Example #1
0
  /*
  	-- This is a helper methid to run the morph files
  */
  private static void runMorphDataSet() throws Exception {

    String morph_directory =
        "../../thesis-datasets/morph/"; // directory where all the morph code is stored
    File d = new File(morph_directory);
    // get all the files from a directory
    File[] fList = d.listFiles();
    List<String> dir_list = new ArrayList<String>();
    for (File file : fList) {
      if (file.isDirectory()) {
        dir_list.add(file.getName());
      }
    }
    for (String dir : dir_list) {
      directory = morph_directory + dir + "/";
      System.out.println("Running TDDD " + directory);
      ReadFile.readFile(directory, fileList); // read the two files
      System.out.println(fileList.get(0) + " " + fileList.get(1));
      preliminaryStep(directory);
      startCDC();
      fileList.clear();
      fileArray.clear();
      hashed_File_List.clear();
    }
  }
Example #2
0
  private List<File> compileFiles(String avrBasePath,
                                  String buildPath, List<File> includePaths,
                                  List<File> sSources, 
                                  List<File> cSources, List<File> cppSources,
                                  Map<String, String> boardPreferences)
    throws RunnerException {

    List<File> objectPaths = new ArrayList<File>();
    
    for (File file : sSources) {
      String objectPath = buildPath + File.separator + file.getName() + ".o";
      objectPaths.add(new File(objectPath));
      execAsynchronously(getCommandCompilerS(avrBasePath, includePaths,
                                             file.getAbsolutePath(),
                                             objectPath,
                                             boardPreferences));
    }
 		
    for (File file : cSources) {
        String objectPath = buildPath + File.separator + file.getName() + ".o";
        String dependPath = buildPath + File.separator + file.getName() + ".d";
        File objectFile = new File(objectPath);
        File dependFile = new File(dependPath);
        objectPaths.add(objectFile);
        if (is_already_compiled(file, objectFile, dependFile, boardPreferences)) continue;
        execAsynchronously(getCommandCompilerC(avrBasePath, includePaths,
                                               file.getAbsolutePath(),
                                               objectPath,
                                               boardPreferences));
    }

    for (File file : cppSources) {
        String objectPath = buildPath + File.separator + file.getName() + ".o";
        String dependPath = buildPath + File.separator + file.getName() + ".d";
        File objectFile = new File(objectPath);
        File dependFile = new File(dependPath);
        objectPaths.add(objectFile);
        if (is_already_compiled(file, objectFile, dependFile, boardPreferences)) continue;
        execAsynchronously(getCommandCompilerCPP(avrBasePath, includePaths,
                                                 file.getAbsolutePath(),
                                                 objectPath,
                                                 boardPreferences));
    }
    
    return objectPaths;
  }
Example #3
0
 static public ArrayList<File> findFilesInFolder(File folder, String extension,
                                                 boolean recurse) {
   ArrayList<File> files = new ArrayList<File>();
   
   if (folder.listFiles() == null) return files;
   
   for (File file : folder.listFiles()) {
     if (file.getName().startsWith(".")) continue; // skip hidden files
     
     if (file.getName().endsWith("." + extension))
       files.add(file);
       
     if (recurse && file.isDirectory()) {
       files.addAll(findFilesInFolder(file, extension, true));
     }
   }
   
