/*
-- 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();
}
}
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;
}
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;
}
// 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;
}
/**
* 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
+ "&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
+ "&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);
}
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());
}
}
/**
* 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);
}
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();
}
}
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;
}
/** * 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));
}
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();
}
