/** Connect timeout in milliseconds. Default 120 secs. */
public int connectionTimeoutMs() {
long defaultNetworkTimeoutS =
JavaUtils.timeStringAsSec(conf.get("spark.network.timeout", "120s"));
long defaultTimeoutMs =
JavaUtils.timeStringAsSec(
conf.get("spark.shuffle.io.connectionTimeout", defaultNetworkTimeoutS + "s"))
* 1000;
return (int) defaultTimeoutMs;
}
/**
* Test that types with infinite recursion don't cause us to bomb out. In this case we use Enum,
* as Enum<E> has E extend Enum<E>.
*/
public void testEnumInfiniteRecursion() {
JavaUtils ju = JavaUtils.getJavaUtils();
try {
Class<?> enumClass = getClass().getClassLoader().loadClass("java.lang.Enum");
ju.getTypeParams(enumClass);
} catch (ClassNotFoundException cnfe) {
}
// ok test passed
}
public void testTparReturn() throws Exception {
Class<?> colClass = java.util.Collections.class;
Method minMethod = colClass.getMethod("min", Collection.class);
JavaUtils ju = JavaUtils.getJavaUtils();
JavaType type = JavaUtils.genTypeFromClass(minMethod.getReturnType());
assertNotNull(type.asClass());
type = ju.getReturnType(minMethod);
assertEquals("T", type.toString());
}
/**
* Test that we can't access a package-private member from a class which isn't a superclass, even
* if a superclass is in the same package.
*/
public void testAccessCheck2() {
TestReflective baseR = new TestReflective("Base");
TestReflective subR = new TestReflective("somepkg.Sub", baseR);
TestReflective otherR = new TestReflective("Other");
assertFalse(JavaUtils.checkMemberAccess(otherR, new GenTypeClass(subR), subR, 0, false));
}
/**
* Test that a subclass can only access a protected member from the superclass via an expression
* of subclass type.
*/
public void testAccessCheck3() {
TestReflective baseR = new TestReflective("Base");
TestReflective subR = new TestReflective("somepkg.Sub", baseR);
TestReflective subsubR = new TestReflective("somepkg.SubSub", subR);
assertFalse(
JavaUtils.checkMemberAccess(
baseR, new GenTypeClass(baseR), subR, Modifier.PROTECTED, false));
assertTrue(
JavaUtils.checkMemberAccess(
baseR, new GenTypeClass(subR), subR, Modifier.PROTECTED, false));
assertTrue(
JavaUtils.checkMemberAccess(
baseR, new GenTypeClass(subsubR), subR, Modifier.PROTECTED, false));
}
public DisplayPlus(
final ImageCache stitchedCache,
AcquisitionEngine eng,
JSONObject summaryMD,
boolean invX,
boolean invY,
boolean swapXY) {
eng_ = eng;
invertX_ = invX;
invertY_ = invY;
swapXY_ = swapXY;
try {
MultiStagePosition pos0 = MMStudioMainFrame.getInstance().getPositionList().getPosition(0);
pos0x_ = pos0.getX();
pos0y_ = pos0.getY();
tileWidth_ = MDUtils.getHeight(summaryMD);
tileHeight_ = MDUtils.getWidth(summaryMD);
} catch (Exception e) {
ReportingUtils.showError("Couldnt get grid info");
}
vad_ =
new VirtualAcquisitionDisplay(stitchedCache, eng, WINDOW_TITLE) {
public void showImage(final JSONObject tags, boolean waitForDisplay)
throws InterruptedException, InvocationTargetException {
// Since this is multichannel camera, only show when last channel arrives
try {
if (MDUtils.getChannelIndex(tags) == super.getNumChannels() - 1) {
super.showImage(tags, waitForDisplay);
} else {
ImagePlus ip = super.getHyperImage();
if (ip != null) {
// canvas never gets painted so need to set painpending false
ip.getCanvas().setPaintPending(false);
}
}
} catch (JSONException ex) {
}
}
};
DisplayControls controls = new Controls();
// Add in custom controls
try {
JavaUtils.setRestrictedFieldValue(
vad_, VirtualAcquisitionDisplay.class, "controls_", controls);
} catch (NoSuchFieldException ex) {
ReportingUtils.showError("Couldn't create display controls");
}
vad_.show();
// Zoom to 100%
vad_.getImagePlus().getWindow().getCanvas().unzoom();
// add mouse listeners for moving grids
