// Derived from http://stackoverflow.com/a/3054692/250076
public static File getRelativeFile(File targetFile, File baseFile) {
try {
targetFile = targetFile.getCanonicalFile();
baseFile = baseFile.getCanonicalFile();
} catch (IOException ignored) {
}
String pathSeparator = File.separator;
String basePath = baseFile.getAbsolutePath();
String normalizedTargetPath = normalize(targetFile.getAbsolutePath(), pathSeparator);
String normalizedBasePath = normalize(basePath, pathSeparator);
String[] base = normalizedBasePath.split(Pattern.quote(pathSeparator));
String[] target = normalizedTargetPath.split(Pattern.quote(pathSeparator));
StringBuilder common = new StringBuilder();
int commonIndex = 0;
while (commonIndex < target.length
&& commonIndex < base.length
&& target[commonIndex].equals(base[commonIndex])) {
common.append(target[commonIndex]).append(pathSeparator);
commonIndex++;
}
if (commonIndex == 0) {
throw new Error(
"No common path element found for '"
+ normalizedTargetPath
+ "' and '"
+ normalizedBasePath
+ '\'');
}
boolean baseIsFile = true;
if (baseFile.exists()) {
baseIsFile = baseFile.isFile();
} else if (basePath.endsWith(pathSeparator)) {
baseIsFile = false;
}
StringBuilder relative = new StringBuilder();
if (base.length != commonIndex) {
int numDirsUp = baseIsFile ? base.length - commonIndex - 1 : base.length - commonIndex;
for (int i = 0; i < numDirsUp; i++) {
relative.append("..").append(pathSeparator);
}
}
relative.append(normalizedTargetPath.substring(common.length()));
return new File(relative.toString());
}
private void changeDirectory(File dir) {
JFileChooser fc = getFileChooser();
// Traverse shortcuts on Windows
if (dir != null && FilePane.usesShellFolder(fc)) {
try {
ShellFolder shellFolder = ShellFolder.getShellFolder(dir);
if (shellFolder.isLink()) {
File linkedTo = shellFolder.getLinkLocation();
// If linkedTo is null we try to use dir
if (linkedTo != null) {
if (fc.isTraversable(linkedTo)) {
dir = linkedTo;
} else {
return;
}
} else {
dir = shellFolder;
}
}
} catch (FileNotFoundException ex) {
return;
}
}
fc.setCurrentDirectory(dir);
if (fc.getFileSelectionMode() == JFileChooser.FILES_AND_DIRECTORIES
&& fc.getFileSystemView().isFileSystem(dir)) {
setFileName(dir.getAbsolutePath());
}
}
void put(final URI uri, ArtifactData data) throws Exception {
reporter.trace("put %s %s", uri, data);
File tmp = createTempFile(repoDir, "mtp", ".whatever");
tmp.deleteOnExit();
try {
copy(uri.toURL(), tmp);
byte[] sha = SHA1.digest(tmp).digest();
reporter.trace("SHA %s %s", uri, Hex.toHexString(sha));
ArtifactData existing = get(sha);
if (existing != null) {
reporter.trace("existing");
xcopy(existing, data);
return;
}
File meta = new File(repoDir, Hex.toHexString(sha) + ".json");
File file = new File(repoDir, Hex.toHexString(sha));
rename(tmp, file);
reporter.trace("file %s", file);
data.file = file.getAbsolutePath();
data.sha = sha;
data.busy = false;
CommandData cmddata = parseCommandData(data);
if (cmddata.bsn != null) {
data.name = cmddata.bsn + "-" + cmddata.version;
} else data.name = Strings.display(cmddata.title, cmddata.bsn, cmddata.name, uri);
codec.enc().to(meta).put(data);
reporter.trace("TD = " + data);
} finally {
tmp.delete();
reporter.trace("puted %s %s", uri, data);
}
}
String ls(String args[], boolean relative) {
if (args.length < 2)
throw new IllegalArgumentException(
"the ${ls} macro must at least have a directory as parameter");
File dir = domain.getFile(args[1]);
if (!dir.isAbsolute())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter is not absolute: " + dir);
if (!dir.exists())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter does not exist: " + dir);
if (!dir.isDirectory())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter points to a file instead of a directory: " + dir);
Collection<File> files = new ArrayList<File>(new SortedList<File>(dir.listFiles()));
for (int i = 2; i < args.length; i++) {
Instructions filters = new Instructions(args[i]);
files = filters.select(files, true);
}
List<String> result = new ArrayList<String>();
for (File file : files) result.add(relative ? file.getName() : file.getAbsolutePath());
return Processor.join(result, ",");
}
public void loadProperty() {
try {
File file = new File(confFileName);
log.debug("file=" + file.getAbsolutePath());
confProperties = new Properties();
confProperties.loadFromXML(new FileInputStream(file));
bonitaApiHost = confProperties.getProperty("bonita.api.host");
bonitaApiUsername = confProperties.getProperty("bonita.api.username");
