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A runtime patcher to introduce extension points into the original ImageJ (1.x). This project offers extension points for use with ImageJ2 and it also offers limited support for headless operations.
/*
* #%L
* ImageJ software for multidimensional image processing and analysis.
* %%
* Copyright (C) 2009 - 2016 Board of Regents of the University of
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
* Institute of Molecular Cell Biology and Genetics.
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package imagej.patcher;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.JarURLConnection;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Enumeration;
import java.util.jar.JarEntry;
import java.util.jar.JarFile;
/**
* Provides some functions originally found in SciJava-common.
*
* The ij1-patcher project was originally part of the ImageJ2 project,
* relying on functions provided by the scijava-common project. However,
* to be as standalone as possible, we replicate the functions here to avoid the
* additional dependency.
*
*
* This class is not part of the API of ij1-patcher; Projects
* which desire to use the functionality contained herein should depend on
* scijava-common instead.
*
*
* @author "Johannes Schindelin"
*/
@Deprecated
class Utils {
/**
* Gets the base location of the given class.
*
* If the class is directly on the file system (e.g.,
* "/path/to/my/package/MyClass.class") then it will return the base directory
* (e.g., "file:/path/to").
*
*
* If the class is within a JAR file (e.g.,
* "/path/to/my-jar.jar!/my/package/MyClass.class") then it will return the
* path to the JAR (e.g., "file:/path/to/my-jar.jar").
*
*
* This method was extracted from SciJava-common's {@code ClassUtils} class.
*
*
* @param c The class whose location is desired.
* @see #urlToFile(URL) to convert the result to a {@link File}.
*/
static URL getLocation(final Class c) {
if (c == null) return null; // could not load the class
// try the easy way first
try {
final URL codeSourceLocation =
c.getProtectionDomain().getCodeSource().getLocation();
if (codeSourceLocation != null) return codeSourceLocation;
}
catch (final SecurityException e) {
// NB: Cannot access protection domain.
}
catch (final NullPointerException e) {
// NB: Protection domain or code source is null.
}
// NB: The easy way failed, so we try the hard way. We ask for the class
// itself as a resource, then strip the class's path from the URL string,
// leaving the base path.
// get the class's raw resource path
final URL classResource = c.getResource(c.getSimpleName() + ".class");
if (classResource == null) return null; // cannot find class resource
final String url = classResource.toString();
final String suffix = c.getCanonicalName().replace('.', '/') + ".class";
if (!url.endsWith(suffix)) return null; // weird URL
// strip the class's path from the URL string
final String base = url.substring(0, url.length() - suffix.length());
String path = base;
// remove the "jar:" prefix and "!/" suffix, if present
if (path.startsWith("jar:")) path = path.substring(4, path.length() - 2);
try {
return new URL(path);
}
catch (final MalformedURLException e) {
e.printStackTrace();
return null;
}
}
/**
* Checks whether a class with the given name exists.
*
* @param className the class name
* @return whether the current thread's context class loader knows the class
*/
static boolean hasClass(final String className) {
return hasClass(className, null);
}
/**
* Checks whether a class with the given name exists.
*
* @param className the class name
* @param classLoader the loader to ask for the class, if {@code null} is
* passed, the current thread's context class loader will be asked
* @return whether the class loader knows the class
*/
static boolean hasClass(final String className,
final ClassLoader classLoader)
{
return loadClass(className, classLoader) != null;
}
/**
* Tries to load the class with the given name.
*
* This method uses the specified {@link ClassLoader} (or the current thread's
* context class loader if {@code null} was passed as the {@code classLoader}
* parameter. If the class cannot be found no exception is thrown but
* {@code null} is returned instead.
*
*
* This method is a stripped down version of the {@code loadClass} method in
* SciJava-common's {@code ClassUtils} class.
*
*
* @param name The name of the class to load.
* @param classLoader The class loader with which to load the class; if null,
* the current thread's context class loader will be used.
*/
static Class loadClass(final String className,
final ClassLoader classLoader)
{
// load the class!
try {
final ClassLoader cl =
classLoader == null ? Thread.currentThread().getContextClassLoader()
: classLoader;
return cl.loadClass(className);
}
catch (final ClassNotFoundException e) {
return null;
}
}
/**
* Recursively lists the contents of the referenced directory.