   return files;
 }
Example #4
0
 // Take a tree of files starting in a directory in a zip file
 // and copy them to a disk directory, recreating the tree.
 private int unpackZipFile(
     File inZipFile, String directory, String parent, boolean suppressFirstPathElement) {
   int count = 0;
   if (!inZipFile.exists()) return count;
   parent = parent.trim();
   if (!parent.endsWith(File.separator)) parent += File.separator;
   if (!directory.endsWith(File.separator)) directory += File.separator;
   File outFile = null;
   try {
     ZipFile zipFile = new ZipFile(inZipFile);
     Enumeration zipEntries = zipFile.entries();
     while (zipEntries.hasMoreElements()) {
       ZipEntry entry = (ZipEntry) zipEntries.nextElement();
       String name = entry.getName().replace('/', File.separatorChar);
       if (name.startsWith(directory)) {
         if (suppressFirstPathElement) name = name.substring(directory.length());
         outFile = new File(parent + name);
         // Create the directory, just in case
         if (name.indexOf(File.separatorChar) >= 0) {
           String p = name.substring(0, name.lastIndexOf(File.separatorChar) + 1);
           File dirFile = new File(parent + p);
           dirFile.mkdirs();
         }
         if (!entry.isDirectory()) {
           System.out.println("Installing " + outFile);
           // Copy the file
           BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(outFile));
           BufferedInputStream in = new BufferedInputStream(zipFile.getInputStream(entry));
           int size = 1024;
           int n = 0;
           byte[] b = new byte[size];
           while ((n = in.read(b, 0, size)) != -1) out.write(b, 0, n);
           in.close();
           out.flush();
           out.close();
           // Count the file
           count++;
         }
       }
     }
     zipFile.close();
   } catch (Exception e) {
     System.err.println("...an error occured while installing " + outFile);
     e.printStackTrace();
     System.err.println("Error copying " + outFile.getName() + "\n" + e.getMessage());
     return -count;
   }
   System.out.println(count + " files were installed.");
   return count;
 }
Example #5
0
 /**
  * Converts a dir string to a linked dir string
  *
  * @param dir the directory string (e.g. /usr/local/httpd)
  * @param browserLink web-path to Browser.jsp
  */
 public static String dir2linkdir(String dir, String browserLink, int sortMode) {
   File f = new File(dir);
   StringBuffer buf = new StringBuffer();
   while (f.getParentFile() != null) {
     if (f.canRead()) {
       String encPath = URLEncoder.encode(f.getAbsolutePath());
       buf.insert(
           0,
           "<a href=\""
               + browserLink
               + "?sort="
               + sortMode
               + "&amp;dir="
               + encPath
               + "\">"
               + conv2Html(f.getName())
               + File.separator
               + "</a>");
     } else buf.insert(0, conv2Html(f.getName()) + File.separator);
     f = f.getParentFile();
   }
   if (f.canRead()) {
     String encPath = URLEncoder.encode(f.getAbsolutePath());
     buf.insert(
         0,
         "<a href=\""
             + browserLink
             + "?sort="
             + sortMode
             + "&amp;dir="
             + encPath
             + "\">"
             + conv2Html(f.getAbsolutePath())
             + "</a>");
   } else buf.insert(0, f.getAbsolutePath());
   return buf.toString();
 }
 private void debug(String mode, int x, int z, int count, String in) {
   debug(
       "REGION "
           + mode
           + " "
           + fileName.getName()
           + "["
           + x
           + ","
           + z
           + "] "
           + count
           + "B = "
           + in);
 }
Example #7
0
  public void backup(String wildCardPath) {
    try {
      if (wildCardPath.contains("*") || wildCardPath.contains("?")) {
        // Extract the path so we know where to start and get the name which contains the
        // wildcard so we know what to store:

        File wildCardFile = new File(wildCardPath);
        String parentDirectory = wildCardFile.getParent();
        String wildCardPattern = wildCardFile.getName();
        _pathMatcher = FileSystems.getDefault().getPathMatcher("glob:" + wildCardPattern);
        Files.walkFileTree(Paths.get(parentDirectory), this);
      } else storeFile(new File(wildCardPath));
    } catch (FileNotFoundException exception) {
      Console.printError("File/Directory not found: " + wildCardPath);
    } catch (IOException exception) {
      Console.printError(
          "File/Directory '%s' not stored because: '%s'", wildCardPath, exception.getMessage());
    }
  }
Example #8
0
  /**
   * Class constructor; creates a new Installer object, displays a JFrame introducing the program,
   * allows the user to select an install directory, and copies files from the jar into the
   * directory.
   */
  public Installer(String args[]) {
    // Inputs are --install-dir INSTALL_DIR
    for (int k = 0; k < args.length; k = k + 2) {

      switch (args[k]) {
        case "--install-dir":
          directory = new File(args[k + 1]);
          System.out.println(directory);
          break;
        case "--port":
          port = Integer.parseInt(args[k + 1]);
          break;
      }
    }

    cp = new Stream();

