website/docs/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html

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  95 <div class="subTitle">compbio.engine.cluster.drmaa</div>
  96 <h2 title="Class AsyncJobRunner" class="title">Class AsyncJobRunner</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.engine.cluster.drmaa.AsyncJobRunner</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt>All Implemented Interfaces:</dt>
 112 <dd><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public class <span class="typeNameLabel">AsyncJobRunner</span>
 117 extends java.lang.Object
 118 implements <a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></pre>
 119 <div class="block">Single cluster job runner class</div>
 120 <dl>
 121 <dt><span class="simpleTagLabel">Version:</span></dt>
 122 <dd>1.0 August 2009
 123
 124           TODO after call to submitJob() no setters really work as the job
 125           template gets deleted, this needs to be taken into account in this
 126           class design!</dd>
 127 <dt><span class="simpleTagLabel">Author:</span></dt>
 128 <dd>pvtroshin</dd>
 129 </dl>
 130 </li>
 131 </ul>
 132 </div>
 133 <div class="summary">
 134 <ul class="blockList">
 135 <li class="blockList">
 136 <!-- =========== FIELD SUMMARY =========== -->
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 139 <!--   -->
 140 </a>
 141 <h3>Field Summary</h3>
 142 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 143 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 144 <tr>
 145 <th class="colFirst" scope="col">Modifier and Type</th>
 146 <th class="colLast" scope="col">Field and Description</th>
 147 </tr>
 148 <tr class="altColor">
 149 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
 150 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#log">log</a></span></code>&nbsp;</td>
 151 </tr>
 152 </table>
 153 </li>
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 155 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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 161 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 162 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 163 <tr>
 164 <th class="colOne" scope="col">Constructor and Description</th>
 165 </tr>
 166 <tr class="altColor">
 167 <td class="colOne"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner--">AsyncJobRunner</a></span>()</code>&nbsp;</td>
 168 </tr>
 169 </table>
 170 </li>
 171 </ul>
 172 <!-- ========== METHOD SUMMARY =========== -->
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 174 <li class="blockList"><a name="method.summary">
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 176 </a>
 177 <h3>Method Summary</h3>
 178 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 179 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 180 <tr>
 181 <th class="colFirst" scope="col">Modifier and Type</th>
 182 <th class="colLast" scope="col">Method and Description</th>
 183 </tr>
 184 <tr id="i0" class="altColor">
 185 <td class="colFirst"><code>boolean</code></td>
 186 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob-java.lang.String-">cancelJob</a></span>(java.lang.String&nbsp;jobId)</code>
 187 <div class="block">Stop running job.</div>
 188 </td>
 189 </tr>
 190 <tr id="i1" class="rowColor">
 191 <td class="colFirst"><code>boolean</code></td>
 192 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup-java.lang.String-">cleanup</a></span>(java.lang.String&nbsp;jobId)</code>
 193 <div class="block">Remove all files and a job directory for a jobid.</div>
 194 </td>
 195 </tr>
 196 <tr id="i2" class="altColor">
 197 <td class="colFirst"><code><a href="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></code></td>
 198 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus-java.lang.String-">getJobStatus</a></span>(java.lang.String&nbsp;jobId)</code>
 199 <div class="block">This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 200  engine cancelled job is the same as failed.</div>
 201 </td>
 202 </tr>
 203 <tr id="i3" class="rowColor">
 204 <td class="colFirst"><code><a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;</code></td>
 205 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;jobId)</code>
 206 <div class="block">Retrieve the results of the job.</div>
 207 </td>
 208 </tr>
