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