engine/compbio/engine/Cleaner.java

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