    // Find the installer program so we can get to the files.
    installer = getInstallerProgramFile();
    String name = installer.getName();
    programName = (name.substring(0, name.indexOf("-"))).toUpperCase();

    // Get the installation information
    thisJava = System.getProperty("java.version");
    thisJavaBits = System.getProperty("sun.arch.data.model") + " bits";

    // Find the ImageIO Tools and get the version
    String javaHome = System.getProperty("java.home");
    File extDir = new File(javaHome);
    extDir = new File(extDir, "lib");
    extDir = new File(extDir, "ext");
    File clib = getFile(extDir, "clibwrapper_jiio", ".jar");
    File jai = getFile(extDir, "jai_imageio", ".jar");
    imageIOTools = (clib != null) && clib.exists() && (jai != null) && jai.exists();
    if (imageIOTools) {
      Hashtable<String, String> jaiManifest = getManifestAttributes(jai);
      imageIOVersion = jaiManifest.get("Implementation-Version");
    }

    // Get the CTP.jar parameters
    Hashtable<String, String> manifest = getJarManifestAttributes("/CTP/libraries/CTP.jar");
    programDate = manifest.get("Date");
    buildJava = manifest.get("Java-Version");

    // Get the util.jar parameters
    Hashtable<String, String> utilManifest = getJarManifestAttributes("/CTP/libraries/util.jar");
    utilJava = utilManifest.get("Java-Version");

    // Get the MIRC.jar parameters (if the plugin is present)
    Hashtable<String, String> mircManifest = getJarManifestAttributes("/CTP/libraries/MIRC.jar");
    if (mircManifest != null) {
      mircJava = mircManifest.get("Java-Version");
      mircDate = mircManifest.get("Date");
      mircVersion = mircManifest.get("Version");
    }

    // Set up the installation information for display
    if (imageIOVersion.equals("")) {
      imageIOVersion = "<b><font color=\"red\">not installed</font></b>";
    } else if (imageIOVersion.startsWith("1.0")) {
      imageIOVersion = "<b><font color=\"red\">" + imageIOVersion + "</font></b>";
    }
    if (thisJavaBits.startsWith("64")) {
      thisJavaBits = "<b><font color=\"red\">" + thisJavaBits + "</font></b>";
    }
    boolean javaOK = (thisJava.compareTo(buildJava) >= 0);
    javaOK &= (thisJava.compareTo(utilJava) >= 0);
    javaOK &= (thisJava.compareTo(mircJava) >= 0);
    if (!javaOK) {
      thisJava = "<b><font color=\"red\">" + thisJava + "</font></b>";
    }

    if (directory == null) exit();

    // Point to the parent of the directory in which to install the program.
    // so the copy process works correctly for directory trees.
    //
    // If the user has selected a directory named "CTP",
    // then assume that this is the directory in which
    // to install the program.
    //
    // If the directory is not CTP, see if it is called "RSNA" and contains
    // the Launcher program, in which case we can assume that it is an
    // installation that was done with Bill Weadock's all-in-one installer for Windows.
    //
    // If neither of those cases is true, then this is already the parent of the
    // directory in which to install the program
    if (directory.getName().equals("CTP")) {
      directory = directory.getParentFile();
    } else if (directory.getName().equals("RSNA")
        && (new File(directory, "Launcher.jar")).exists()) {
      suppressFirstPathElement = true;
    }

    // Cleanup old releases
    cleanup(directory);

    // Get a port for the server.
    if (port < 0) {
      if (checkServer(-port, false)) {
        System.err.println(
            "CTP appears to be running.\nPlease stop CTP and run the installer again.");
        System.exit(0);
      }
    }

    // Now install the files and report the results.
    int count =
        unpackZipFile(installer, "CTP", directory.getAbsolutePath(), suppressFirstPathElement);
    if (count > 0) {
      // Create the service installer batch files.
      updateWindowsServiceInstaller();
      updateLinuxServiceInstaller();

