1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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18 package compbio.engine;
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20 import java.io.File;
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21 import java.util.List;
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23 import org.apache.log4j.Logger;
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25 import compbio.engine.conf.PropertyHelperManager;
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26 import compbio.engine.client.ConfiguredExecutable;
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27 import compbio.engine.client.PathValidator;
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28 import compbio.engine.local.ExecutableWrapper;
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29 import compbio.util.PropertyHelper;
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34 // understand what this class does and why it was set as deprecated ...
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35 // how to check timestamps of files before deleting
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36 public class Cleaner {
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38 private static final Logger log = Logger.getLogger(Cleaner.class);
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41 * This method returns true if all files specified by List files were
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42 * successfully removed or there was no files to remove (files list was
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45 * @param workDirectory
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47 * @return This method returns true if all files specified by List files
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48 * were successfully removed, false otherwise
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50 public static boolean deleteFiles(ConfiguredExecutable<?> exec) {
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53 throw new IllegalArgumentException("Executable must be provided!");
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56 List<String> files = exec.getCreatedFiles();
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57 for (String fname : files) {
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58 assert PathValidator.isAbsolutePath(fname) : " Absolute path must be provided but got: "
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62 // Remove process std output and error capture files, do not care
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63 // whether succeed or not
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64 // as these are only created for local processes, so may not exist
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65 removeFile(exec.getWorkDirectory() + File.separator + ExecutableWrapper.PROC_OUT_FILE);
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66 removeFile(exec.getWorkDirectory() + File.separator + ExecutableWrapper.PROC_ERR_FILE);
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67 // Remove the task directory if all files were successfully removed
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68 return removeFile(exec.getWorkDirectory());
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71 static boolean removeFile(String filename) {
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72 File outfile = new File(filename);
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73 boolean success = false;
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74 if (outfile.exists()) {
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75 String type = outfile.isDirectory() ? "Directory " : "File ";
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76 success = outfile.delete();
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78 log.trace(type + filename + " was successfully removed");
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80 log.debug("Could not remove "
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84 + " reportedly created by executable. Insufficient access right?");
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87 log.debug("File: " + filename
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88 + " does not appear ro exist. Could have been removed?");
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93 public static boolean deleteAllFiles(String directory) {
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94 if (compbio.util.Util.isEmpty(directory)) {
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95 throw new NullPointerException("Directory must be provided! ");
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97 File rootdir = new File(directory);
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98 if (!rootdir.exists()) {
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99 log.error("Directory " + directory + " does not exist. Have been deleted already?");
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102 if (!rootdir.isDirectory()) {
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103 log.error("Directory is expected by file given! Skipping... ");
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107 File[] files = rootdir.listFiles();
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108 int deletedCount = 0;
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109 for (File f : files) {
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110 if (f.isDirectory()) {
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111 log.error("Cannot delete subdirectories! Skipping...");
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119 return deletedCount == files.length;
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122 public static boolean deleteDirectory(String directory) {
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123 if (deleteAllFiles (directory)) {
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124 File rootdir = new File(directory);
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125 return rootdir.delete();
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