Added KEGG overview XML files that are no longer available through th…

…e API and method for loading from resources

src/de/zbit/kegg/io/KEGGImporter.java

@@ -22,6 +22,9 @@
 
 import java.awt.event.ActionEvent;
 import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
 
 import javax.swing.SwingWorker;
 
@@ -41,6 +44,11 @@
  * @version $Rev$
  */
 public class KEGGImporter extends NotifyingWorker<Object> {
+  /**
+   * This directory will be used as target for downloaded pathways.
+   * This string must end with a "/" and will be prepended to the file.
+   */
+  private final static String localPathwayCacheDir = "res/kgml/";
   /**
    * 
    */
@@ -106,7 +114,26 @@ protected Object doInBackground() throws Exception {
       // PART1: Download
       String localFile = null;
       try {
-        localFile = KGMLSelectAndDownload.downloadPathway(KEGGpathwayID, false);
+        if (KGMLSelectAndDownload.class.getResource("kgml/" + KEGGpathwayID + ".xml") != null) {
+          System.out.println("Pathway in resources...");
+          InputStream is = KGMLSelectAndDownload.class.getResourceAsStream("kgml/" + KEGGpathwayID + ".xml");
+          System.out.println("Copying file...");
+          localFile = localPathwayCacheDir + KEGGpathwayID + ".xml";
+          new File("res/kgml/").mkdirs();
+          OutputStream os = new FileOutputStream(localFile);
+          int read = 0;
+          byte[] bytes = new byte[1024];
+
+          while ((read = is.read(bytes)) != -1) {
+            os.write(bytes, 0, read);
+          }
+          is.close();
+          os.close();
+          System.out.println("Done...");
+        } else {
+          System.out.println("Pathway NOT in resources...");
+          localFile = KGMLSelectAndDownload.downloadPathway(KEGGpathwayID, false);
+        }
       } catch (Exception exc) {
         // Mostly 1) pathway does not exists for organism or 2) no connection to server
         GUITools.showErrorMessage(null, exc);