runner/compbio/runner/disorder/Jronn.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.disorder;\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.IOException;\r
  25 import java.io.InputStream;\r
  26 import java.util.Arrays;\r
  27 import java.util.List;\r
  28 \r
  29 import org.apache.log4j.Logger;\r
  30 \r
  31 import compbio.data.sequence.ScoreManager;\r
  32 import compbio.data.sequence.SequenceUtil;\r
  33 import compbio.data.sequence.UnknownFileFormatException;\r
  34 import compbio.engine.client.CommandBuilder;\r
  35 import compbio.engine.client.Executable;\r
  36 import compbio.engine.client.SkeletalExecutable;\r
  37 import compbio.metadata.ResultNotAvailableException;\r
  38 import compbio.runner.Util;\r
  39 \r
  40 /**\r
  41  * Command line\r
  42  * \r
  43  * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
  44  * \r
  45  * @author pvtroshin\r
  46  * \r
  47  */\r
  48 public class Jronn extends SkeletalExecutable<Jronn> {\r
  49 \r
  50         private static Logger log = Logger.getLogger(Jronn.class);\r
  51 \r
  52 /*\r
  53  * Number of cores to use, defaults to 1 for local execution or the value of\r
  54  * "jronn.cluster.cpunum" property for cluster execution\r
  55  */\r
  56         private int ncoreNumber = 0;\r
  57 \r
  58         private final String ncorePrm = "-n=";\r
  59 \r
  60         public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
  61         public static final String STAT_FILE = "stat.txt";\r
  62 \r
  63         public Jronn() {\r
  64                 addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE, "-f=H"));\r
  65         }\r
  66 \r
  67         @SuppressWarnings("unchecked")\r
  68         @Override\r
  69         public ScoreManager getResults(String workDirectory)\r
  70                         throws ResultNotAvailableException {\r
  71                 ScoreManager sequences = null;\r
  72                 try {\r
  73                         InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
  74                         sequences = ScoreManager.newInstanceSingleScore(SequenceUtil.readJRonn(inStream));\r
  75                         inStream.close();\r
  76                 } catch (FileNotFoundException e) {\r
  77                         log.error(e.getMessage(), e.getCause());\r
  78                         throw new ResultNotAvailableException(e);\r
  79                 } catch (IOException e) {\r
  80                         log.error(e.getMessage(), e.getCause());\r
  81                         throw new ResultNotAvailableException(e);\r
  82                 } catch (UnknownFileFormatException e) {\r
  83                         log.error(e.getMessage(), e.getCause());\r
  84                         throw new ResultNotAvailableException(e);\r
  85                 } catch (NullPointerException e) {\r
  86                         log.error(e.getMessage(), e.getCause());\r
  87                         throw new ResultNotAvailableException(e);\r
  88                 }\r
  89                 return sequences;\r
  90         }\r
  91 \r
  92         private static String getLibPath() {\r
  93                 String settings = ph.getProperty("jronn.jar.file");\r
  94                 if (compbio.util.Util.isEmpty(settings)) {\r
  95                         throw new NullPointerException(\r
  96                                         "Please define jronn.jar.file property in Executable.properties file"\r
  97                                                         + "and initialize it with the location of jronn jar file");\r
  98                 }\r
  99                 if (new File(settings).isAbsolute()) {\r
 100                         // Jronn jar can be found so no actions necessary\r
 101                         // no further actions is necessary\r
 102                         return settings;\r
 103                 }\r
 104                 return compbio.engine.client.Util.convertToAbsolute(settings);\r
 105         }\r
 106 \r
 107         @Override\r
 108         public List<String> getCreatedFiles() {\r
 109                 return Arrays.asList(getOutput(), getError());\r
 110         }\r
 111 \r
 112         @Override\r
 113         public Jronn setInput(String inFile) {\r
 114                 super.setInput(inFile);\r
 115                 cbuilder.setParam("-i=" + inFile);\r
 116                 return this;\r
 117         }\r
 118 \r
 119         @Override\r
 120         public Jronn setOutput(String outFile) {\r
 121                 super.setOutput(outFile);\r
 122                 cbuilder.setParam("-o=" + outFile);\r
 123                 return this;\r
 124         }\r
 125 \r
 126         @SuppressWarnings("unchecked")\r
 127         @Override\r
 128         public Class<Jronn> getType() {\r
 129                 return (Class<Jronn>) this.getClass();\r
 130         }\r
 131 \r
 132         public static String getStatFile() {\r
 133                 return STAT_FILE;\r
 134         }\r
 135 \r
 136         public void setNCore(int ncoreNumber) {\r
 137                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 138                         throw new IndexOutOfBoundsException(\r
 139                                         "Number of cores must be within 1 and 100 ");\r
 140                 }\r
 141                 this.ncoreNumber = ncoreNumber;\r
 142                 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
 143         }\r
 144 \r
 145         int getNCore() {\r
 146                 return ncoreNumber;\r
 147         }\r
 148 \r
 149         @Override\r
 150         public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
 151                 // If number of cores is provided, set it for the cluster execution only!\r
 152                 if (provider == Executable.ExecProvider.Cluster) {\r
 153                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 154                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 155                         setNCore(cpunum);\r
 156                 } else {\r
 157                         // Limit number of cores to 1 for ANY execution which does not set\r
 158                         // Ncores explicitly using setNCore method or is run on local VM\r
 159                         if (ncoreNumber == 0) {\r
 160                                 setNCore(1);\r
 161                         }\r
 162                 }\r
 163                 return super.getParameters(provider);\r
 164         }\r
 165 \r
 166 }\r