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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29 public class Cleaner {
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31 private static final Logger log = Logger.getLogger(Cleaner.class);
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34 * This method returns true if all files specified by List files were
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35 * successfully removed or there was no files to remove (files list was
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38 * @param workDirectory
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42 public static boolean deleteFiles(ConfiguredExecutable<?> exec) {
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45 throw new IllegalArgumentException("Executable must be provided!");
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48 List<String> files = exec.getCreatedFiles();
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49 for (String fname : files) {
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50 assert PathValidator.isAbsolutePath(fname) : " Absolute path must be provided but got: "
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54 // Remove process std output and error capture files, do not care
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55 // whether succeed or not
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56 // as these are only created for local processes, so may not exist
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57 removeFile(exec.getWorkDirectory() + File.separator
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58 + ExecutableWrapper.PROC_OUT_FILE);
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59 removeFile(exec.getWorkDirectory() + File.separator
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60 + ExecutableWrapper.PROC_ERR_FILE);
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61 // Remove the task directory if all files were successfully removed
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62 return removeFile(exec.getWorkDirectory());
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65 static boolean removeFile(String filename) {
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66 File outfile = new File(filename);
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67 boolean success = false;
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68 if (outfile.exists()) {
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69 String type = outfile.isDirectory() ? "Directory " : "File ";
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70 success = outfile.delete();
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72 log.trace(type + filename + " was successfully removed");
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75 .debug("Could not remove "
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79 + " reportedly created by executable. Insufficient access right?");
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82 log.debug("File: " + filename
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83 + " does not appear ro exist. Could have been removed?");
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88 public static boolean deleteAllFiles(String directory) {
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89 if (compbio.util.Util.isEmpty(directory)) {
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90 throw new NullPointerException("Direcotry must be provided! ");
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92 File rootdir = new File(directory);
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93 if (!rootdir.exists()) {
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94 log.error("Directory " + directory
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95 + " does not exist. Have been deleted already?");
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98 if (!rootdir.isDirectory()) {
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99 log.error("Directory is expected by file given! Skipping... ");
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103 File[] files = rootdir.listFiles();
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104 int deletedCount = 0;
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105 for (File f : files) {
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106 if (f.isDirectory()) {
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107 log.error("Cannot delete subdirecotries! Skipping...");
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109 boolean deleted = f.delete();
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115 return deletedCount == files.length;
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