updated javadoc
[jabaws.git] / website / full_javadoc / compbio / engine / cluster / drmaa / JobRunner.html
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7 JobRunner\r
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79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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91 compbio.engine.cluster.drmaa</FONT>\r
92 <BR>\r
93 Class JobRunner</H2>\r
94 <PRE>\r
95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
96   <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.JobRunner</B>\r
97 </PRE>\r
98 <DL>\r
99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DD>\r
100 </DL>\r
101 <HR>\r
102 <DL>\r
103 <DT><PRE>public class <B>JobRunner</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DL>\r
104 </PRE>\r
105 \r
106 <P>\r
107 Single cluster job runner class\r
108 <P>\r
109 \r
110 <P>\r
111 <DL>\r
112 <DT><B>Author:</B></DT>\r
113   <DD>pvtroshin</DD>\r
114 </DL>\r
115 <HR>\r
116 \r
117 <P>\r
118 \r
119 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
120 \r
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125 <B>Constructor Summary</B></FONT></TH>\r
126 </TR>\r
127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
128 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
129 \r
130 <BR>\r
131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
132 </TR>\r
133 </TABLE>\r
134 &nbsp;\r
135 <!-- ========== METHOD SUMMARY =========== -->\r
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141 <B>Method Summary</B></FONT></TH>\r
142 </TR>\r
143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
145 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
146 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()">cancelJob</A></B>()</CODE>\r
147 \r
148 <BR>\r
149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops running job.</TD>\r
150 </TR>\r
151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
153 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
154 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()">cleanup</A></B>()</CODE>\r
155 \r
156 <BR>\r
157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clean up after the job</TD>\r
158 </TR>\r
159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
161 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
162 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()">deepClean</A></B>()</CODE>\r
163 \r
164 <BR>\r
165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
166 </TR>\r
167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
169 <CODE>&nbsp;void</CODE></FONT></TD>\r
170 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
171 \r
172 <BR>\r
173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute the job</TD>\r
174 </TR>\r
175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
177 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
178 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
179 \r
180 <BR>\r
181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
182 </TR>\r
183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
185 <CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
186 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()">getJobInfo</A></B>()</CODE>\r
187 \r
188 <BR>\r
189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method will block before the calculation has completed and then
190  return the object containing a job execution statistics</TD>\r
191 </TR>\r
192 <TR BGCOLOR="white" CLASS="TableRowColor">\r
193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
194 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
195 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
196 \r
197 <BR>\r
198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</TD>\r
199 </TR>\r
200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
202 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
203 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
204 \r
205 <BR>\r
206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
207 </TR>\r
208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
210 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
211 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
212 \r
213 <BR>\r
214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
215 </TR>\r
216 </TABLE>\r
217 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
218 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
219 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
220 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
221 </TR>\r
222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
223 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
224 </TR>\r
225 </TABLE>\r
226 &nbsp;\r
227 <P>\r
228 \r
229 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
230 \r
231 <A NAME="constructor_detail"><!-- --></A>\r
232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
233 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
234 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
235 <B>Constructor Detail</B></FONT></TH>\r
236 </TR>\r
237 </TABLE>\r
238 \r
239 <A NAME="JobRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
240 JobRunner</H3>\r
241 <PRE>\r
242 public <B>JobRunner</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)\r
243           throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
244 <DL>\r
245 <DL>\r
246 \r
247 <DT><B>Throws:</B>\r
248 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
249 </DL>\r
250 \r
251 <!-- ============ METHOD DETAIL ========== -->\r
252 \r
253 <A NAME="method_detail"><!-- --></A>\r
254 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
255 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
256 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
257 <B>Method Detail</B></FONT></TH>\r
258 </TR>\r
259 </TABLE>\r
260 \r
261 <A NAME="deepClean()"><!-- --></A><H3>\r
262 deepClean</H3>\r
263 <PRE>\r
264 public boolean <B>deepClean</B>()</PRE>\r
265 <DL>\r
266 <DD><DL>\r
267 </DL>\r
268 </DD>\r
269 <DD><DL>\r
270 </DL>\r
271 </DD>\r
272 </DL>\r
273 <HR>\r
274 \r
275 <A NAME="cleanup()"><!-- --></A><H3>\r
276 cleanup</H3>\r
277 <PRE>\r
278 public boolean <B>cleanup</B>()</PRE>\r
279 <DL>\r
280 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>\r
281 <DD>Clean up after the job\r
282 <P>\r
283 <DD><DL>\r
284 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
285 </DD>\r
286 <DD><DL>\r
287 \r
288 <DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
289 </DD>\r
290 </DL>\r
291 <HR>\r
292 \r
293 <A NAME="cancelJob()"><!-- --></A><H3>\r
294 cancelJob</H3>\r
295 <PRE>\r
296 public boolean <B>cancelJob</B>()</PRE>\r
297 <DL>\r
298 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>\r
299 <DD>Stops running job. 
