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