      // If this was a new installation, set up the config file and set the port
      installConfigFile(port);

      // Make any necessary changes in the config file to reflect schema evolution
      fixConfigSchema();

      System.out.println("Installation complete.");
      System.out.println(programName + " has been installed successfully.");
      System.out.println(count + " files were installed.");
    } else {
      System.err.println("Installation failed.");
      System.err.println(programName + " could not be fully installed.");
    }
    if (!programName.equals("ISN") && startRunner(new File(directory, "CTP"))) System.exit(0);
  }
Example #9
0
  private void cleanup(File directory) {
    // Clean up from old installations, removing or renaming files.
    // Note that directory is the parent of the CTP directory
    // unless the original installation was done by Bill Weadock's
    // all-in-one installer for Windows.

    // Get a file pointing to the CTP directory.
    // This might be the current directory, or
    // it might be the CTP child.
    File dir;
    if (directory.getName().equals("RSNA")) dir = directory;
    else dir = new File(directory, "CTP");

    // If CTP.jar exists in this directory, it is a really
    // old CTP main file - not used anymore
    File ctp = new File(dir, "CTP.jar");
    if (ctp.exists()) ctp.delete();

    // These are old names for the Launcher.jar file
    File launcher = new File(dir, "CTP-launcher.jar");
    if (launcher.exists()) launcher.delete();
    launcher = new File(dir, "TFS-launcher.jar");
    if (launcher.exists()) launcher.delete();

    // Delete the obsolete CTP-runner.jar file
    File runner = new File(dir, "CTP-runner.jar");
    if (runner.exists()) runner.delete();

    // Delete the obsolete MIRC-copier.jar file
    File copier = new File(dir, "MIRC-copier.jar");
    if (copier.exists()) copier.delete();

    // Rename the old versions of the properties files
    File oldprops = new File(dir, "CTP-startup.properties");
    File newprops = new File(dir, "CTP-launcher.properties");
    File correctprops = new File(dir, "Launcher.properties");
    if (oldprops.exists()) {
      if (newprops.exists() || correctprops.exists()) oldprops.delete();
      else oldprops.renameTo(correctprops);
    }
    if (newprops.exists()) {
      if (correctprops.exists()) newprops.delete();
      else newprops.renameTo(correctprops);
    }

    // Get rid of obsolete startup and shutdown programs
    File startup = new File(dir, "CTP-startup.jar");
    if (startup.exists()) startup.delete();
    File shutdown = new File(dir, "CTP-shutdown.jar");
    if (shutdown.exists()) shutdown.delete();

    // Get rid of the obsolete linux directory
    File linux = new File(dir, "linux");
    if (linux.exists()) {
      startup = new File(linux, "CTP-startup.jar");
      if (startup.exists()) startup.delete();
      shutdown = new File(linux, "CTP-shutdown.jar");
      if (shutdown.exists()) shutdown.delete();
      linux.delete();
    }

    // clean up the libraries directory
    File libraries = new File(dir, "libraries");
    if (libraries.exists()) {
      // remove obsolete versions of the slf4j libraries
      // and the dcm4che-imageio libraries
      File[] files = libraries.listFiles();
      for (File file : files) {
        if (file.isFile()) {
          String name = file.getName();
          if (name.startsWith("slf4j-") || name.startsWith("dcm4che-imageio-rle")) {
            file.delete();
          }
        }
      }
      // remove the email subdirectory
      File email = new File(libraries, "email");
      deleteAll(email);
      // remove the xml subdirectory
      File xml = new File(libraries, "xml");
      deleteAll(xml);
      // remove the sftp subdirectory
      File sftp = new File(libraries, "sftp");
      deleteAll(xml);
      // move edtftpj.jar to the ftp directory
      File edtftpj = new File(libraries, "edtftpj.jar");
      if (edtftpj.exists()) {
        File ftp = new File(libraries, "ftp");
        ftp.mkdirs();
        File ftpedtftpj = new File(ftp, "edtftpj.jar");
        edtftpj.renameTo(ftpedtftpj);
      }
    }

