/* Copyright (c) 2005 Stanford University and Christopher Bruns * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the * "Software"), to deal in the Software without restriction, including * without limitation the rights to use, copy, modify, merge, publish, * distribute, sublicense, and/or sell copies of the Software, and to * permit persons to whom the Software is furnished to do so, subject * to the following conditions: * * The above copyright notice and this permission notice shall be included * in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* * Created on Oct 25, 2005 * Original author: Christopher Bruns */ package org.simtk.isimsu; import java.io.*; import java.net.*; import java.util.*; import java.util.jar.*; import org.simtk.gui.*; /** * @author Christopher Bruns * * Manages external process whose executable is named and stored in a directory of a jar file */ public class JarDefinedExecutableThread extends ExternalProcessThread implements MonitoredProcess { private boolean isUnpackedAlready = false; private boolean isCancelled = false; private boolean isFailed = false; private boolean isSuccessful = false; /** * Make sure executable file exists. Unpack it if it doesn't. * Get the platform-specific command name from a file in the jar file. * * @returns Vector of Strings with executable name and initial arguments */ Vector unpackExecutable( String jarDirectory, String executableNameFileName, File programDirectory ) throws IOException { // TODO getResource returns null on a directory in a jar file // URL directoryURL = getClass().getClassLoader().getResource(jarDirectory); // System.out.println("Executable directory URL = " + directoryURL); // What is the name of the executable? // First open a "name file" that contains the name of the executable // This indirection is to the variety of names that an executable can have URL exeNameURL = getClass().getClassLoader().getResource(jarDirectory + "/" + executableNameFileName); if (exeNameURL == null) throw new IOException("Unable to find executable-name file " + executableNameFileName); // for debugging System.out.println("jar directory = " + jarDirectory); System.out.println("executable file name file = " + executableNameFileName); System.out.println("program directory = " + programDirectory); System.out.println("Exe file name-file URL = " + exeNameURL); InputStream exeNameStream = exeNameURL.openConnection().getInputStream(); BufferedReader exeNameReader = new BufferedReader(new InputStreamReader(exeNameStream)); Vector initialArgs = new Vector(); // Arguments are on separate lines in the executable name file String line; while ( (line = exeNameReader.readLine()) != null) { initialArgs.add(line); } if (initialArgs.size() < 1) throw new FileNotFoundException("Failed to parse name file " + executableNameFileName); // If the file is already unpacked (for some reason?), we don't need to unpack again. if (isUnpackedAlready) return initialArgs; // The first LINE of the file-name file contains the name of the executable, e.g. "python" // (subsequent lines contain arguments?) e.g. "pdb2pqr.py" String exeName = (String) initialArgs.elementAt(0); // e.g. "python" or "pdb2pqr.exe" // This is no good because it is not there in the case of python on mac and linux // File exeFile = new File(programDirectory, exeName); // if (exeFile.exists()) return initialArgs; // It's already unpacked // Unpack directory from jar file // Find directory in jar file // e.g. "jar:file:/C:/cygwin/home/cmbruns/eclipse/ISIM-SU/source/webstart/pdb2pqr_win32.jar!/pdb2pqr" // URL exeNameURL = getClass().getClassLoader().getResource(jarDirectory + "/" + executableNameFileName); // URL directoryURL = getClass().getClassLoader().getResource(jarDirectory + "/"); // String directoryURLString = directoryURL.toString(); // String jarURLEnd = "!/" + jarDirectory; // e.g. "!/pdb2pqr" String exeNameURLString = exeNameURL.toString(); try { if (exeNameURLString.startsWith("jar:file:")) { // Directory is inside of a jar file JarURLConnection exeNameJuc = (JarURLConnection) exeNameURL.openConnection(); JarFile jarFile = exeNameJuc.getJarFile(); // Consider each entry in the jar file, until we find the one we want Enumeration entries = jarFile.entries(); jarEntryLoop: while (entries.hasMoreElements()) { JarEntry entry = (JarEntry) entries.nextElement(); // Only look at entries in the "pdb2pqr" directory if (! entry.getName().startsWith(jarDirectory)) continue jarEntryLoop; if (entry.isDirectory()) continue jarEntryLoop; String outFileName = entry.getName().substring(jarDirectory.length() + 1); if (outFileName.length() < 1) continue jarEntryLoop; // Copy this file to the program area File outFile = new File(programDirectory, outFileName); StreamCopy.copy(jarFile.getInputStream(entry), new FileOutputStream(outFile)); // Try to make executable file executable if (outFile.getName().equals(exeName)) { System.out.println("Found executable " + exeName); try { Process setExecutableBitProcess = Runtime.getRuntime().exec("chmod +x " + exeName, null, programDirectory); setExecutableBitProcess.waitFor(); if (setExecutableBitProcess.exitValue() == 0) { System.out.println("Set executable bit succeeded on " + exeName); } else { System.out.println("Set executable bit failed on " + exeName); } } catch (Exception exc) {} // It's OK if attempt fails, e.g. on Windows } } // if (exeFile.exists()) // Declare success at this point isUnpackedAlready = true; return initialArgs; // It's already unpacked // TODO but the executable might not be there in the case of python // else throw new FileNotFoundException("Unable to find executable file " + exeFile + "in directory " + programDirectory + ", even after unpacking " + jarDirectory); } else { setFailed(); throw new FileNotFoundException("Could not understand URL: " + exeNameURLString); } } catch (IOException exc) { setFailed(); throw exc; } } public void setFailed() { isFailed = true; isSuccessful = false; } public void setSuccessful() { isSuccessful = true; isFailed = false; } public int getMinimum() {return 0;} // TODO public int getMaximum() {return 0;} // TODO public int getProgress() {return 0;} // TODO public boolean isFailed() {return this.isFailed;} public boolean isSuccessful() {return this.isSuccessful;} public synchronized void abort() { isCancelled = true; interrupt(); } }