1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.engine.client;
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21 import java.io.File;
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22 import java.io.FileInputStream;
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23 import java.io.IOException;
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24 import java.io.InputStream;
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25 import java.util.ArrayList;
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26 import java.util.Collections;
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27 import java.util.List;
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28 import java.util.Map;
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30 import javax.xml.bind.JAXBException;
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32 import org.apache.log4j.Logger;
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34 import compbio.engine.conf.PropertyHelperManager;
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35 import compbio.engine.conf.RunnerConfigMarshaller;
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36 import compbio.metadata.Limit;
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37 import compbio.metadata.LimitsManager;
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38 import compbio.metadata.PresetManager;
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39 import compbio.metadata.ResultNotAvailableException;
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40 import compbio.metadata.RunnerConfig;
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41 import compbio.metadata.UnsupportedRuntimeException;
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42 import compbio.util.FileUtil;
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43 import compbio.util.PropertyHelper;
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44 import compbio.util.SysPrefs;
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45 import compbio.util.Util;
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47 public class ConfExecutable<T> implements ConfiguredExecutable<T> {
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49 private static final Logger log = Logger.getLogger(ConfExecutable.class);
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51 private static final PropertyHelper ph = PropertyHelperManager
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52 .getPropertyHelper();
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53 public final static String CLUSTER_TASK_ID_PREFIX = "@";
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55 private String workDirectory;
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56 private String taskDirectory;
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58 private ExecProvider provider;
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59 private Executable<T> exec;
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61 public ConfExecutable(Executable<T> executable, String taskDirectory) {
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62 this.exec = executable;
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63 assert !compbio.util.Util.isEmpty(taskDirectory);
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64 this.taskDirectory = taskDirectory;
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67 // TODO think about appropriate exception here
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68 ConfExecutable(RunConfiguration rconf) {
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70 exec = (Executable<T>) Class.forName(rconf.runnerClassName)
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72 } catch (InstantiationException e) {
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73 e.printStackTrace();
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74 } catch (IllegalAccessException e) {
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75 e.printStackTrace();
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76 } catch (ClassNotFoundException e) {
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77 e.printStackTrace();
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79 exec.loadRunConfiguration(rconf);
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80 setWorkDirectory(rconf.workDirectory);
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81 this.taskDirectory = rconf.taskId;
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85 public ExecProvider getExecProvider() {
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89 public void setExecProvider(ExecProvider provider) {
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90 assert provider != null && provider != ExecProvider.Any;
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91 this.provider = provider;
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92 if (provider == Executable.ExecProvider.Cluster) {
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93 this.taskDirectory = CLUSTER_TASK_ID_PREFIX + taskDirectory;
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98 public String getCommand(ExecProvider provider)
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99 throws UnsupportedRuntimeException {
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100 String command = compbio.engine.client.Util.getCommand(provider,
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102 if (Util.isEmpty(command)) {
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103 throw new UnsupportedRuntimeException(
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105 + this.exec.getClass().getSimpleName()
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106 + " is not supported by the current runtime environment! Current runtime environment is "
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107 + (SysPrefs.isWindows
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109 : "Linux/Unix/Mac"));
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115 public ExecProvider getSupportedRuntimes() {
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116 return compbio.engine.client.Util.getSupportedRuntimes(exec.getClass());
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120 public Limit<T> getLimit(String presetName) {
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121 return exec.getLimit(presetName);
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125 public LimitsManager<T> getLimits() {
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126 return exec.getLimits();
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130 public String getTaskId() {
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131 return taskDirectory;
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135 public void setWorkDirectory(String workDirectory) {
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136 assert !compbio.util.Util.isEmpty(workDirectory);
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137 this.workDirectory = workDirectory;
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141 public String getWorkDirectory() {
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142 return this.workDirectory;
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146 public Executable<T> addParameters(List<String> parameters) {
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147 exec.addParameters(parameters);
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152 public String getOutput() {
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153 return exec.getOutput();
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157 public String getError() {
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158 return exec.getError();
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162 public List<String> getCreatedFiles() {
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163 return getFullPath(exec.getCreatedFiles());
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166 List<String> getFullPath(List<String> fileNames) {
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167 List<String> files = new ArrayList<String>();
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168 for (String fileName : fileNames) {
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169 files.add(compbio.engine.client.Util.getFullPath(workDirectory,
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176 * Not all input paths are relative! Input path could be absolute!
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178 * @see compbio.engine.client.Executable#getInputFiles()
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181 public String getInput() {
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182 String path = exec.getInput();
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183 if (PathValidator.isAbsolutePath(path)) {
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186 return compbio.engine.client.Util.getFullPath(workDirectory, path);
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190 public CommandBuilder<T> getParameters() {
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191 return exec.getParameters(provider);
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195 public CommandBuilder<T> getParameters(
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196 compbio.engine.client.Executable.ExecProvider provider) {
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197 return getParameters();
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201 public Executable<T> getExecutable() {
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206 public <V> V getResults() throws ResultNotAvailableException {
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207 return (V) exec.getResults(workDirectory);
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211 * This is just a pass through method (non-Javadoc)
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213 * @see compbio.runner.Executable#getResults(java.lang.String)
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216 public <V> V getResults(String directory)
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217 throws ResultNotAvailableException {
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218 return (V) exec.getResults(directory);
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222 * This method should be executed once and result of its execution reused.