 209 <tr id="i4" class="altColor">
 210 <td class="colFirst"><code>java.lang.String</code></td>
 211 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory-java.lang.String-">getWorkDirectory</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 212 </tr>
 213 <tr id="i5" class="rowColor">
 214 <td class="colFirst"><code>java.lang.String</code></td>
 215 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob</a></span>(<a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;executable)</code>
 216 <div class="block">Submits job for the execution
 217  Immediate execution is not guaranteed, this method puts the job in the queue.</div>
 218 </td>
 219 </tr>
 220 </table>
 221 <ul class="blockList">
 222 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 223 <!--   -->
 224 </a>
 225 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 226 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 227 </ul>
 228 </li>
 229 </ul>
 230 </li>
 231 </ul>
 232 </div>
 233 <div class="details">
 234 <ul class="blockList">
 235 <li class="blockList">
 236 <!-- ============ FIELD DETAIL =========== -->
 237 <ul class="blockList">
 238 <li class="blockList"><a name="field.detail">
 239 <!--   -->
 240 </a>
 241 <h3>Field Detail</h3>
 242 <a name="log">
 243 <!--   -->
 244 </a>
 245 <ul class="blockListLast">
 246 <li class="blockList">
 247 <h4>log</h4>
 248 <pre>private static&nbsp;org.apache.log4j.Logger log</pre>
 249 </li>
 250 </ul>
 251 </li>
 252 </ul>
 253 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 254 <ul class="blockList">
 255 <li class="blockList"><a name="constructor.detail">
 256 <!--   -->
 257 </a>
 258 <h3>Constructor Detail</h3>
 259 <a name="AsyncJobRunner--">
 260 <!--   -->
 261 </a>
 262 <ul class="blockListLast">
 263 <li class="blockList">
 264 <h4>AsyncJobRunner</h4>
 265 <pre>public&nbsp;AsyncJobRunner()</pre>
 266 </li>
 267 </ul>
 268 </li>
 269 </ul>
 270 <!-- ============ METHOD DETAIL ========== -->
 271 <ul class="blockList">
 272 <li class="blockList"><a name="method.detail">
 273 <!--   -->
 274 </a>
 275 <h3>Method Detail</h3>
 276 <a name="submitJob-compbio.engine.client.ConfiguredExecutable-">
 277 <!--   -->
 278 </a>
 279 <ul class="blockList">
 280 <li class="blockList">
 281 <h4>submitJob</h4>
 282 <pre>public&nbsp;java.lang.String&nbsp;submitJob(<a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;executable)
 283                            throws <a href="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 284 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html#submitJob-compbio.engine.client.ConfiguredExecutable-">AsyncExecutor</a></code></span></div>
 285 <div class="block">Submits job for the execution
 286  Immediate execution is not guaranteed, this method puts the job in the queue.
 287  All it guarantees that the job will be eventually executed.
 288  The start of execution will depend on the number of jobs in the queue.</div>
 289 <dl>
 290 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 291 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#submitJob-compbio.engine.client.ConfiguredExecutable-">submitJob</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 292 <dt><span class="returnLabel">Returns:</span></dt>
 293 <dd>unique job identifier</dd>
 294 <dt><span class="throwsLabel">Throws:</span></dt>
 295 <dd><code><a href="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - if submission fails. This usually happens due to the problem on a server side.</dd>
 296 </dl>
 297 </li>
 298 </ul>
 299 <a name="cancelJob-java.lang.String-">
 300 <!--   -->
 301 </a>
 302 <ul class="blockList">
 303 <li class="blockList">
 304 <h4>cancelJob</h4>
 305 <pre>public&nbsp;boolean&nbsp;cancelJob(java.lang.String&nbsp;jobId)</pre>
 306 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html#cancelJob-java.lang.String-">AsyncExecutor</a></code></span></div>
 307 <div class="block">Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.</div>
 308 <dl>
 309 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 310 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#cancelJob-java.lang.String-">cancelJob</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 311 <dt><span class="returnLabel">Returns:</span></dt>
 312 <dd>true if job was cancelled successfully, false otherwise</dd>
 313 </dl>
 314 </li>
