runner/compbio/runner/conservation/AACon.java

   1 /*\r
   2  * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
   3  * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
   4  * and/or modify it under the terms of the Apache License version 2 as published\r
   5  * by the Apache Software Foundation This library is distributed in the hope\r
   6  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
   7  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
   8  * Apache License for more details. A copy of the license is in\r
   9  * apache_license.txt. It is also available here:\r
  10  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
  11  * derived work distributed in source code form must include this copyright and\r
  12  * license notice.\r
  13  */\r
  14 \r
  15 package compbio.runner.conservation;\r
  16 \r
  17 import java.io.File;\r
  18 import java.io.FileInputStream;\r
  19 import java.io.FileNotFoundException;\r
  20 import java.io.IOException;\r
  21 import java.io.InputStream;\r
  22 import java.util.Arrays;\r
  23 import java.util.List;\r
  24 \r
  25 import org.apache.log4j.Logger;\r
  26 \r
  27 import compbio.conservation.Method;\r
  28 import compbio.conservation.ResultReader;\r
  29 import compbio.data.sequence.MultiAnnotatedSequence;\r
  30 import compbio.engine.client.CommandBuilder;\r
  31 import compbio.engine.client.Executable;\r
  32 import compbio.engine.client.SkeletalExecutable;\r
  33 import compbio.metadata.Limit;\r
  34 import compbio.metadata.LimitsManager;\r
  35 import compbio.metadata.ResultNotAvailableException;\r
  36 import compbio.runner.Util;\r
  37 \r
  38 /**\r
  39  * Command line\r
  40  * \r
  41  * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
  42  * \r
  43  * @author pvtroshin\r
  44  * \r
  45  */\r
  46 public class AACon extends SkeletalExecutable<AACon> {\r
  47 \r
  48         private static Logger log = Logger.getLogger(AACon.class);\r
  49 \r
  50         /**\r
  51          * Number of cores to use, defaults to 1 for local execution or the value of\r
  52          * "jronn.cluster.cpunum" property for cluster execution\r
  53          */\r
  54         private int ncoreNumber = 0;\r
  55 \r
  56         private final String ncorePrm = "-n=";\r
  57 \r
  58         // Cache for Limits information\r
  59         private static LimitsManager<AACon> limits;\r
  60 \r
  61         public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
  62         public static final String STAT_FILE = "stat.txt";\r
  63 \r
  64         public AACon() {\r
  65                 addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,\r
  66                                 "-f=RESULT_NO_ALIGNMENT"));\r
  67         }\r
  68 \r
  69         @SuppressWarnings("unchecked")\r
  70         @Override\r
  71         public MultiAnnotatedSequence<Method> getResults(String workDirectory)\r
  72                         throws ResultNotAvailableException {\r
  73                 MultiAnnotatedSequence<Method> annotations = null;\r
  74                 try {\r
  75                         InputStream inStream = new FileInputStream(new File(workDirectory,\r
  76                                         getOutput()));\r
  77                         annotations = ResultReader.readResults(inStream);\r
  78                         inStream.close();\r
  79                 } catch (FileNotFoundException e) {\r
  80                         log.error(e.getMessage(), e.getCause());\r
  81                         throw new ResultNotAvailableException(e);\r
  82                 } catch (IOException 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 annotations;\r
  90         }\r
  91 \r
  92         private static String getLibPath() {\r
  93 \r
  94                 String settings = ph.getProperty("aacon.jar.file");\r
  95                 if (compbio.util.Util.isEmpty(settings)) {\r
  96                         throw new NullPointerException(\r
  97                                         "Please define aacon.jar.file property in Executable.properties file"\r
  98                                                         + "and initialize it with the location of jronn jar file");\r
  99                 }\r
 100                 if (new File(settings).isAbsolute()) {\r
 101                         // Jronn jar can be found so no actions necessary\r
 102                         // no further actions is necessary\r
 103                         return settings;\r
 104                 }\r
 105                 return compbio.engine.client.Util.convertToAbsolute(settings);\r
 106         }\r
 107 \r
 108         @Override\r
 109         public List<String> getCreatedFiles() {\r
 110                 return Arrays.asList(getOutput(), getError());\r
 111         }\r
 112 \r
 113         @Override\r
 114         public AACon setInput(String inFile) {\r
 115                 super.setInput(inFile);\r
 116                 cbuilder.setParam("-i=" + inFile);\r
 117                 return this;\r
 118         }\r
 119 \r
 120         @Override\r
 121         public AACon setOutput(String outFile) {\r
 122                 super.setOutput(outFile);\r
 123                 cbuilder.setParam("-o=" + outFile);\r
 124                 return this;\r
 125         }\r
 126 \r
 127         @Override\r
 128         public Limit<AACon> getLimit(String presetName) {\r
 129                 if (limits == null) {\r
 130                         limits = getLimits();\r
 131                 }\r
 132                 Limit<AACon> limit = null;\r
 133                 if (limits != null) {\r
 134                         // this returns default limit if preset is undefined!\r
 135                         limit = limits.getLimitByName(presetName);\r
 136                 }\r
 137                 // If limit is not defined for a particular preset, then return default\r
 138                 // limit\r
 139                 if (limit == null) {\r
 140                         log.debug("Limit for the preset " + presetName\r
 141                                         + " is not found. Using default");\r
 142                         limit = limits.getDefaultLimit();\r
 143                 }\r
 144                 return limit;\r
 145         }\r
 146 \r
 147         @Override\r
 148         public LimitsManager<AACon> getLimits() {\r
 149                 // synchronise on static field\r
 150                 synchronized (log) {\r
 151                         if (limits == null) {\r
 152                                 limits = Util.getLimits(this.getClass());\r
 153                         }\r
 154                 }\r
 155                 return limits;\r
 156         }\r
 157 \r
 158         @Override\r
 159         public Class<? extends Executable<?>> getType() {\r
 160                 return this.getClass();\r
 161         }\r
 162 \r
 163         public static String getStatFile() {\r
 164                 return STAT_FILE;\r
 165         }\r
 166 \r
 167         public void setNCore(int ncoreNumber) {\r
 168                 if (ncoreNumber < 1 || ncoreNumber > 100) {\r
 169                         throw new IndexOutOfBoundsException(\r
 170                                         "Number of cores must be within 1 and 100 ");\r
 171                 }\r
 172                 this.ncoreNumber = ncoreNumber;\r
 173                 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
 174         }\r
 175 \r
 176         int getNCore() {\r
 177                 return ncoreNumber;\r
 178         }\r
 179 \r
 180         @Override\r
 181         public CommandBuilder<AACon> getParameters(ExecProvider provider) {\r
 182                 // If number of cores is provided, set it for the cluster execution\r
 183                 // only!\r
 184                 if (provider == Executable.ExecProvider.Cluster) {\r
 185                         int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
 186                         cpunum = (cpunum == 0) ? 1 : cpunum;\r
 187                         setNCore(cpunum);\r
 188                 } else {\r
 189                         // Limit number of cores to 1 for ANY execution which does not set\r
 190                         // Ncores explicitly using setNCore method or is run on local VM\r
 191                         if (ncoreNumber == 0) {\r
 192                                 setNCore(1);\r
 193                         }\r
 194                 }\r
 195                 return super.getParameters(provider);\r
 196         }\r
 197 \r
 198 }\r