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