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