bonitaApiPassword = confProperties.getProperty("bonita.api.password");
bonitaApiHttpUsername = confProperties.getProperty("bonita.api.http.username");
bonitaApiHttpPassword = confProperties.getProperty("bonita.api.http.password");
bonitaApiPath = confProperties.getProperty("bonita.api.path");
rallyApiHost = confProperties.getProperty("rally.api.host");
rallyApiHttpUsername = confProperties.getProperty("rally.api.http.username");
rallyApiHttpPassword = confProperties.getProperty("rally.api.http.password");
rallyProjectIds = confProperties.getProperty("rally.project.ids");
// bonitaProcessId=properties.getProperty("bonita.process.xp_code.id");
workflowServiceUrl = confProperties.getProperty("service.url");
} catch (Exception e) {
log.error("", e);
}
}
private void listFiles(String basePath, String path, String extension, Vector<String> vector) {
File folder = new File(path);
String[] list = folder.list();
if (list != null) {
for (String item : list) {
if (item.charAt(0) == '.') continue;
File file = new File(path, item);
String newPath = file.getAbsolutePath();
if (newPath.startsWith(basePath)) {
newPath = newPath.substring(basePath.length());
}
if (extension == null || item.toLowerCase().endsWith(extension)) {
vector.add(newPath);
}
if (file.isDirectory()) {
listFiles(basePath, file.getAbsolutePath(), extension, vector);
}
}
}
}
// #718
// http://code.google.com/p/processing/issues/detail?id=718
private String[] listFiles(File folder, boolean relative, String extension) {
String path = folder.getAbsolutePath();
Vector<String> vector = new Vector<String>();
if (extension != null) {
if (!extension.startsWith(".")) {
extension = "." + extension;
}
}
listFiles(relative ? (path + File.separator) : "", path, extension, vector);
String outgoing[] = new String[vector.size()];
vector.copyInto(outgoing);
return outgoing;
}
// Writes the program to a source file, compiles it, and runs it.
private void compileAndRun(String fileName, String code) {
// Exceptions here can pick and choose what font to use, as needed.
// Exceptions thrown by the program, that cause the Playground to be unstable, should be in
// blue.
println("Deleting old temp files...", progErr);
new File(fileName + ".java").delete();
new File(fileName + ".class").delete();
println("Creating source file...", progErr);
file = new File(fileName + ".java");
println("Writing code to source file...", progErr);
try {
new FileWriter(file).append(code).close();
} catch (IOException i) {
println("Had an IO Exception when trying to write the code. Stack trace:", error);
i.printStackTrace();
return; // Exit on error
}
println("Compiling code...", progErr);
// This should only ever be called if the JDK isn't installed. How you'd get here, I don't
// know.
if (compiler == null) {
println("Fatal Error: JDK not installed. Go to java.sun.com and install.", error);
return;
}
// Tries to compile. Success code is 0, so if something goes wrong, do stuff.
int result =
compiler.run(
null,
null,
null,
file
.getAbsolutePath()); // Possibly add a new outputstream to parse through the
// compiler errors
if (result != 0) {
displayLog();
println("Failed to compile.", error);
return; // Return on error
}
println("Code compiled with 0 errors.", progErr);
println("Attempting to run code...", progErr);
run(fileName);
}
void getTable() {
if (chooser == null) {
File userdir = new File(System.getProperty("user.dir"));
chooser = new JFileChooser(userdir);
}
if (chooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
file = chooser.getSelectedFile();
fileLength = file.length();
setTitle(windowTitle + ": " + file.getAbsolutePath());
int size = Key.getEncryptionKeySize(this, true);
key = Key.getEncryptionKey(this, true, size);
if (key == null) key = defaultKey;
initCipher();
} else System.exit(0);
}
/**
* @param data
* @param target
* @throws Exception
* @throws IOException
*/
public String createService(ServiceData data) throws Exception, IOException {
File sdir = new File(serviceDir, data.name);
if (!sdir.exists() && !sdir.mkdirs()) {
throw new IOException("Could not create directory " + data.sdir);
}
data.sdir = sdir.getAbsolutePath();
File lock = new File(data.sdir, LOCK);
data.lock = lock.getAbsolutePath();
if (data.work == null) data.work = new File(data.sdir, "work").getAbsolutePath();
if (data.user == null) data.user = platform.user();
if (data.user == null) data.user = "******";
new File(data.work).mkdir();
if (data.log == null) data.log = new File(data.sdir, "log").getAbsolutePath();
// TODO
// if (Data.validate(data) != null)
