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.LimitsManager;\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         private 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         /**\r
  55          * For now just assume that all parameters which came in needs setting it\r
  56          * will be a client responsibility to prepare RunnerConfig object then\r
  57          * \r
  58          * @param rconfig\r
  59          * @return\r
  60          * \r
  61          *         public static List<String> toOptionString(RunnerConfig<?>\r
  62          *         rconfig) { String option = ""; List<String> options = new\r
  63          *         ArrayList<String>(); for (Parameter<?> par :\r
  64          *         rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())\r
  65          *         { option = par.getOptionName(); } else { option =\r
  66          *         par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
  67          *         separate options options.add(option); } return options; }\r
  68          */\r
  69 \r
  70         public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {\r
  71                 LimitsManager<T> limits = null;\r
  72                 try {\r
  73                         limits = ConfExecutable.getRunnerLimits(clazz);\r
  74                 } catch (FileNotFoundException e) {\r
  75                         log.warn(\r
  76                                         "No limits are found for " + clazz + " executable! "\r
  77                                                         + e.getLocalizedMessage(), e.getCause());\r
  78                         // its ok, limit may not be initialized\r
  79                 } catch (IOException e) {\r
  80                         log.warn("IO exception while attempting to read limits for "\r
  81                                         + clazz + " executable! " + e.getLocalizedMessage(),\r
  82                                         e.getCause());\r
  83                 }\r
  84                 return limits;\r
  85         }\r
  86 \r
  87         public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
  88                         Class<? extends Executable<T>> clazz) {\r
  89                 try {\r
  90                         return ConfExecutable.getRunnerOptions(clazz);\r
  91                 } catch (FileNotFoundException e) {\r
  92                         log.error(\r
  93                                         "Could not load " + clazz + " Parameters !"\r
  94                                                         + e.getMessage(), e.getCause());\r
  95                 } catch (IOException e) {\r
  96                         log.error("IO exception while reading " + clazz + " Parameters !"\r
  97                                         + e.getMessage(), e.getCause());\r
  98                 }\r
  99                 return null;\r
 100         }\r
 101 \r
 102         public static <T> PresetManager<T> getPresets(\r
 103                         Class<? extends Executable<T>> clazz) {\r
 104                 try {\r
 105                         return ConfExecutable.getRunnerPresets(clazz);\r
 106                 } catch (FileNotFoundException e) {\r
 107                         log.warn(\r
 108                                         "No presets are found for " + clazz + " executable! "\r
 109                                                         + e.getLocalizedMessage(), e.getCause());\r
 110                 } catch (IOException e) {\r
 111                         log.warn("IO exception while reading presents! for " + clazz\r
 112                                         + " executable! " + e.getLocalizedMessage(), e.getCause());\r
 113                 }\r
 114                 return null;\r
 115         }\r
 116 \r
 117         public static final Alignment readClustalFile(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("CLUSTAL 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 ClustalAlignmentUtil.readClustalFile(cfile);\r
 131         }\r
 132 \r
 133         public static final Map<String, Score> readJronnFile(String workDirectory,\r
 134                         String clustFile) throws UnknownFileFormatException, IOException,\r
 135                         FileNotFoundException, NullPointerException {\r
 136                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 137                 assert !compbio.util.Util.isEmpty(clustFile);\r
 138                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
 139                                 workDirectory, clustFile));\r
 140                 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
 141                 if (!(cfile.exists() && cfile.length() > 0)) {\r
 142                         throw new FileNotFoundException("Result for the jobId "\r
 143                                         + workDirectory + " with file name " + clustFile\r
 144                                         + " is not found!");\r
 145                 }\r
 146                 return SequenceUtil.readJRonn(cfile);\r
 147         }\r
 148 \r
 149         public static void writeInput(List<FastaSequence> sequences,\r
 150                         ConfiguredExecutable<?> exec) {\r
 151 \r
 152                 File filein = new File(exec.getInput());\r
 153                 try {\r
 154                         FileOutputStream fout = new FileOutputStream(filein);\r
 155                         log.debug("File path: " + filein.getAbsolutePath());\r
 156                         SequenceUtil.writeFasta(fout, sequences);\r
 157                         fout.close();\r
 158                 } catch (FileNotFoundException e) {\r
 159                         e.printStackTrace();\r
 160                 } catch (IOException e) {\r
 161                         e.printStackTrace();\r
 162                 }\r
 163         }\r
 164 \r
 165 }\r