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223 * If not used carefully it could slow down the system!
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225 public static <V> RunnerConfig<V> getRunnerOptions(
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226 Class<? extends Executable<V>> clazz) throws IOException {
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227 String parametersFile = clazz.getSimpleName().toLowerCase()
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228 + ".parameters.file";
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229 return (RunnerConfig<V>) getRunnerConfiguration(clazz,
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230 RunnerConfig.class, parametersFile);
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234 * This method should be executed once and result of its execution reused.
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235 * If not used carefully it could slow down the system!
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237 public static <V> PresetManager<V> getRunnerPresets(
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238 Class<? extends Executable<V>> clazz) throws IOException {
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239 String parametersFile = clazz.getSimpleName().toLowerCase()
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241 PresetManager<V> presets = (PresetManager<V>) getRunnerConfiguration(
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242 clazz, PresetManager.class, parametersFile);
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247 * This method should be executed once and result of its execution reused.
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248 * If not used carefully it could slow down the system!
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252 * @return LimitsManager instance
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253 * @throws IOException
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255 public static <V> LimitsManager<V> getRunnerLimits(Class<V> clazz)
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256 throws IOException {
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257 String parametersFile = clazz.getSimpleName().toLowerCase()
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259 LimitsManager<V> limits = (LimitsManager<V>) getRunnerConfiguration(
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260 clazz, LimitsManager.class, parametersFile);
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264 static <V> Object getRunnerConfiguration(Class<V> clazz,
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265 Class<?> configurationHolder, String propertyName)
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266 throws IOException {
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268 Object rconf = null;
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269 FileInputStream confFileStream = null;
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271 RunnerConfigMarshaller<V> rcm = new RunnerConfigMarshaller<V>(
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272 configurationHolder);
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273 String path = ph.getProperty(propertyName);
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274 if (compbio.util.Util.isEmpty(path)) {
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275 log.debug("Configuration " + path + " is not provided");
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278 log.debug("Loading Configuration from " + path + " Config type:"
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279 + configurationHolder);
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280 File confFile = new File(PropertyHelperManager.getLocalPath()
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282 confFileStream = new FileInputStream(confFile);
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283 rconf = rcm.read(confFileStream, configurationHolder);
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284 confFileStream.close();
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285 } catch (JAXBException e) {
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286 log.error(e.getLocalizedMessage(), e.getCause());
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288 FileUtil.closeSilently(log, confFileStream);
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294 public Map<String, String> getEnvironment() {
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295 String envProperty = ph.getProperty(exec.getClass().getSimpleName()
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298 if (envProperty == null) {
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299 return Collections.emptyMap();
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302 return EnvVariableProcessor.getEnvVariables(envProperty,
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307 public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf) {
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308 if (rconf == null) {
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309 throw new NullPointerException("RunConfiguration is expected!");
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311 return new ConfExecutable(rconf);
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314 public static ConfiguredExecutable<?> newConfExecutable(
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315 RunConfiguration rconf) {
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316 if (rconf == null) {
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317 throw new NullPointerException("RunConfiguration is expected!");
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319 return new ConfExecutable(rconf);
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323 public boolean saveRunConfiguration() throws IOException {
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324 RunConfiguration rconf = getRunConfiguration();
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325 return RunConfiguration.write(rconf);
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328 public RunConfiguration getRunConfiguration() {
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330 * Distinguish between dynamic settings and static settings (set in conf
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331 * or class) The latter does not need saving (as if they change there
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332 * were a good reason for this and it make it impossible/dangerous to
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333 * rerun the task with old settings)
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335 // Set within Executable
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336 // String taskId = executable.getTaskId();
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339 * All things below are handled by Executable
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341 * getInput() && getOutput()
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343 * // Handle PipedExecutables String error = executable.getError(); if
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344 * (error != null) {
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346 * } String output = executable.getOutput(); if (output != null) {
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348 * } List<String> outputs = executable.getCreatedFiles(); List<String>
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349 * inputs = executable.getInputFiles();
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351 * /* Environment is defined only declaratively. Map<String,String> env
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352 * = executable.getEnvironment();
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354 * List<String> params = executable.getParameters();
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356 RunConfiguration rconf = new RunConfiguration(this);
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361 public ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
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362 throws IOException {
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363 RunConfiguration rconf = RunConfiguration.load(input);
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364 log.info("Loaded saved RunConfiguration " + rconf);
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365 return new ConfExecutable(rconf);
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369 public String toString() {
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370 String value = "Work dir: " + this.workDirectory + "\n";
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371 value += "TaskId: " + this.taskDirectory + "\n";
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372 value += "Params: " + this.getParameters() + "\n";
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373 value += exec.toString();
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378 public String getClusterJobSettings() {
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379 return exec.getClusterJobSettings();
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