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 public class Cleaner {\r
  30 \r
  31         private static final Logger log = Logger.getLogger(Cleaner.class);\r
  32 \r
  33         /**\r
  34          * This method returns true if all files specified by List files were\r
  35          * successfully removed or there was no files to remove (files list was\r
  36          * empty)\r
  37          * \r
  38          * @param workDirectory\r
  39          * @param files\r
  40          * @return\r
  41          */\r
  42         public static boolean deleteFiles(ConfiguredExecutable<?> exec) {\r
  43 \r
  44                 if (exec == null) {\r
  45                         throw new IllegalArgumentException("Executable must be provided!");\r
  46                 }\r
  47 \r
  48                 List<String> files = exec.getCreatedFiles();\r
  49                 for (String fname : files) {\r
  50                         assert PathValidator.isAbsolutePath(fname) : " Absolute path must be provided but got: "\r
  51                                         + fname;\r
  52                         removeFile(fname);\r
  53                 }\r
  54                 // Remove process std output and error capture files, do not care\r
  55                 // whether succeed or not\r
  56                 // as these are only created for local processes, so may not exist\r
  57                 removeFile(exec.getWorkDirectory() + File.separator\r
  58                                 + ExecutableWrapper.PROC_OUT_FILE);\r
  59                 removeFile(exec.getWorkDirectory() + File.separator\r
  60                                 + ExecutableWrapper.PROC_ERR_FILE);\r
  61                 // Remove the task directory if all files were successfully removed\r
  62                 return removeFile(exec.getWorkDirectory());\r
  63         }\r
  64 \r
  65         static boolean removeFile(String filename) {\r
  66                 File outfile = new File(filename);\r
  67                 boolean success = false;\r
  68                 if (outfile.exists()) {\r
  69                         String type = outfile.isDirectory() ? "Directory " : "File ";\r
  70                         success = outfile.delete();\r
  71                         if (success) {\r
  72                                 log.trace(type + filename + " was successfully removed");\r
  73                         } else {\r
  74                                 log\r
  75                                                 .debug("Could not remove "\r
  76                                                                 + type\r
  77                                                                 + ": "\r
  78                                                                 + filename\r
  79                                                                 + " reportedly created by executable. Insufficient access right?");\r
  80                         }\r
  81                 } else {\r
  82                         log.debug("File: " + filename\r
  83                                         + " does not appear ro exist. Could have been removed?");\r
  84                 }\r
  85                 return success;\r
  86         }\r
  87 \r
  88         public static boolean deleteAllFiles(String directory) {\r
  89                 if (compbio.util.Util.isEmpty(directory)) {\r
  90                         throw new NullPointerException("Direcotry must be provided! ");\r
  91                 }\r
  92                 File rootdir = new File(directory);\r
  93                 if (!rootdir.exists()) {\r
  94                         log.error("Directory " + directory\r
  95                                         + " does not exist. Have been deleted already?");\r
  96                         return false;\r
  97                 }\r
  98                 if (!rootdir.isDirectory()) {\r
  99                         log.error("Directory is expected by file given! Skipping... ");\r
 100                         return false;\r
 101                 }\r
 102 \r
 103                 File[] files = rootdir.listFiles();\r
 104                 int deletedCount = 0;\r
 105                 for (File f : files) {\r
 106                         if (f.isDirectory()) {\r
 107                                 log.error("Cannot delete subdirecotries! Skipping...");\r
 108                         } else {\r
 109                                 boolean deleted = f.delete();\r
 110                                 if (deleted) {\r
 111                                         deletedCount++;\r
 112                                 }\r
 113                         }\r
 114                 }\r
 115                 return deletedCount == files.length;\r
 116         }\r
 117 \r
 118 }\r