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