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.client.ConfiguredExecutable;
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26 import compbio.engine.client.PathValidator;
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27 import compbio.engine.local.ExecutableWrapper;
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32 // understand what this class does and why it was set as deprecated ...
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33 // how to check timestamps of files before deleting
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34 public class Cleaner {
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36 private static final Logger log = Logger.getLogger(Cleaner.class);
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39 * This method returns true if all files specified by List files were
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40 * successfully removed or there was no files to remove (files list was
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43 * @param workDirectory
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45 * @return This method returns true if all files specified by List files
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46 * were successfully removed, false otherwise
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48 public static boolean deleteFiles(ConfiguredExecutable<?> exec) {
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51 throw new IllegalArgumentException("Executable must be provided!");
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54 List<String> files = exec.getCreatedFiles();
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55 for (String fname : files) {
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56 assert PathValidator.isAbsolutePath(fname) : " Absolute path must be provided but got: "
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60 // Remove process std output and error capture files, do not care
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61 // whether succeed or not
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62 // as these are only created for local processes, so may not exist
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63 removeFile(exec.getWorkDirectory() + File.separator + ExecutableWrapper.PROC_OUT_FILE);
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64 removeFile(exec.getWorkDirectory() + File.separator + ExecutableWrapper.PROC_ERR_FILE);
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65 // Remove the task directory if all files were successfully removed
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66 return removeFile(exec.getWorkDirectory());
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69 static boolean removeFile(String filename) {
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70 File outfile = new File(filename);
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71 boolean success = false;
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72 if (outfile.exists()) {
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73 String type = outfile.isDirectory() ? "Directory " : "File ";
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74 success = outfile.delete();
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76 log.trace(type + filename + " was successfully removed");
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78 log.debug("Could not remove "
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82 + " reportedly created by executable. Insufficient access right?");
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85 log.debug("File: " + filename
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86 + " does not appear ro exist. Could have been removed?");
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91 public static boolean deleteAllFiles(String directory) {
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92 if (compbio.util.Util.isEmpty(directory)) {
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93 throw new NullPointerException("Directory must be provided! ");
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95 File rootdir = new File(directory);
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96 if (!rootdir.exists()) {
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97 log.error("Directory " + directory + " does not exist. Have been deleted already?");
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100 if (!rootdir.isDirectory()) {
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101 log.error("Directory is expected by file given! Skipping... ");
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105 File[] files = rootdir.listFiles();
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106 int deletedCount = 0;
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107 for (File f : files) {
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108 if (f.isDirectory()) {
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109 log.error("Cannot delete subdirectories! Skipping...");
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113 log.debug("file " + f.getName() + " removed");
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115 log.debug("file " + f.getName() + " is not removed");
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121 return deletedCount == files.length;
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124 public static boolean deleteDirectory(String directory) {
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125 if (deleteAllFiles (directory)) {
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126 File rootdir = new File(directory);
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127 return rootdir.delete();
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