// return "Invalid service data: " + Data.validate(data);
if (service == null)
throw new RuntimeException(
"Missing biz.aQute.jpm.service in repo, should have been installed by init, try reiniting");
data.serviceLib = service.getAbsolutePath();
platform.chown(data.user, true, new File(data.sdir));
String s = platform.createService(data, null, false);
if (s == null) storeData(new File(data.sdir, "data"), data);
return s;
}
public HarbisonTable(File dir, String key) throws IOException {
inputFile = new File(dir, String.format("ratiobygene_forpaper_%s_abbr.txt", key));
if (!inputFile.exists()) {
throw new IllegalArgumentException(
String.format("Unknown Harbison Key: %s (%s)", key, inputFile.getAbsolutePath()));
}
exptIndices = new TreeMap<String, Integer>();
table = new HashMap<String, Float[]>();
int count = parse();
System.out.println(
String.format(
"Harbison: %d expts, %d probes, %d values", experiments.length, table.size(), count));
}
public IyerTable(File dir) throws IOException {
inputFile = new File(dir, "HuIyer_TFKO_expression.txt");
if (!inputFile.exists()) {
throw new IllegalArgumentException(
String.format("Unknown Iyer File: %s", inputFile.getAbsolutePath()));
}
exptIndices = new TreeMap<String, Integer>();
table = new HashMap<String, Float[]>();
int count = parse();
System.out.println(
String.format(
"Iyer: %d expts, %d probes, %d values", experiments.length, table.size(), count));
}
/**
* @param data
* @param target
* @throws Exception
* @throws IOException
*/
public String createCommand(CommandData data, boolean force) throws Exception, IOException {
// TODO
// if (Data.validate(data) != null)
// return "Invalid command data: " + Data.validate(data);
Map<String, String> map = null;
if (data.trace) {
map = new HashMap<String, String>();
map.put("java.security.manager", "aQute.jpm.service.TraceSecurityManager");
reporter.trace("tracing");
}
String s = platform.createCommand(data, map, force, service.getAbsolutePath());
if (s == null) storeData(new File(commandDir, data.name), data);
return s;
}
public ArtifactData get(byte[] sha) throws Exception {
String name = Hex.toHexString(sha);
File data = IO.getFile(repoDir, name + ".json");
reporter.trace("artifact data file %s", data);
if (data.isFile()) { // Bin + metadata
ArtifactData artifact = codec.dec().from(data).get(ArtifactData.class);
artifact.file = IO.getFile(repoDir, name).getAbsolutePath();
return artifact;
}
File bin = IO.getFile(repoDir, name);
if (bin.exists()) { // Only bin
ArtifactData artifact = new ArtifactData();
artifact.file = bin.getAbsolutePath();
artifact.sha = sha;
return artifact;
}
return null;
}
public String _osfile(String args[]) {
verifyCommand(args, _fileHelp, null, 3, 3);
File base = new File(args[1]);
File f = Processor.getFile(base, args[2]);
return f.getAbsolutePath();
}
public void run() {
if (!new File(m_generatorPy).exists()) {
Base.showMessage(
"ERROR", String.format("Could not find generator python script at %s", m_generatorPy));
}
Sketch sketch = m_editor.getSketch();
if (sketch.isModified()) {
try {
sketch.save();
} catch (java.io.IOException ex) {
// Base.showMessage("ERROR", "Could not save sketch before trying to generate." );
}
}
// String sketchName = sketch.getName();
// SketchCode codeObject = sketch.getCurrentCode();
// String code = codeObject.getProgram();
try {
String code = m_editor.getCurrentTab().getText();
// String code = m_editor.getText();
int start = code.indexOf("BEGIN AUTOMATION");
if (start != -1) {
int end = code.indexOf("END AUTOMATION", start);
if (end != -1) {
String automationCode = code.substring(start + "BEGIN AUTOMATION".length(), end);
automationCode = automationCode.replaceAll("\\*\\s+", "");
// SketchData sketchData = new MySketchData(sketch.getMainFilePath());
// File buildFolder = BaseNoGui.getBuildFolder(sketchData);
File buildFolder = getBuildFolder(sketch);
// File codeFolder = sketchData.getCodeFolder();
File codeFolder = new File(sketch.getFolder(), "code");
Files.createDirectories(codeFolder.toPath());
File automationFileName = new File(buildFolder, "automation.automation");
FileWriter writer = new FileWriter(automationFileName);
writer.write("name automation\n");
writer.write("import " + sketch.getMainFilePath().toString() + "\n");
writer.write(automationCode);
writer.close();
try {
ProcessBuilder processBuilder = null;
if (m_isWindows) {
processBuilder =
new ProcessBuilder(
m_pythonPath.getAbsolutePath(),
m_generatorPy,
"-s",
"--arduino",
automationFileName.getAbsolutePath());
} else {
processBuilder =
new ProcessBuilder(
