engine/compbio/engine/client/ConfExecutable.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.engine.client;\r
  20 \r
  21 import java.io.File;\r
  22 import java.io.FileInputStream;\r
  23 import java.io.IOException;\r
  24 import java.io.InputStream;\r
  25 import java.util.ArrayList;\r
  26 import java.util.Collections;\r
  27 import java.util.List;\r
  28 import java.util.Map;\r
  29 \r
  30 import javax.xml.bind.JAXBException;\r
  31 \r
  32 import org.apache.log4j.Logger;\r
  33 \r
  34 import compbio.engine.conf.PropertyHelperManager;\r
  35 import compbio.engine.conf.RunnerConfigMarshaller;\r
  36 import compbio.metadata.Limit;\r
  37 import compbio.metadata.LimitsManager;\r
  38 import compbio.metadata.PresetManager;\r
  39 import compbio.metadata.ResultNotAvailableException;\r
  40 import compbio.metadata.RunnerConfig;\r
  41 import compbio.metadata.UnsupportedRuntimeException;\r
  42 import compbio.util.FileUtil;\r
  43 import compbio.util.PropertyHelper;\r
  44 import compbio.util.SysPrefs;\r
  45 import compbio.util.Util;\r
  46 \r
  47 public class ConfExecutable<T> implements ConfiguredExecutable<T> {\r
  48 \r
  49         private static final Logger log = Logger.getLogger(ConfExecutable.class);\r
  50 \r
  51         private static final PropertyHelper ph = PropertyHelperManager\r
  52                         .getPropertyHelper();\r
  53         public final static String CLUSTER_TASK_ID_PREFIX = "@";\r
  54 \r
  55         private String workDirectory;\r
  56         private String taskDirectory;\r
  57 \r
  58         private ExecProvider provider;\r
  59         private Executable<T> exec;\r
  60 \r
  61         public ConfExecutable(Executable<T> executable, String taskDirectory) {\r
  62                 this.exec = executable;\r
  63                 assert !compbio.util.Util.isEmpty(taskDirectory);\r
  64                 this.taskDirectory = taskDirectory;\r
  65         }\r
  66 \r
  67         // TODO think about appropriate exception here\r
  68         ConfExecutable(RunConfiguration rconf) {\r
  69                 try {\r
  70                         exec = (Executable<T>) Class.forName(rconf.runnerClassName)\r
  71                                         .newInstance();\r
  72                 } catch (InstantiationException e) {\r
  73                         e.printStackTrace();\r
  74                 } catch (IllegalAccessException e) {\r
  75                         e.printStackTrace();\r
  76                 } catch (ClassNotFoundException e) {\r
  77                         e.printStackTrace();\r
  78                 }\r
  79                 exec.loadRunConfiguration(rconf);\r
  80                 setWorkDirectory(rconf.workDirectory);\r
  81                 this.taskDirectory = rconf.taskId;\r
  82         }\r
  83 \r
  84         @Override\r
  85         public ExecProvider getExecProvider() {\r
  86                 return provider;\r
  87         }\r
  88 \r
  89         public void setExecProvider(ExecProvider provider) {\r
  90                 assert provider != null && provider != ExecProvider.Any;\r
  91                 this.provider = provider;\r
  92                 if (provider == Executable.ExecProvider.Cluster) {\r
  93                         this.taskDirectory = CLUSTER_TASK_ID_PREFIX + taskDirectory;\r
  94                 }\r
  95         }\r
  96 \r
  97         @Override\r
  98         public String getCommand(ExecProvider provider)\r
  99                         throws UnsupportedRuntimeException {\r
 100                 String command = compbio.engine.client.Util.getCommand(provider, exec\r
 101                                 .getClass());\r
 102                 if (Util.isEmpty(command)) {\r
 103                         throw new UnsupportedRuntimeException(\r
 104                                         "Executable "\r
 105                                                         + this.exec.getClass().getSimpleName()\r
 106                                                         + " is not supported by the current runtime environment! Current runtime environment is "\r
 107                                                         + (SysPrefs.isWindows ? "Windows "\r
 108                                                                         : "Linux/Unix/Mac"));\r
 109                 }\r
 110                 return command;\r
 111         }\r
 112 \r
 113         @Override\r
 114         public ExecProvider getSupportedRuntimes() {\r
 115                 return compbio.engine.client.Util.getSupportedRuntimes(exec.getClass());\r
 116         }\r
 117 \r
 118         @Override\r
 119         public Limit<T> getLimit(String presetName) {\r
 120                 return exec.getLimit(presetName);\r
 121         }\r
 122 \r
 123         @Override\r
 124         public LimitsManager<T> getLimits() {\r
 125                 return exec.getLimits();\r
 126         }\r
 127 \r
 128         @Override\r
 129         public String getTaskId() {\r
 130                 return taskDirectory;\r
 131         }\r
 132 \r
 133         @Override\r
 134         public void setWorkDirectory(String workDirectory) {\r
 135                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 136                 this.workDirectory = workDirectory;\r
 137         }\r
 138 \r
 139         @Override\r
 140         public String getWorkDirectory() {\r
 141                 return this.workDirectory;\r
 142         }\r
 143 \r