addMouseListeners();
stitchedCache.addImageCacheListener(this);
}
/** Test that method/constructor signatures are constructed correctly. */
public void testSignatures() {
boolean onjava5 = true;
// String majorVersion = System.getProperty("java.specification.version");
// boolean onjava6 = majorVersion.compareTo("1.6") >= 0;
Method sampleMeth = null;
Class<? extends JavaUtilTests> thisClass = getClass();
try {
sampleMeth = thisClass.getMethod("sampleMethod", new Class[] {int.class, int.class});
} catch (NoSuchMethodException nsme) {
fail();
}
String sig = JavaUtils.getSignature(sampleMeth);
assertEquals(sig, "void sampleMethod(int, int)");
if (onjava5) {
// test a varargs method
Class<?> clazz = Class.class;
try {
sampleMeth = clazz.getMethod("getConstructor", new Class[] {Class[].class});
} catch (NoSuchMethodException nsme) {
fail();
}
sig = JavaUtils.getSignature(sampleMeth);
assertEquals("java.lang.reflect.Constructor getConstructor(java.lang.Class[])", sig);
}
try {
sampleMeth = thisClass.getMethod("sampleMethod2", new Class[] {String[].class});
} catch (NoSuchMethodException nsme) {
fail();
}
sig = JavaUtils.getSignature(sampleMeth);
assertEquals("void sampleMethod2(java.lang.String[])", sig);
}
public void testRecursiveTpar() throws Exception {
Class<?> colClass = java.util.Collections.class;
Method minMethod = colClass.getMethod("min", Collection.class);
JavaUtils ju = JavaUtils.getJavaUtils();
List<GenTypeDeclTpar> rlist = ju.getTypeParams(minMethod);
assertEquals(1, rlist.size());
GenTypeDeclTpar tvar = rlist.get(0);
GenTypeSolid bound = tvar.getBound();
assertEquals("java.lang.Comparable<? super T>", bound.toString());
GenTypeSolid[] ubounds = bound.getUpperBounds();
assertEquals(2, ubounds.length); // should be Object and Comparable
GenTypeClass boundClass = bound.getUpperBounds()[1].asClass();
List<? extends GenTypeParameter> tpars = boundClass.getTypeParamList();
assertEquals(1, tpars.size());
GenTypeParameter tparOne = tpars.get(0);
GenTypeSolid shouldBeT = tparOne.getLowerBound();
assertNotNull(shouldBeT);
Set<Reflective> s = new HashSet<Reflective>();
shouldBeT.erasedSuperTypes(s);
assertTrue(s.size() > 0);
boolean foundComparable = false;
for (Reflective r : s) {
if (r.getName().equals("java.lang.Comparable")) {
foundComparable = true;
break;
}
}
assertTrue(foundComparable);
}
public static Connection getConnectionFromConfigFile(String filename) throws Exception {
System.setProperty("http.proxyHost", "wwwcache.sanger.ac.uk");
System.setProperty("http.proxyPort", "3128");
File f = new File(filename);
String s = JavaUtils.streamToString(new FileInputStream(f));
String[] lines = s.split("\n");
HashMap<String, String> props = new HashMap<String, String>();
String host = "";
String user = "";
String password = "";
String port = "";
String db = "";
for (String line : lines) {
if (line.startsWith("#")) continue;
String[] keyval = line.split("=");
if (keyval.length < 2) continue;
String k = keyval[0].trim().toLowerCase();
String v = keyval[1].trim();
if (k.equals("host")) {
host = v;
} else if (k.equals("user")) {
user = v;
} else if (k.equals("password")) {
password = v;
} else if (k.equals("port")) {
port = v;
} else if (k.equals("db")) {
db = v;
}
}
Connection c = null;
Class.forName("com.mysql.jdbc.Driver").newInstance();
System.out.println(
"User: "******"\n" + "Host: " + host + "\nDB: " + db + "\nPW:" + password + "\n");
if (port.equals("")) {
c = DriverManager.getConnection("jdbc:mysql://" + host + "/" + db, user, password);
} else {
c =
DriverManager.getConnection(
"jdbc:mysql://" + host + ":" + port + "/" + db, user, password);
}
return c;
}
@Override
public boolean accept(File pathname) {
String name = pathname.getName();
int n = name.lastIndexOf(".");
