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