 144         @Override\r
 145         public Executable<T> addParameters(List<String> parameters) {\r
 146                 exec.addParameters(parameters);\r
 147                 return exec;\r
 148         }\r
 149 \r
 150         @Override\r
 151         public String getOutput() {\r
 152                 return exec.getOutput();\r
 153         }\r
 154 \r
 155         @Override\r
 156         public String getError() {\r
 157                 return exec.getError();\r
 158         }\r
 159 \r
 160         @Override\r
 161         public List<String> getCreatedFiles() {\r
 162                 return getFullPath(exec.getCreatedFiles());\r
 163         }\r
 164 \r
 165         List<String> getFullPath(List<String> fileNames) {\r
 166                 List<String> files = new ArrayList<String>();\r
 167                 for (String fileName : fileNames) {\r
 168                         files.add(compbio.engine.client.Util.getFullPath(workDirectory,\r
 169                                         fileName));\r
 170                 }\r
 171                 return files;\r
 172         }\r
 173 \r
 174         /**\r
 175          * Not all input paths are relative! Input path could be absolute!\r
 176          * \r
 177          * @see compbio.engine.client.Executable#getInputFiles()\r
 178          */\r
 179         @Override\r
 180         public String getInput() {\r
 181                 String path = exec.getInput();\r
 182                 if (PathValidator.isAbsolutePath(path)) {\r
 183                         return path;\r
 184                 }\r
 185                 return compbio.engine.client.Util.getFullPath(workDirectory, path);\r
 186         }\r
 187 \r
 188         @Override\r
 189         public CommandBuilder<T> getParameters() {\r
 190                 return exec.getParameters(provider);\r
 191         }\r
 192 \r
 193         @Override\r
 194         public CommandBuilder<T> getParameters(\r
 195                         compbio.engine.client.Executable.ExecProvider provider) {\r
 196                 return getParameters();\r
 197         }\r
 198 \r
 199         @Override\r
 200         public Executable<T> getExecutable() {\r
 201                 return exec;\r
 202         }\r
 203 \r
 204         @Override\r
 205         public <V> V getResults() throws ResultNotAvailableException {\r
 206                 return (V) exec.getResults(workDirectory);\r
 207         }\r
 208 \r
 209         /*\r
 210          * This is just a pass through method (non-Javadoc)\r
 211          * \r
 212          * @see compbio.runner.Executable#getResults(java.lang.String)\r
 213          */\r
 214         @Override\r
 215         public <V> V getResults(String directory)\r
 216                         throws ResultNotAvailableException {\r
 217                 return (V) exec.getResults(directory);\r
 218         }\r
 219 \r
 220         /*\r
 221          * This method should be executed once and result of its execution reused.\r
 222          * If not used carefully it could slow down the system!\r
 223          */\r
 224         public static <V> RunnerConfig<V> getRunnerOptions(\r
 225                         Class<? extends Executable<V>> clazz) throws IOException {\r
 226                 String parametersFile = clazz.getSimpleName().toLowerCase()\r
 227                                 + ".parameters.file";\r
 228                 return (RunnerConfig<V>) getRunnerConfiguration(clazz,\r
 229                                 RunnerConfig.class, parametersFile);\r
 230         }\r
 231 \r
 232         /*\r
 233          * This method should be executed once and result of its execution reused.\r
 234          * If not used carefully it could slow down the system!\r
 235          */\r
 236         public static <V> PresetManager<V> getRunnerPresets(\r
 237                         Class<? extends Executable<V>> clazz) throws IOException {\r
 238                 String parametersFile = clazz.getSimpleName().toLowerCase()\r
 239                                 + ".presets.file";\r
 240                 PresetManager<V> presets = (PresetManager<V>) getRunnerConfiguration(\r
 241                                 clazz, PresetManager.class, parametersFile);\r
 242                 return presets;\r
 243         }\r
 244 \r
 245         /**\r
 246          * This method should be executed once and result of its execution reused.\r
 247          * If not used carefully it could slow down the system!\r
 248          * \r
 249          * @param <V>\r
 250          * @param clazz\r
 251          * @return\r
 252          * @throws IOException\r
 253          */\r
 254         public static <V> LimitsManager<V> getRunnerLimits(\r
 255                         Class<? extends Executable<V>> clazz) throws IOException {\r
 256                 String parametersFile = clazz.getSimpleName().toLowerCase()\r
 257                                 + ".limits.file";\r
 258                 LimitsManager<V> limits = (LimitsManager<V>) getRunnerConfiguration(\r
 259                                 clazz, LimitsManager.class, parametersFile);\r
 260                 return limits;\r
 261         }\r
 262 \r
 263         static <V> Object getRunnerConfiguration(\r
 264                         Class<? extends Executable<V>> clazz, Class<?> configurationHolder,\r
 265                         String propertyName) throws IOException {\r
 266 \r
 267                 Object rconf = null;\r
