runner/compbio/runner/Util.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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 \r
  19 package compbio.runner;\r
  20 \r
  21 import java.io.File;\r
  22 import java.io.FileInputStream;\r
  23 import java.io.FileReader;\r
  24 import java.io.BufferedReader;\r
  25 import java.io.FileNotFoundException;\r
  26 import java.io.FileOutputStream;\r
  27 import java.io.IOException;\r
  28 import java.util.List;\r
  29 import java.util.Map;\r
  30 \r
  31 import org.apache.log4j.Logger;\r
  32 \r
  33 import compbio.data.sequence.Alignment;\r
  34 import compbio.data.sequence.ClustalAlignmentUtil;\r
  35 import compbio.data.sequence.FastaSequence;\r
  36 import compbio.data.sequence.RNAstruct;\r
  37 import compbio.data.sequence.Score;\r
  38 import compbio.data.sequence.SequenceUtil;\r
  39 import compbio.data.sequence.UnknownFileFormatException;\r
  40 import compbio.engine.client.ConfExecutable;\r
  41 import compbio.engine.client.ConfiguredExecutable;\r
  42 import compbio.engine.client.Executable;\r
  43 import compbio.engine.conf.PropertyHelperManager;\r
  44 import compbio.metadata.JobSubmissionException;\r
  45 import compbio.metadata.PresetManager;\r
  46 import compbio.metadata.RunnerConfig;\r
  47 import compbio.util.PropertyHelper;\r
  48 \r
  49 public final class Util {\r
  50 \r
  51         public static Logger log = Logger.getLogger(Util.class);\r
  52 \r
  53         private static final PropertyHelper ph = PropertyHelperManager\r
  54                         .getPropertyHelper();\r
  55 \r
  56         public static final String SPACE = " ";\r
  57 \r
  58         public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
  59                         Class<? extends Executable<T>> clazz) {\r
  60                 try {\r
  61                         return ConfExecutable.getRunnerOptions(clazz);\r
  62                 } catch (FileNotFoundException e) {\r
  63                         log.error(\r
  64                                         "Could not load " + clazz + " Parameters !"\r
  65                                                         + e.getMessage(), e.getCause());\r
  66                 } catch (IOException e) {\r
  67                         log.error("IO exception while reading " + clazz + " Parameters !"\r
  68                                         + e.getMessage(), e.getCause());\r
  69                 }\r
  70                 return null;\r
  71         }\r
  72 \r
  73         public static <T> PresetManager<T> getPresets(\r
  74                         Class<? extends Executable<T>> clazz) {\r
  75                 try {\r
  76                         return ConfExecutable.getRunnerPresets(clazz);\r
  77                 } catch (FileNotFoundException e) {\r
  78                         log.warn(\r
  79                                         "No presets are found for " + clazz + " executable! "\r
  80                                                         + e.getLocalizedMessage(), e.getCause());\r
  81                 } catch (IOException e) {\r
  82                         log.warn("IO exception while reading presents! for " + clazz\r
  83                                         + " executable! " + e.getLocalizedMessage(), e.getCause());\r
  84                 }\r
  85                 return null;\r
  86         }\r
  87 \r
  88         public static final Alignment readClustalFile(String workDirectory,\r
  89                         String clustFile) throws UnknownFileFormatException, IOException,\r
  90                         FileNotFoundException, NullPointerException {\r
  91                 assert !compbio.util.Util.isEmpty(workDirectory);\r
  92                 assert !compbio.util.Util.isEmpty(clustFile);\r
  93                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
  94                                 workDirectory, clustFile));\r
  95                 log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
  96                 if (!(cfile.exists() && cfile.length() > 0)) {\r
  97                         throw new FileNotFoundException("Result for the jobId "\r
  98                                         + workDirectory + " with file name " + clustFile\r
  99                                         + " is not found!");\r
 100                 }\r
 101                 return ClustalAlignmentUtil.readClustalFile(cfile);\r
 102         }\r
 103 \r
 104         public static final Map<String, Score> readJronnFile(String workDirectory,\r
 105                         String clustFile) throws UnknownFileFormatException, IOException,\r
 106                         FileNotFoundException, NullPointerException {\r
 107                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 108                 assert !compbio.util.Util.isEmpty(clustFile);\r
 109                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
 110                                 workDirectory, clustFile));\r
 111                 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
 112                 if (!(cfile.exists() && cfile.length() > 0)) {\r
 113                         throw new FileNotFoundException("Result for the jobId "\r