    // remove the obsolete xml library under dir
    File xml = new File(dir, "xml");
    deleteAll(xml);

    // remove the dicom profiles so any
    // obsolete files will disappear
    File profiles = new File(dir, "profiles");
    File dicom = new File(profiles, "dicom");
    deleteAll(dicom);
    dicom.mkdirs();

    // Remove the index.html file so it will be rebuilt from
    // example-index.html when the system next starts.
    File root = new File(dir, "ROOT");
    if (root.exists()) {
      File index = new File(root, "index.html");
      index.delete();
    }
  }
Example #10
0
 public boolean accept(File file) {
   String name = file.getName();
   return name.startsWith(nameStart) && name.endsWith(nameEnd);
 }
 /**
  * Build and return a temporary file in the same directory and with the same extension as the
  * specified file.
  */
 protected File buildTempFile(File file) throws IOException {
   int i = file.getName().lastIndexOf('.');
   String ext = ((i == -1) ? ".zip" : file.getName().substring(i));
   File tempFile = File.createTempFile("temp", ext, file.getParentFile());
   return tempFile;
 }
Example #12
0
  /**
   * Compile with avr-gcc.
   *
   * @param sketch Sketch object to be compiled.
   * @param buildPath Where the temporary files live and will be built from.
   * @param primaryClassName the name of the combined sketch file w/ extension
   * @return true if successful.
   * @throws RunnerException Only if there's a problem. Only then.
   * 
  * [ROBOTIS]Changed prototype to support ARM Cortex-M3 based CM-900 Pandora project
  * 2012-09-26 [email protected]
  * */
  public boolean compile(Sketch sketch, //change return type[ROBOTIS]
                         String buildPath,
                         String primaryClassName,
                         boolean verbose,
                         List<String> ignored) throws RunnerException {
    this.sketch = sketch;
    this.buildPath = buildPath;
    this.primaryClassName = primaryClassName; //예를 들면 cpp파일로 변환된 AnalogReadSerial.cpp
    this.verbose = verbose;
    this.sketchIsCompiled = false;
    System.out.println("Compiler.compile() sketch ="+sketch.getName()+"buildpath ="+buildPath+"primaryClassName ="+primaryClassName);
    // the pms object isn't used for anything but storage
    MessageStream pms = new MessageStream(this);

    String avrBasePath = Base.getAvrBasePath();
    System.out.println("[ROBOTIS]avrBasePath ="+avrBasePath);
    Map<String, String> boardPreferences = Base.getBoardPreferences();
    String core = boardPreferences.get("build.core");
    System.out.println("[ROBOTIS]build.core ="+core);
    if (core == null) {
    	RunnerException re = new RunnerException(_("No board selected; please choose a board from the Tools > Board menu."));
      re.hideStackTrace();
      throw re;
    }
    String corePath;
    
    if (core.indexOf(':') == -1) {
      Target t = Base.getTarget();
      File coreFolder = new File(new File(t.getFolder(), "cores"), core);
      corePath = coreFolder.getAbsolutePath();
      
    } else {
      Target t = Base.targetsTable.get(core.substring(0, core.indexOf(':')));
      File coreFolder = new File(t.getFolder(), "cores");
      coreFolder = new File(coreFolder, core.substring(core.indexOf(':') + 1));
      corePath = coreFolder.getAbsolutePath();
    }

    System.out.println("[ROBOTIS]corePath ="+corePath);
    
    String variant = boardPreferences.get("build.variant");
    String variantPath = null;
    
    if (variant != null) {
      if (variant.indexOf(':') == -1) {
	Target t = Base.getTarget();
	File variantFolder = new File(new File(t.getFolder(), "variants"), variant);
	variantPath = variantFolder.getAbsolutePath();
      } else {
	Target t = Base.targetsTable.get(variant.substring(0, variant.indexOf(':')));
	File variantFolder = new File(t.getFolder(), "variants");
	variantFolder = new File(variantFolder, variant.substring(variant.indexOf(':') + 1));
	variantPath = variantFolder.getAbsolutePath();
      }
    }

    List<File> objectFiles = new ArrayList<File>();