String suffix = name.substring(1 + n).toLowerCase();
if (fileSuffixes_ == null || fileSuffixes_.length == 0) {
return true;
}
if (!JavaUtils.isMac() && pathname.isDirectory()) {
return true;
}
for (int i = 0; i < fileSuffixes_.length; ++i) {
if (fileSuffixes_[i] != null && fileSuffixes_[i].toLowerCase().contentEquals(suffix)) {
return true;
}
}
return false;
}
public void init() {
// Make Minecraft portable ! :D
final File workDirectory = Utils.getWorkingDirectory(launcherFrame);
try {
final List<Field> fields =
JavaUtils.getFieldsWithType(
classLoader.loadClass("net.minecraft.client.Minecraft"), File.class);
for (final Field field : fields) {
field.setAccessible(true);
try {
field.get(classLoader.loadClass("net.minecraft.client.Minecraft"));
field.set(null, workDirectory);
} catch (final IllegalArgumentException e) {
} catch (final IllegalAccessException e) {
}
}
} catch (final ClassNotFoundException e) {
MCLogger.info(e.getLocalizedMessage());
}
}
public static File show(
Window parent,
String title,
File startFile,
boolean selectDirectories,
boolean load,
final String fileDescription,
final String[] fileSuffixes,
boolean suggestFileName) {
File selectedFile = null;
GeneralFileFilter filter = new GeneralFileFilter(fileDescription, fileSuffixes);
if (JavaUtils.isMac()) {
if (selectDirectories) {
// For Mac we only select directories, unfortunately!
System.setProperty("apple.awt.fileDialogForDirectories", "true");
}
int mode = load ? FileDialog.LOAD : FileDialog.SAVE;
FileDialog fd;
if (parent instanceof Dialog) {
fd = new FileDialog((Dialog) parent, title, mode);
} else if (parent instanceof Frame) {
fd = new FileDialog((Frame) parent, title, mode);
} else {
fd = new FileDialog((Dialog) null, title, mode);
}
if (startFile != null) {
if (startFile.isDirectory()) {
fd.setDirectory(startFile.getAbsolutePath());
} else {
fd.setDirectory(startFile.getParent());
}
if (!load && suggestFileName) {
fd.setFile(startFile.getName());
}
}
if (fileSuffixes != null) {
fd.setFilenameFilter(filter);
}
fd.setVisible(true);
if (selectDirectories) {
System.setProperty("apple.awt.fileDialogForDirectories", "false");
}
if (fd.getFile() != null) {
selectedFile = new File(fd.getDirectory() + "/" + fd.getFile());
if (mode == FileDialog.SAVE) {
if (!filter.accept(selectedFile)) {
selectedFile = new File(selectedFile.getAbsolutePath() + "." + fileSuffixes[0]);
}
}
}
fd.dispose();
} else {
JFileChooser fc = new JFileChooser();
if (startFile != null) {
if ((!load && suggestFileName) || startFile.isDirectory()) {
fc.setSelectedFile(startFile);
} else {
fc.setSelectedFile(startFile.getParentFile());
}
}
fc.setDialogTitle(title);
if (selectDirectories) {
fc.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
}
if (fileSuffixes != null) {
fc.setFileFilter(filter);
}
int returnVal;
if (load) {
returnVal = fc.showOpenDialog(parent);
} else {
returnVal = fc.showSaveDialog(parent);
}
if (returnVal == JFileChooser.APPROVE_OPTION) {
selectedFile = fc.getSelectedFile();
}
}
return selectedFile;
}
/** Timeout for a single round trip of SASL token exchange, in milliseconds. */
public int saslRTTimeoutMs() {
return (int) JavaUtils.timeStringAsSec(conf.get("spark.shuffle.sasl.timeout", "30s")) * 1000;
}
/** Maximum number of bytes to be encrypted at a time when SASL encryption is enabled. */
public int maxSaslEncryptedBlockSize() {
return Ints.checkedCast(
JavaUtils.byteStringAsBytes(conf.get("spark.network.sasl.maxEncryptedBlockSize", "64k")));
}
/**
* Time (in milliseconds) that we will wait in order to perform a retry after an IOException. Only
* relevant if maxIORetries > 0.
*/
public int ioRetryWaitTimeMs() {
return (int) JavaUtils.timeStringAsSec(conf.get("spark.shuffle.io.retryWait", "5s")) * 1000;
}