 268                 FileInputStream confFileStream = null;\r
 269                 try {\r
 270                         RunnerConfigMarshaller<V> rcm = new RunnerConfigMarshaller<V>(\r
 271                                         configurationHolder);\r
 272                         String path = ph.getProperty(propertyName);\r
 273                         if (compbio.util.Util.isEmpty(path)) {\r
 274                                 log.debug("Configuration " + path + " is not provided");\r
 275                                 return null;\r
 276                         }\r
 277                         log.debug("Loading Configuration from " + path + " Config type:"\r
 278                                         + configurationHolder);\r
 279                         File confFile = new File(PropertyHelperManager.getLocalPath()\r
 280                                         + path);\r
 281                         confFileStream = new FileInputStream(confFile);\r
 282                         rconf = rcm.read(confFileStream, configurationHolder);\r
 283                         confFileStream.close();\r
 284                 } catch (JAXBException e) {\r
 285                         log.error(e.getLocalizedMessage(), e.getCause());\r
 286                 } finally {\r
 287                         FileUtil.closeSilently(log, confFileStream);\r
 288                 }\r
 289                 return rconf;\r
 290         }\r
 291 \r
 292         @Override\r
 293         public Map<String, String> getEnvironment() {\r
 294                 String envProperty = ph.getProperty(exec.getClass().getSimpleName()\r
 295                                 .toLowerCase()\r
 296                                 + ".bin.env");\r
 297                 if (envProperty == null) {\r
 298                         return Collections.emptyMap();\r
 299                 }\r
 300 \r
 301                 return EnvVariableProcessor.getEnvVariables(envProperty, this\r
 302                                 .getClass());\r
 303         }\r
 304 \r
 305         @Override\r
 306         public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf) {\r
 307                 if (rconf == null) {\r
 308                         throw new NullPointerException("RunConfiguration is expected!");\r
 309                 }\r
 310                 return new ConfExecutable(rconf);\r
 311         }\r
 312 \r
 313         public static ConfiguredExecutable<?> newConfExecutable(\r
 314                         RunConfiguration rconf) {\r
 315                 if (rconf == null) {\r
 316                         throw new NullPointerException("RunConfiguration is expected!");\r
 317                 }\r
 318                 return new ConfExecutable(rconf);\r
 319         }\r
 320 \r
 321         @Override\r
 322         public boolean saveRunConfiguration() throws IOException {\r
 323                 RunConfiguration rconf = getRunConfiguration();\r
 324                 return RunConfiguration.write(rconf);\r
 325         }\r
 326 \r
 327         public RunConfiguration getRunConfiguration() {\r
 328                 /*\r
 329                  * Distinguish between dynamic settings and static settings (set in conf\r
 330                  * or class) The latter does not need saving (as if they change there\r
 331                  * were a good reason for this and it make it impossible/dangerous to\r
 332                  * rerun the task with old settings)\r
 333                  */\r
 334                 // Set within Executable\r
 335                 // String taskId = executable.getTaskId();\r
 336 \r
 337                 /*\r
 338                  * All things below are handled by Executable\r
 339                  * \r
 340                  * getInput() && getOutput()\r
 341                  * \r
 342                  * // Handle PipedExecutables String error = executable.getError(); if\r
 343                  * (error != null) {\r
 344                  * \r
 345                  * } String output = executable.getOutput(); if (output != null) {\r
 346                  * \r
 347                  * } List<String> outputs = executable.getCreatedFiles(); List<String>\r
 348                  * inputs = executable.getInputFiles();\r
 349                  * \r
 350                  * /* Environment is defined only declaratively. Map<String,String> env\r
 351                  * = executable.getEnvironment();\r
 352                  * \r
 353                  * List<String> params = executable.getParameters();\r
 354                  */\r
 355                 RunConfiguration rconf = new RunConfiguration(this);\r
 356                 return rconf;\r
 357         }\r
 358 \r
 359         @Override\r
 360         public ConfiguredExecutable<?> loadRunConfiguration(InputStream input)\r
 361                         throws IOException {\r
 362                 RunConfiguration rconf = RunConfiguration.load(input);\r
 363                 log.info("Loaded saved RunConfiguration " + rconf);\r
 364                 return new ConfExecutable(rconf);\r
 365         }\r
 366 \r
 367         @Override\r
 368         public String toString() {\r
 369                 String value = "Work dir: " + this.workDirectory + "\n";\r
 370                 value += "TaskId: " + this.taskDirectory + "\n";\r
 371                 value += "Params: " + this.getParameters() + "\n";\r
 372                 value += exec.toString();\r
 373                 return value;\r
 374         }\r
 375 }\r