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 STAT_FILE = "stat.txt";\r
  61 \r
  62         public Jronn() {\r
  63                 addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE, "-f=H"));\r
  64         }\r
  65 \r
  66         @SuppressWarnings("unchecked")\r
  67         @Override\r
  68         public ScoreManager getResults(String workDirectory)\r
  69                         throws ResultNotAvailableException {\r
  70                 ScoreManager sequences = null;\r
  71                 try {\r
  72                         InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
  73                         sequences = ScoreManager.newInstanceSingleScore(SequenceUtil.readJRonn(inStream));\r
  74                         inStream.close();\r
  75                 } catch (FileNotFoundException e) {\r
  76                         log.error(e.getMessage(), e.getCause());\r
  77                         throw new ResultNotAvailableException(e);\r
  78                 } catch (IOException e) {\r
  79                         log.error(e.getMessage(), e.getCause());\r
  80                         throw new ResultNotAvailableException(e);\r
  81                 } catch (UnknownFileFormatException e) {\r
  82                         log.error(e.getMessage(), e.getCause());\r
  83                         throw new ResultNotAvailableException(e);\r
  84                 } catch (NullPointerException e) {\r
  85                         log.error(e.getMessage(), e.getCause());\r
  86                         throw new ResultNotAvailableException(e);\r
  87                 }\r
  88                 return sequences;\r
  89         }\r
  90 \r
  91         private static String getLibPath() {\r
  92                 String settings = ph.getProperty("jronn.jar.file");\r
  93                 if (compbio.util.Util.isEmpty(settings)) {\r
  94                         throw new NullPointerException(\r
  95                         "Please define jronn.jar.file property in Executable.properties file and initialize it with the location of jronn jar file");\r
  96                 }\r
  97                 if (new File(settings).isAbsolute()) {\r
  98                         // Jronn jar can be found so no actions necessary\r
  99                         // no further actions is necessary\r
 100                         return settings;\r
 101                 }\r
 102                 return compbio.engine.client.Util.convertToAbsolute(settings);\r
 103         }\r
 104 \r
 105         @Override\r
 106         public List<String> getCreatedFiles() {\r
 107                 return Arrays.asList(getOutput(), getError());\r
 108         }\r
 109 \r
 110         @Override\r
 111         public Jronn setInput(String inFile) {\r
 112                 super.setInput(inFile);\r
 113                 cbuilder.setParam("-i=" + inFile);\r
 114                 return this;\r
 115         }\r
 116 \r
 117         @Override\r
 118         public Jronn setOutput(String outFile) {\r
 119                 super.setOutput(outFile);\r
 120                 cbuilder.setParam("-o=" + outFile);\r
 121                 return this;\r
 122         }\r
 123 \r
 124         @SuppressWarnings("unchecked")\r
 125         @Override\r
 126         public Class<Jronn> getType() {\r
 127                 return (Class<Jronn>) this.getClass();\r
 128         }\r
 129 \r
 130         public static String getStatFile() {\r
 131                 return STAT_FILE;\r
 132         }\r
 133 \r
 134         public void setNCore(int ncoreNumber) {\r
 135                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 136                         throw new IndexOutOfBoundsException(\r
 137                                         "Number of cores must be within 1 and 100 ");\r
 138                 }\r
 139                 this.ncoreNumber = ncoreNumber;\r
 140                 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
 141         }\r
 142 \r
 143         int getNCore() {\r
 144                 return ncoreNumber;\r
 145         }\r
 146 \r
 147         @Override\r
 148         public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
 149                 // If number of cores is provided, set it for the cluster execution only!\r
 150                 if (provider == Executable.ExecProvider.Cluster) {\r
 151                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 152                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 153                         setNCore(cpunum);\r
 154                 } else {\r
 155                         // Limit number of cores to 1 for ANY execution which does not set\r
 156                         // Ncores explicitly using setNCore method or is run on local VM\r
 157                         if (ncoreNumber == 0) {\r
 158                                 setNCore(1);\r
 159                         }\r
 160                 }\r
 161                 return super.getParameters(provider);\r
 162         }\r
 163 \r
 164 }\r