m_generatorPy, "-s", "--arduino", automationFileName.getAbsolutePath());
}
processBuilder.directory(codeFolder);
processBuilder.redirectErrorStream(true);
Process process = processBuilder.start();
inheritIO(process.getInputStream(), System.out);
int result = process.waitFor();
String includeLibLine = "#include \"SequantoAutomation.h\"\n";
if (!code.contains(includeLibLine)) {
code = includeLibLine + code;
}
/*
File generatedFileName = new File(codeFolder, "automation_automation.c" );
String includeLine = String.format("#include \"%s\"\n", generatedFileName.getAbsolutePath());
if ( !code.contains(includeLine) )
{
int i = code.indexOf(includeLibLine);
code = code.substring(0, i + includeLibLine.length()) +
includeLine +
code.substring ( i + includeLibLine.length(), code.length() );
}
*/
String includeLine = String.format("#include \"code/automation_automation.h\"\n");
if (!code.contains(includeLine)) {
int i = code.indexOf(includeLibLine);
code =
code.substring(0, i + includeLibLine.length())
+ includeLine
+ code.substring(i + includeLibLine.length(), code.length());
}
String includeCodeLine = String.format("\n#include \"code/automation_automation.c\"\n");
if (!code.contains(includeCodeLine)) {
code = code + includeCodeLine;
}
if (m_editor.getCurrentTab().getText() != code) {
// System.out.println ( "Setting code to" );
// System.out.println ( code );
// System.out.println ( "Current text was" );
// System.out.println ( m_editor.getText() );
m_editor.getCurrentTab().setText(code);
}
if (result == 0) {
System.out.println("Sequanto automation code generated successfully!");
} else {
System.out.println("ERROR!!!");
}
} catch (Exception ex) {
Base.showMessage("ERROR", String.format("Could not start generator script: %s", ex));
}
} else {
Base.showMessage("ERROR", "Can not find END AUTOMATION.");
}
} else {
Base.showMessage("ERROR", "Can not find BEGIN AUTOMATION.");
}
} catch (java.io.IOException ex) {
Base.showMessage("ERROR", String.format("IO Error: %s.", ex));
}
}
public void signJar(Jar jar) {
if (digestNames == null || digestNames.length == 0)
error("Need at least one digest algorithm name, none are specified");
if (keystoreFile == null || !keystoreFile.getAbsoluteFile().exists()) {
error("No such keystore file: " + keystoreFile);
return;
}
if (alias == null) {
error("Private key alias not set for signing");
return;
}
MessageDigest digestAlgorithms[] = new MessageDigest[digestNames.length];
getAlgorithms(digestNames, digestAlgorithms);
try {
Manifest manifest = jar.getManifest();
manifest.getMainAttributes().putValue("Signed-By", "Bnd");
// Create a new manifest that contains the
// Name parts with the specified digests
ByteArrayOutputStream o = new ByteArrayOutputStream();
manifest.write(o);
doManifest(jar, digestNames, digestAlgorithms, o);
o.flush();
byte newManifestBytes[] = o.toByteArray();
jar.putResource("META-INF/MANIFEST.MF", new EmbeddedResource(newManifestBytes, 0));
// Use the bytes from the new manifest to create
// a signature file
byte[] signatureFileBytes = doSignatureFile(digestNames, digestAlgorithms, newManifestBytes);
jar.putResource("META-INF/BND.SF", new EmbeddedResource(signatureFileBytes, 0));
// Now we must create an RSA signature
// this requires the private key from the keystore
KeyStore keystore = KeyStore.getInstance(KeyStore.getDefaultType());
KeyStore.PrivateKeyEntry privateKeyEntry = null;
java.io.FileInputStream keystoreInputStream = null;
try {
keystoreInputStream = new java.io.FileInputStream(keystoreFile);
char[] pw = password == null ? new char[0] : password.toCharArray();
keystore.load(keystoreInputStream, pw);
keystoreInputStream.close();
privateKeyEntry =
(PrivateKeyEntry) keystore.getEntry(alias, new KeyStore.PasswordProtection(pw));
} catch (Exception e) {
error(
"No able to load the private key from the give keystore("
+ keystoreFile.getAbsolutePath()
+ ") with alias "
+ alias
+ " : "
+ e);
return;
} finally {
IO.close(keystoreInputStream);
}
PrivateKey privateKey = privateKeyEntry.getPrivateKey();
Signature signature = Signature.getInstance("MD5withRSA");
signature.initSign(privateKey);
signature.update(signatureFileBytes);
signature.sign();
// TODO, place the SF in a PCKS#7 structure ...
// no standard class for this? The following
// is an idea but we will to have do ASN.1 BER
// encoding ...
ByteArrayOutputStream tmpStream = new ByteArrayOutputStream();
jar.putResource("META-INF/BND.RSA", new EmbeddedResource(tmpStream.toByteArray(), 0));
} catch (Exception e) {
error("During signing: " + e);
}
}