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.PresetManager;\r
  41 import compbio.metadata.RunnerConfig;\r
  42 import compbio.util.PropertyHelper;\r
  43 \r
  44 public final class Util {\r
  45 \r
  46         public static Logger log = Logger.getLogger(Util.class);\r
  47 \r
  48         private static final PropertyHelper ph = PropertyHelperManager\r
  49                         .getPropertyHelper();\r
  50 \r
  51         public static final String SPACE = " ";\r
  52 \r
  53         public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
  54                         Class<? extends Executable<T>> clazz) {\r
  55                 try {\r
  56                         return ConfExecutable.getRunnerOptions(clazz);\r
  57                 } catch (FileNotFoundException e) {\r
  58                         log.error(\r
  59                                         "Could not load " + clazz + " Parameters !"\r
  60                                                         + e.getMessage(), e.getCause());\r
  61                 } catch (IOException e) {\r
  62                         log.error("IO exception while reading " + clazz + " Parameters !"\r
  63                                         + e.getMessage(), e.getCause());\r
  64                 }\r
  65                 return null;\r
  66         }\r
  67 \r
  68         public static <T> PresetManager<T> getPresets(\r
  69                         Class<? extends Executable<T>> clazz) {\r
  70                 try {\r
  71                         return ConfExecutable.getRunnerPresets(clazz);\r
  72                 } catch (FileNotFoundException e) {\r
  73                         log.warn(\r
  74                                         "No presets are found for " + clazz + " executable! "\r
  75                                                         + e.getLocalizedMessage(), e.getCause());\r
  76                 } catch (IOException e) {\r
  77                         log.warn("IO exception while reading presents! for " + clazz\r
  78                                         + " executable! " + e.getLocalizedMessage(), e.getCause());\r
  79                 }\r
  80                 return null;\r
  81         }\r
  82 \r
  83         public static final Alignment readClustalFile(String workDirectory,\r
  84                         String clustFile) throws UnknownFileFormatException, IOException,\r
  85                         FileNotFoundException, NullPointerException {\r
  86                 assert !compbio.util.Util.isEmpty(workDirectory);\r
  87                 assert !compbio.util.Util.isEmpty(clustFile);\r
  88                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
  89                                 workDirectory, clustFile));\r
  90                 log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
  91                 if (!(cfile.exists() && cfile.length() > 0)) {\r
  92                         throw new FileNotFoundException("Result for the jobId "\r
  93                                         + workDirectory + " with file name " + clustFile\r
  94                                         + " is not found!");\r
  95                 }\r
  96                 return ClustalAlignmentUtil.readClustalFile(cfile);\r
  97         }\r
  98 \r
  99         public static final Map<String, Score> readJronnFile(String workDirectory,\r
 100                         String clustFile) throws UnknownFileFormatException, IOException,\r
 101                         FileNotFoundException, NullPointerException {\r
 102                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 103                 assert !compbio.util.Util.isEmpty(clustFile);\r
 104                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
 105                                 workDirectory, clustFile));\r
 106                 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
 107                 if (!(cfile.exists() && cfile.length() > 0)) {\r
 108                         throw new FileNotFoundException("Result for the jobId "\r
 109                                         + workDirectory + " with file name " + clustFile\r
 110                                         + " is not found!");\r
 111                 }\r
 112                 return SequenceUtil.readJRonn(cfile);\r
 113         }\r
 114 \r
 115         public static void writeInput(List<FastaSequence> sequences,\r
 116                         ConfiguredExecutable<?> exec) {\r
 117 \r
 118                 File filein = new File(exec.getInput());\r
 119                 try {\r
 120                         FileOutputStream fout = new FileOutputStream(filein);\r
 121                         log.debug("File path: " + filein.getAbsolutePath());\r
 122                         SequenceUtil.writeFasta(fout, sequences);\r
 123                         fout.close();\r
 124                 } catch (FileNotFoundException e) {\r
 125                         e.printStackTrace();\r
 126                 } catch (IOException e) {\r
 127                         e.printStackTrace();\r
 128                 }\r
 129         }\r
 130 \r
 131 }\r