 315 </ul>
 316 <a name="getJobStatus-java.lang.String-">
 317 <!--   -->
 318 </a>
 319 <ul class="blockList">
 320 <li class="blockList">
 321 <h4>getJobStatus</h4>
 322 <pre>public&nbsp;<a href="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a>&nbsp;getJobStatus(java.lang.String&nbsp;jobId)</pre>
 323 <div class="block">This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 324  engine cancelled job is the same as failed. Cancelled jobs needs to be
 325  tracked manually!</div>
 326 <dl>
 327 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 328 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#getJobStatus-java.lang.String-">getJobStatus</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 329 <dt><span class="returnLabel">Returns:</span></dt>
 330 <dd>The JobStatus object representing the status of the job</dd>
 331 <dt><span class="seeLabel">See Also:</span></dt>
 332 <dd><a href="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><code>JobStatus</code></a></dd>
 333 </dl>
 334 </li>
 335 </ul>
 336 <a name="cleanup-java.lang.String-">
 337 <!--   -->
 338 </a>
 339 <ul class="blockList">
 340 <li class="blockList">
 341 <h4>cleanup</h4>
 342 <pre>public&nbsp;boolean&nbsp;cleanup(java.lang.String&nbsp;jobId)</pre>
 343 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html#cleanup-java.lang.String-">AsyncExecutor</a></code></span></div>
 344 <div class="block">Remove all files and a job directory for a jobid.</div>
 345 <dl>
 346 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 347 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#cleanup-java.lang.String-">cleanup</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 348 <dt><span class="returnLabel">Returns:</span></dt>
 349 <dd>true if job directory was successfully removed, false otherwise.</dd>
 350 </dl>
 351 </li>
 352 </ul>
 353 <a name="getResults-java.lang.String-">
 354 <!--   -->
 355 </a>
 356 <ul class="blockList">
 357 <li class="blockList">
 358 <h4>getResults</h4>
 359 <pre>public&nbsp;<a href="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;getResults(java.lang.String&nbsp;jobId)
 360                                    throws <a href="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 361 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html#getResults-java.lang.String-">AsyncExecutor</a></code></span></div>
 362 <div class="block">Retrieve the results of the job. Please not that current implementations of this method
 363  blocks if the task is running until the end of the calculation.</div>
 364 <dl>
 365 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 366 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#getResults-java.lang.String-">getResults</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 367 <dt><span class="paramLabel">Parameters:</span></dt>
 368 <dd><code>jobId</code> - job identifier obtained at the job submission</dd>
 369 <dt><span class="returnLabel">Returns:</span></dt>
 370 <dd>ConfiguredExecutable object from which result can be obtained</dd>
 371 <dt><span class="throwsLabel">Throws:</span></dt>
 372 <dd><code><a href="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code> - if the result is not available for whatever reason.
 373  Could be due to execution failure, or due to the results being removed from the server at
 374  the time of request.</dd>
 375 </dl>
 376 </li>
 377 </ul>
 378 <a name="getWorkDirectory-java.lang.String-">
 379 <!--   -->
 380 </a>
 381 <ul class="blockListLast">
 382 <li class="blockList">
 383 <h4>getWorkDirectory</h4>
 384 <pre>public&nbsp;java.lang.String&nbsp;getWorkDirectory(java.lang.String&nbsp;jobId)</pre>
 385 <dl>
 386 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 387 <dd><code><a href="../../../../compbio/engine/AsyncExecutor.html#getWorkDirectory-java.lang.String-">getWorkDirectory</a></code>&nbsp;in interface&nbsp;<code><a href="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></dd>
 388 <dt><span class="paramLabel">Parameters:</span></dt>
 389 <dd><code>jobId</code> - unique job identifier</dd>
 390 <dt><span class="returnLabel">Returns:</span></dt>
 391 <dd>task working directory</dd>
 392 </dl>
 393 </li>
 394 </ul>
 395 </li>
 396 </ul>
 397 </li>
 398 </ul>
 399 </div>
 400 </div>
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