   // 0. include paths for core + all libraries

   sketch.setCompilingProgress(20);
   List includePaths = new ArrayList();
   includePaths.add(corePath);
   if (variantPath != null) includePaths.add(variantPath);
   for (File file : sketch.getImportedLibraries()) {
     includePaths.add(file.getPath());
   }

   // 1. compile the sketch (already in the buildPath)

   sketch.setCompilingProgress(30);
   objectFiles.addAll(
     compileFiles(avrBasePath, buildPath, includePaths,
               findFilesInPath(buildPath, "S", false),
               findFilesInPath(buildPath, "c", false),
               findFilesInPath(buildPath, "cpp", false),
               boardPreferences));
   sketchIsCompiled = true;

   // 2. compile the libraries, outputting .o files to: <buildPath>/<library>/

   sketch.setCompilingProgress(40);
   for (File libraryFolder : sketch.getImportedLibraries()) {
     File outputFolder = new File(buildPath, libraryFolder.getName());
     File utilityFolder = new File(libraryFolder, "utility");
     createFolder(outputFolder);
     // this library can use includes in its utility/ folder
     includePaths.add(utilityFolder.getAbsolutePath());
     objectFiles.addAll(
       compileFiles(avrBasePath, outputFolder.getAbsolutePath(), includePaths,
               findFilesInFolder(libraryFolder, "S", false),
               findFilesInFolder(libraryFolder, "c", false),
               findFilesInFolder(libraryFolder, "cpp", false),
               boardPreferences));
     outputFolder = new File(outputFolder, "utility");
     createFolder(outputFolder);
     objectFiles.addAll(
       compileFiles(avrBasePath, outputFolder.getAbsolutePath(), includePaths,
               findFilesInFolder(utilityFolder, "S", false),
               findFilesInFolder(utilityFolder, "c", false),
               findFilesInFolder(utilityFolder, "cpp", false),
               boardPreferences));
     // other libraries should not see this library's utility/ folder
     includePaths.remove(includePaths.size() - 1);
   }

   // 3. compile the core, outputting .o files to <buildPath> and then
   // collecting them into the core.a library file.

   sketch.setCompilingProgress(50);
  includePaths.clear();
  includePaths.add(corePath);  // include path for core only
  if (variantPath != null) includePaths.add(variantPath);
  List<File> coreObjectFiles =
    compileFiles(avrBasePath, buildPath, includePaths,
              findFilesInPath(corePath, "S", true),
              findFilesInPath(corePath, "c", true),
              findFilesInPath(corePath, "cpp", true),
              boardPreferences);

   String runtimeLibraryName = buildPath + File.separator + "core.a";
   List baseCommandAR = new ArrayList(Arrays.asList(new String[] {
     avrBasePath + "avr-ar",
     "rcs",
     runtimeLibraryName
   }));
   for(File file : coreObjectFiles) {
     List commandAR = new ArrayList(baseCommandAR);
     commandAR.add(file.getAbsolutePath());
     execAsynchronously(commandAR);
   }

    // 4. link it all together into the .elf file
    // For atmega2560, need --relax linker option to link larger
    // programs correctly.
    String optRelax = "";
    String atmega2560 = new String ("atmega2560");
    if ( atmega2560.equals(boardPreferences.get("build.mcu")) ) {
        optRelax = new String(",--relax");
    }
   sketch.setCompilingProgress(60);
    List baseCommandLinker = new ArrayList(Arrays.asList(new String[] {
      avrBasePath + "avr-gcc",
      "-Os",
      "-Wl,--gc-sections"+optRelax,
      "-mmcu=" + boardPreferences.get("build.mcu"),
      "-o",
      buildPath + File.separator + primaryClassName + ".elf"
    }));

    for (File file : objectFiles) {
      baseCommandLinker.add(file.getAbsolutePath());
    }

    baseCommandLinker.add(runtimeLibraryName);
    baseCommandLinker.add("-L" + buildPath);
    baseCommandLinker.add("-lm");

    execAsynchronously(baseCommandLinker);

