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