summary.Summary
-import org.apache.commons.io.IOUtils
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
-import scala.collection.JavaConversions._
+import nl.lumc.sasc.biopet.utils.IoUtils
 
 /**
  * Created by pjvan_thof on 3/27/15.
@@ -92,7 +91,7 @@ trait ReportBuilder extends ToolCommand {
     )
 
     for (resource <- extFiles.par) {
-      ReportBuilder.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), true)
+      IoUtils.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), true)
     }
 
     logger.info("Parsing summary")
@@ -162,37 +161,11 @@ object ReportBuilder {
       case Some(template) => template
       case _ => {
         val tempFile = File.createTempFile("ssp-template", new File(location).getName)
-        copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
+        IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
         templateCache += location -> tempFile
         tempFile
       }
     }
     engine.layout(TemplateSource.fromFile(templateFile), args)
   }
-
-  //TODO: move to utils
-  def copyFile(in: File, out: File, createDirs: Boolean = false): Unit = {
-    copyStreamToFile(new FileInputStream(in), out, createDirs)
-  }
-
-  def copyStreamToFile(in: InputStream, out: File, createDirs: Boolean = false): Unit = {
-    if (createDirs) out.getParentFile.mkdirs()
-    val os = new FileOutputStream(out)
-
-    org.apache.commons.io.IOUtils.copy(in, os)
-    os.close()
-    in.close()
-  }
-
-  def copyDir(inputDir: File, externalDir: File): Unit = {
-    require(inputDir.isDirectory)
-    externalDir.mkdirs()
-    for (srcFile <- inputDir.listFiles) {
-      if (srcFile.isDirectory) copyDir(new File(inputDir, srcFile.getName), new File(externalDir, srcFile.getName))
-      else {
-        val newFile = new File(externalDir, srcFile.getName)
-        copyFile(srcFile, newFile)
-      }
-    }
-  }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala

+package nl.lumc.sasc.biopet.utils
+
+import java.io.{ FileOutputStream, InputStream, FileInputStream, File }
+
+/**
+ * Created by pjvan_thof on 6/4/15.
+ */
+object IoUtils {
+  def copyFile(in: File, out: File, createDirs: Boolean = false): Unit = {
+    copyStreamToFile(new FileInputStream(in), out, createDirs)
+  }
+
+  def copyStreamToFile(in: InputStream, out: File, createDirs: Boolean = false): Unit = {
+    if (createDirs) out.getParentFile.mkdirs()
+    val os = new FileOutputStream(out)
+
+    org.apache.commons.io.IOUtils.copy(in, os)
+    os.close()
+    in.close()
+  }
+
+  def copyDir(inputDir: File, externalDir: File): Unit = {
+    require(inputDir.isDirectory)
+    externalDir.mkdirs()
+    for (srcFile <- inputDir.listFiles) {
+      if (srcFile.isDirectory) copyDir(new File(inputDir, srcFile.getName), new File(externalDir, srcFile.getName))
+      else {
+        val newFile = new File(externalDir, srcFile.getName)
+        copyFile(srcFile, newFile)
+      }
+    }
+  }
+}