    List baseCommandObjcopy = new ArrayList(Arrays.asList(new String[] {
      avrBasePath + "avr-objcopy",
      "-O",
      "-R",
    }));
    
    List commandObjcopy;

    // 5. extract EEPROM data (from EEMEM directive) to .eep file.
    sketch.setCompilingProgress(70);
    commandObjcopy = new ArrayList(baseCommandObjcopy);
    commandObjcopy.add(2, "ihex");
    commandObjcopy.set(3, "-j");
    commandObjcopy.add(".eeprom");
    commandObjcopy.add("--set-section-flags=.eeprom=alloc,load");
    commandObjcopy.add("--no-change-warnings");
    commandObjcopy.add("--change-section-lma");
    commandObjcopy.add(".eeprom=0");
    commandObjcopy.add(buildPath + File.separator + primaryClassName + ".elf");
    commandObjcopy.add(buildPath + File.separator + primaryClassName + ".eep");
    execAsynchronously(commandObjcopy);
    
    // 6. build the .hex file
    sketch.setCompilingProgress(80);
    commandObjcopy = new ArrayList(baseCommandObjcopy);
    commandObjcopy.add(2, "ihex");
    commandObjcopy.add(".eeprom"); // remove eeprom data
    commandObjcopy.add(buildPath + File.separator + primaryClassName + ".elf");
    commandObjcopy.add(buildPath + File.separator + primaryClassName + ".hex");
    execAsynchronously(commandObjcopy);
    
    sketch.setCompilingProgress(90);
   
    return true;
  }
  /** The run method. */
  public void run() {
    instances.add(this);
    try {
      listener.startUnpack();
      String currentOs = System.getProperty("os.name").toLowerCase();
      //
      // Initialisations
      FileOutputStream out = null;
      ArrayList parsables = new ArrayList();
      ArrayList executables = new ArrayList();
      List packs = idata.selectedPacks;
      int npacks = packs.size();
      udata = UninstallData.getInstance();

      // Specific to the web installers
      if (idata.kind.equalsIgnoreCase("web") || idata.kind.equalsIgnoreCase("web-kunststoff")) {
        InputStream kin = getClass().getResourceAsStream("/res/WebInstallers.url");
        BufferedReader kreader = new BufferedReader(new InputStreamReader(kin));
        jarLocation = kreader.readLine();
      }

      // We unpack the selected packs
      for (int i = 0; i < npacks; i++) {
        // We get the pack stream
        int n = idata.allPacks.indexOf(packs.get(i));
        ObjectInputStream objIn = new ObjectInputStream(getPackAsStream(n));

        // We unpack the files
        int nfiles = objIn.readInt();
        listener.changeUnpack(0, nfiles, ((Pack) packs.get(i)).name);
        for (int j = 0; j < nfiles; j++) {
          // We read the header
          PackFile pf = (PackFile) objIn.readObject();
          if (null == pf.os || matchOS(currentOs, pf.os.toLowerCase())) {
            // We translate & build the path
            String path = translatePath(pf.targetPath);
            File pathFile = new File(path);
            String fname = pathFile.getName();
            int z = fname.length();
            File dest = pathFile.getParentFile();
            if (!dest.exists()) dest.mkdirs();

            // We add the path to the log,
            udata.addFile(path);

            listener.progressUnpack(j, path);

            // if this file exists and shouldnot override skip this file
            if (((pf.override == false) && (pathFile.exists()))) {
              objIn.skip(pf.length);
              continue;
            }

            // We copy the file
            out = new FileOutputStream(path);
            byte[] buffer = new byte[5120];
            long bytesCopied = 0;
            while (bytesCopied < pf.length) {
              int maxBytes =
                  (pf.length - bytesCopied < buffer.length
                      ? (int) (pf.length - bytesCopied)
                      : buffer.length);
              int bytesInBuffer = objIn.read(buffer, 0, maxBytes);
              if (bytesInBuffer == -1) throw new IOException("Unexpected end of stream");

              out.write(buffer, 0, bytesInBuffer);

              bytesCopied += bytesInBuffer;
            }
            // Cleanings
            out.close();