300  Clean up is not performed.\r
301 <P>\r
302 <DD><DL>\r
303 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
304 </DD>\r
305 <DD><DL>\r
306 \r
307 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
308 </DD>\r
309 </DL>\r
310 <HR>\r
311 \r
312 <A NAME="getWorkDirectory()"><!-- --></A><H3>\r
313 getWorkDirectory</H3>\r
314 <PRE>\r
315 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getWorkDirectory</B>()</PRE>\r
316 <DL>\r
317 <DD><DL>\r
318 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
319 </DD>\r
320 <DD><DL>\r
321 \r
322 <DT><B>Returns:</B><DD>working directory if the task</DL>\r
323 </DD>\r
324 </DL>\r
325 <HR>\r
326 \r
327 <A NAME="executeJob()"><!-- --></A><H3>\r
328 executeJob</H3>\r
329 <PRE>\r
330 public void <B>executeJob</B>()\r
331                 throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
332 <DL>\r
333 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>\r
334 <DD>Execute the job\r
335 <P>\r
336 <DD><DL>\r
337 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
338 </DD>\r
339 <DD><DL>\r
340 \r
341 <DT><B>Throws:</B>\r
342 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
343 </DD>\r
344 </DL>\r
345 <HR>\r
346 \r
347 <A NAME="getJobInfo()"><!-- --></A><H3>\r
348 getJobInfo</H3>\r
349 <PRE>\r
350 public org.ggf.drmaa.JobInfo <B>getJobInfo</B>()\r
351                                  throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
352 <DL>\r
353 <DD>This method will block before the calculation has completed and then
354  return the object containing a job execution statistics\r
355 <P>\r
356 <DD><DL>\r
357 </DL>\r
358 </DD>\r
359 <DD><DL>\r
360 \r
361 <DT><B>Returns:</B><DD>\r
362 <DT><B>Throws:</B>\r
363 <DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
364 </DD>\r
365 </DL>\r
366 <HR>\r
367 \r
368 <A NAME="waitForResult()"><!-- --></A><H3>\r
369 waitForResult</H3>\r
370 <PRE>\r
371 public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>waitForResult</B>()\r
372                                       throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
373 <DL>\r
374 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>\r
375 <DD>Call to this method block for as long as it is required for an executable to finish its job. 
376  If the calculation has been completed already, the this method returns results immediately. 
377  This could return the result directly, but that would be type unsafe\r
378 <P>\r
379 <DD><DL>\r
380 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
381 </DD>\r
382 <DD><DL>\r
383 \r
384 <DT><B>Returns:</B><DD>object from wich the result can be obtained\r
385 <DT><B>Throws:</B>\r
386 <DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
387 </DD>\r
388 </DL>\r
389 <HR>\r
390 \r
391 <A NAME="getJobStatus()"><!-- --></A><H3>\r
392 getJobStatus</H3>\r
393 <PRE>\r
394 public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
395 <DL>\r
396 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>\r
397 <DD>Query the status of the job by its id.\r
398 <P>\r
399 <DD><DL>\r
400 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>\r
401 </DD>\r
402 <DD><DL>\r
403 \r
404 <DT><B>Returns:</B><DD>- JobStatus</DL>\r
405 </DD>\r
406 </DL>\r
407 <HR>\r
408 \r
409 <A NAME="getInstance(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
410 getInstance</H3>\r
411 <PRE>\r
412 public static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A> <B>getInstance</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
413                              throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
414 <DL>\r
415 <DD><DL>\r
416 </DL>\r
417 </DD>\r
418 <DD><DL>\r
419 \r
420 <DT><B>Throws:</B>\r
421 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
422 </DD>\r
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