*
* Directories are excluded from the result. Supported protocols include
* {@code file} and {@code jar}.
*
*
* This method was extracted from SciJava-common's {@code FileUtils} class.
*
*
* @param directory The directory whose contents should be listed.
* @return A collection of {@link URL}s representing the directory's contents.
* @see #listContents(URL, boolean, boolean)
*/
static Collection listContents(final URL directory) {
return appendContents(new ArrayList(), directory, true, true);
}
/**
* Add contents from the referenced directory to an existing collection.
*
* Supported protocols include {@code file} and {@code jar}.
*
*
* This method was extracted from SciJava-common's {@code FileUtils} class.
*
*
* @param result The collection to which contents should be added.
* @param directory The directory whose contents should be listed.
* @param recurse Whether to append contents recursively, as opposed to only
* the directory's direct contents.
* @param filesOnly Whether to exclude directories in the resulting collection
* of contents.
* @return A collection of {@link URL}s representing the directory's contents.
*/
static Collection appendContents(final Collection result,
final URL directory, final boolean recurse, final boolean filesOnly)
{
if (directory == null) return result; // nothing to append
final String protocol = directory.getProtocol();
if (protocol.equals("file")) {
final File dir = urlToFile(directory);
final File[] list = dir.listFiles();
if (list != null) {
for (final File file : list) {
try {
if (!filesOnly || file.isFile()) {
result.add(file.toURI().toURL());
}
if (recurse && file.isDirectory()) {
appendContents(result, file.toURI().toURL(), recurse, filesOnly);
}
}
catch (final MalformedURLException e) {
e.printStackTrace();
}
}
}
}
else if (protocol.equals("jar")) {
try {
final String url = directory.toString();
final int bang = url.indexOf("!/");
if (bang < 0) return result;
final String prefix = url.substring(bang + 2);
final String baseURL = url.substring(0, bang + 2);
final JarURLConnection connection =
(JarURLConnection) new URL(baseURL).openConnection();
final JarFile jar = connection.getJarFile();
final Enumeration entries = jar.entries();
while (entries.hasMoreElements()) {
final JarEntry entry = entries.nextElement();
final String urlEncoded =
new URI(null, null, entry.getName(), null).toString();
if (urlEncoded.length() > prefix.length() && // omit directory itself
urlEncoded.startsWith(prefix))
{
if (filesOnly && urlEncoded.endsWith("/")) {
// URL is directory; exclude it
continue;
}
if (!recurse) {
// check whether this URL is a *direct* child of the directory
final int slash = urlEncoded.indexOf("/", prefix.length());
if (slash >= 0 && slash != urlEncoded.length() - 1) {
// not a direct child
continue;
}
}
result.add(new URL(baseURL + urlEncoded));
}
}
jar.close();
}
catch (final IOException e) {
e.printStackTrace();
}
catch (final URISyntaxException e) {
throw new IllegalArgumentException(e);
}
}
return result;
}
/**
* Converts the given URL string to its corresponding {@link File}.
*
* This method was extracted from SciJava-common's {@code FileUtils} class.
*
*
* @param url The URL to convert.
* @return A file path suitable for use with e.g. {@link FileInputStream}
* @throws IllegalArgumentException if the URL does not correspond to a file.
*/
static File urlToFile(final URL url) {
String path = url.toString();
if (path.startsWith("jar:")) {
// remove "jar:" prefix and "!/" suffix
final int index = path.indexOf("!/");
path = path.substring(4, index);
}
try {
return new File(new URL(path).toURI());
}
catch (final MalformedURLException e) {
// NB: URL is not completely well-formed.
}
catch (final URISyntaxException e) {
// NB: URL is not completely well-formed.
}
if (path.startsWith("file:")) {
// pass through the URL as-is, minus "file:" prefix
path = path.substring(5);
return new File(path);
}
throw new IllegalArgumentException("Invalid URL: " + url);
}
/**
* Determines whether the current stack trace contains the specified string.
*
* @param needles the text(s) to find
* @return whether the stack trace contains the text
*/
static boolean stackTraceContains(String... needles) {
final StringWriter writer = new StringWriter();
final PrintWriter out = new PrintWriter(writer);
new Exception().printStackTrace(out);
out.close();
final String haystack = writer.toString();
for (final String needle : needles) {
if (haystack.contains(needle)) return true;
}
return false;
}
}