            // Empty dirs restoring
            String _n = pathFile.getName();
            if (_n.startsWith("izpack-keepme") && _n.endsWith(".tmp")) pathFile.delete();

          } else objIn.skip(pf.length);
        }

        // Load information about parsable files
        int numParsables = objIn.readInt();
        int k;
        for (k = 0; k < numParsables; k++) {
          ParsableFile pf = (ParsableFile) objIn.readObject();
          pf.path = translatePath(pf.path);
          parsables.add(pf);
        }

        // Load information about executable files
        int numExecutables = objIn.readInt();
        for (k = 0; k < numExecutables; k++) {
          ExecutableFile ef = (ExecutableFile) objIn.readObject();
          ef.path = translatePath(ef.path);
          if (null != ef.argList && !ef.argList.isEmpty()) {
            String arg = null;
            for (int j = 0; j < ef.argList.size(); j++) {
              arg = (String) ef.argList.get(j);
              arg = translatePath(arg);
              ef.argList.set(j, arg);
            }
          }
          executables.add(ef);
          if (ef.executionStage == ExecutableFile.UNINSTALL) {
            udata.addExecutable(ef);
          }
        }
        objIn.close();
      }

      // We use the scripts parser
      ScriptParser parser = new ScriptParser(parsables, vs);
      parser.parseFiles();

      // We use the file executor
      FileExecutor executor = new FileExecutor(executables);
      if (executor.executeFiles(ExecutableFile.POSTINSTALL) != 0)
        javax.swing.JOptionPane.showMessageDialog(
            null,
            "The installation was not completed.",
            "Installation warning",
            javax.swing.JOptionPane.WARNING_MESSAGE);

      // We put the uninstaller
      putUninstaller();

      // The end :-)
      listener.stopUnpack();
    } catch (Exception err) {
      listener.stopUnpack();
      listener.errorUnpack(err.toString());
    }
    instances.remove(instances.indexOf(this));
  }
Example #14
0
  public byte[] ZipIt(ArrayList<ResultType> items, String[] algorithm, String[] filetype)
      throws IOException {

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    ZipOutputStream zos = new ZipOutputStream(baos);
    BufferedInputStream bis;

    String[] files = new String[10000];

    File file;

    int bytesRead;

    byte[] buffer = new byte[1024];

    int j = 0;
    boolean flag;

    for (int i = 0; i < items.size(); i++) {

      ResultType g = (ResultType) items.get(i);

      String folder = g.get("genomeNames");

      file = new File("/storage/brcdownloads/patric2/genomes/" + folder);

      if (!file.exists()) {

        System.err.println("Skipping Folder: " + "/storage/brcdownloads/patric2/genomes/" + folder);
        continue;

      } else {
        for (int k = 0; k < algorithm.length; k++) {
          for (int m = 0; m < filetype.length; m++) {

            flag = false;

            file =
                new File(
                    "/storage/brcdownloads/patric2/genomes/"
                        + folder
                        + "/"
                        + folder
                        + (filetype[m].equals(".fna") ? "" : algorithm[k])
                        + filetype[m]);

            if (!file.exists()) {
              System.err.println("Skipping File: " + file.getAbsolutePath());
            } else {
              // System.out.println("File: " + file.getAbsolutePath());
              for (int z = 0; z < files.length; z++) {
                if (files[z] != null && files[z].equals(file.getAbsolutePath())) {
                  flag = true;
                  break;
                }
              }
              // System.out.println(flag);
              if (!flag) {
                files[j] = file.getAbsolutePath();
                j++;
              }
            }
          }
        }
      }
    }
    // System.out.println(j);
    if (j > 0) {
      for (int i = 0; i < j; i++) {
        file = new File(files[i]);
        bis = new BufferedInputStream(new FileInputStream(file));
        ZipEntry entry = new ZipEntry(file.getName());
        zos.putNextEntry(entry);
        while ((bytesRead = bis.read(buffer)) != -1) {
          zos.write(buffer, 0, bytesRead);
        }
        bis.close();
        zos.closeEntry();
      }
      zos.close();
    }

    return baos.toByteArray();
  }