 114                                         + workDirectory + " with file name " + clustFile\r
 115                                         + " is not found!");\r
 116                 }\r
 117                 return SequenceUtil.readJRonn(cfile);\r
 118         }\r
 119 \r
 120         public static void writeInput(List<FastaSequence> sequences,\r
 121                         ConfiguredExecutable<?> exec) throws JobSubmissionException {\r
 122 \r
 123                 try {\r
 124                         File filein = new File(exec.getInput());\r
 125                         FileOutputStream fout = new FileOutputStream(filein);\r
 126                         log.debug("File path: " + filein.getAbsolutePath());\r
 127                         SequenceUtil.writeFasta(fout, sequences);\r
 128                         fout.close();\r
 129                 } catch (IOException e) {\r
 130                         log.error("IOException while writing input file into the disk: "\r
 131                                         + e.getLocalizedMessage(), e);\r
 132                         throw new JobSubmissionException(\r
 133                                         "We are sorry by JABAWS server seems to have a problem! "\r
 134                                                         + e.getLocalizedMessage(), e);\r
 135                 }\r
 136         }\r
 137         \r
 138         public static void writeClustalInput(List<FastaSequence> sequences,\r
 139                         ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {\r
 140                 \r
 141                 try {\r
 142                         File filein = new File(exec.getInput());\r
 143                         FileOutputStream fout = new FileOutputStream(filein);\r
 144                         log.debug("File path: " + filein.getAbsolutePath());\r
 145                         SequenceUtil.writeClustal(fout, sequences, gapChar);\r
 146                         fout.close();\r
 147                 } catch (IOException e) {\r
 148                         log.error("IOException while writing input file into the disk: "\r
 149                                         + e.getLocalizedMessage(), e);\r
 150                         throw new JobSubmissionException(\r
 151                                         "We are sorry but JABAWS server seems to have a problem! "\r
 152                                                 + e.getLocalizedMessage(), e);\r
 153                 }\r
 154         }\r
 155         \r
 156         // OUT OF USE\r
 157         \r
 158 //      public static final RNAstruct readRNAStructFile(String workDirectory,\r
 159 //                      String structFile) throws IOException, FileNotFoundException {\r
 160 //              assert !compbio.util.Util.isEmpty(workDirectory);\r
 161 //              assert !compbio.util.Util.isEmpty(structFile);\r
 162 //              File sfile = new File(compbio.engine.client.Util.getFullPath(\r
 163 //                              workDirectory, structFile));\r
 164 //              if(!(sfile.exists() && sfile.length() > 0)) {\r
 165 //                      throw new FileNotFoundException("Result for the jobId "\r
 166 //                                      + workDirectory + "with file name " + structFile\r
 167 //                                      + " is not found!");\r
 168 //              }\r
 169 //              return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(\r
 170 //                              new FileInputStream(sfile));\r
 171 //      }\r
 172         \r
 173         public static String readRNAStruct(String workDirectory,\r
 174                         String structFile) throws IOException, FileNotFoundException {\r
 175                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 176                 assert !compbio.util.Util.isEmpty(structFile);\r
 177                 File sfile = new File(compbio.engine.client.Util.getFullPath(\r
 178                                 workDirectory, structFile));\r
 179                 if(!(sfile.exists() && sfile.length() > 0)) {\r
 180                         throw new FileNotFoundException("Result for the jobId "\r
 181                                         + workDirectory + "with file name " + structFile\r
 182                                         + " is not found!");\r
 183                 }\r
 184                 return readFile(sfile);\r
 185         }\r
 186         \r
 187         public static String readFile(File inputFile) throws \r
 188                         FileNotFoundException, IOException {\r
 189 \r
 190                 BufferedReader input    = new BufferedReader(new FileReader(inputFile));\r
 191 \r
 192                 String file = new String();\r
 193                 String line = new String();\r
 194 \r
 195                 while (true) {\r
 196                         line = input.readLine();\r
 197 \r
 198                         if (line != null) {\r
 199                                 file = file + line + "\r\n";\r
 200                         } else break;\r
 201                 }\r
 202                 // Close file\r
 203                 input.close();\r
 204                 return file;\r
 205         }\r
 206         \r
 207         \r
 208 \r
 209 }\r