runner/compbio/runner/Util.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \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.FileNotFoundException;\r
  23 import java.io.FileOutputStream;\r
  24 import java.io.IOException;\r
  25 import java.util.List;\r
  26 import java.util.Map;\r
  27 \r
  28 import org.apache.log4j.Logger;\r
  29 \r
  30 import compbio.data.sequence.Alignment;\r
  31 import compbio.data.sequence.ClustalAlignmentUtil;\r
  32 import compbio.data.sequence.FastaSequence;\r
  33 import compbio.data.sequence.Score;\r
  34 import compbio.data.sequence.SequenceUtil;\r
  35 import compbio.data.sequence.UnknownFileFormatException;\r
  36 import compbio.engine.client.ConfExecutable;\r
  37 import compbio.engine.client.ConfiguredExecutable;\r
  38 import compbio.engine.client.Executable;\r
  39 import compbio.engine.conf.PropertyHelperManager;\r
  40 import compbio.metadata.JobSubmissionException;\r
  41 import compbio.metadata.PresetManager;\r
  42 import compbio.metadata.RunnerConfig;\r
  43 import compbio.util.PropertyHelper;\r
  44 \r
  45 public final class Util {\r
  46 \r
  47         public static Logger log = Logger.getLogger(Util.class);\r
  48 \r
  49         private static final PropertyHelper ph = PropertyHelperManager\r
  50                         .getPropertyHelper();\r
  51 \r
  52         public static final String SPACE = " ";\r
  53 \r
  54         public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
  55                         Class<? extends Executable<T>> clazz) {\r
  56                 try {\r
  57                         return ConfExecutable.getRunnerOptions(clazz);\r
  58                 } catch (FileNotFoundException e) {\r
  59                         log.error(\r
  60                                         "Could not load " + clazz + " Parameters !"\r
  61                                                         + e.getMessage(), e.getCause());\r
  62                 } catch (IOException e) {\r
  63                         log.error("IO exception while reading " + clazz + " Parameters !"\r
  64                                         + e.getMessage(), e.getCause());\r
  65                 }\r
  66                 return null;\r
  67         }\r
  68 \r
  69         public static <T> PresetManager<T> getPresets(\r
  70                         Class<? extends Executable<T>> clazz) {\r
  71                 try {\r
  72                         return ConfExecutable.getRunnerPresets(clazz);\r
  73                 } catch (FileNotFoundException e) {\r
  74                         log.warn(\r
  75                                         "No presets are found for " + clazz + " executable! "\r
  76                                                         + e.getLocalizedMessage(), e.getCause());\r
  77                 } catch (IOException e) {\r
  78                         log.warn("IO exception while reading presents! for " + clazz\r
  79                                         + " executable! " + e.getLocalizedMessage(), e.getCause());\r
  80                 }\r
  81                 return null;\r
  82         }\r
  83 \r
  84         public static final Alignment readClustalFile(String workDirectory,\r
  85                         String clustFile) throws UnknownFileFormatException, IOException,\r
  86                         FileNotFoundException, NullPointerException {\r
  87                 assert !compbio.util.Util.isEmpty(workDirectory);\r
  88                 assert !compbio.util.Util.isEmpty(clustFile);\r
  89                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
  90                                 workDirectory, clustFile));\r
  91                 log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
  92                 if (!(cfile.exists() && cfile.length() > 0)) {\r
  93                         throw new FileNotFoundException("Result for the jobId "\r
  94                                         + workDirectory + " with file name " + clustFile\r
  95                                         + " is not found!");\r
  96                 }\r
  97                 return ClustalAlignmentUtil.readClustalFile(cfile);\r
  98         }\r
  99 \r
 100         public static final Map<String, Score> readJronnFile(String workDirectory,\r
 101                         String clustFile) throws UnknownFileFormatException, IOException,\r
 102                         FileNotFoundException, NullPointerException {\r
 103                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 104                 assert !compbio.util.Util.isEmpty(clustFile);\r
 105                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
 106                                 workDirectory, clustFile));\r
 107                 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
 108                 if (!(cfile.exists() && cfile.length() > 0)) {\r
 109                         throw new FileNotFoundException("Result for the jobId "\r
 110                                         + workDirectory + " with file name " + clustFile\r
 111                                         + " is not found!");\r
 112                 }\r
 113                 return SequenceUtil.readJRonn(cfile);\r
 114         }\r
 115 \r
 116         public static void writeInput(List<FastaSequence> sequences,\r
 117                         ConfiguredExecutable<?> exec) throws JobSubmissionException {\r
 118 \r
 119                 try {\r
 120                         File filein = new File(exec.getInput());\r
 121                         FileOutputStream fout = new FileOutputStream(filein);\r
 122                         log.debug("File path: " + filein.getAbsolutePath());\r
 123                         SequenceUtil.writeFasta(fout, sequences);\r
 124                         fout.close();\r
 125                 } catch (IOException e) {\r
 126                         log.error("IOException while writing input file into the disk: "\r
 127                                         + e.getLocalizedMessage(), e);\r
 128                         throw new JobSubmissionException(\r
 129                                         "We are sorry by JABAWS server seems to have a problem! "\r
 130                                                         + e.getLocalizedMessage(), e);\r
 131                 }\r
 132         }\r
 133 \r
 134 }\r