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

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   7 AsyncJobRunner\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 AsyncJobRunner</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.AsyncJobRunner</B>\r
  97 </PRE>\r
  98 <DL>\r
  99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 103 <DT><PRE>public class <B>AsyncJobRunner</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/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</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>Version:</B></DT>\r
 113   <DD>1.0 August 2009
 114
 115           TODO after call to submitJob() no setters really work as the job
 116           template gets deleted, this needs to be taken into account in this
 117           class design!</DD>\r
 118 <DT><B>Author:</B></DT>\r
 119   <DD>pvtroshin</DD>\r
 120 </DL>\r
 121 <HR>\r
 122 \r
 123 <P>\r
 124 \r
 125 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 126 \r
 127 <A NAME="constructor_summary"><!-- --></A>\r
 128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 129 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 130 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 131 <B>Constructor Summary</B></FONT></TH>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()">AsyncJobRunner</A></B>()</CODE>\r
 135 \r
 136 <BR>\r
 137 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 138 </TR>\r
 139 </TABLE>\r
 140 &nbsp;\r
 141 <!-- ========== METHOD SUMMARY =========== -->\r
 142 \r
 143 <A NAME="method_summary"><!-- --></A>\r
 144 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 145 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 146 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 147 <B>Method Summary</B></FONT></TH>\r
 148 </TR>\r
 149 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 151 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 152 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)">cancelJob</A></B>(<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>&nbsp;jobId)</CODE>\r
 153 \r
 154 <BR>\r
 155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job.</TD>\r
 156 </TR>\r
 157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 159 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 160 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)">cleanup</A></B>(<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>&nbsp;jobId)</CODE>\r
 161 \r
 162 <BR>\r
 163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</TD>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 167 <CODE>&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 168 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(<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>&nbsp;jobId)</CODE>\r
 169 \r
 170 <BR>\r
 171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 172  engine cancelled job is the same as failed.</TD>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 177 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(<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>&nbsp;jobId)</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <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
 185 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(<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>&nbsp;jobId)</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 192 <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
 193 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 194 \r
 195 <BR>\r
 196 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
 197  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
 198 </TR>\r
 199 </TABLE>\r
 200 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 201 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 202 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 203 <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
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <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
 207 </TR>\r
 208 </TABLE>\r
 209 &nbsp;\r
 210 <P>\r
 211 \r
 212 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 213 \r
 214 <A NAME="constructor_detail"><!-- --></A>\r
 215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 216 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 217 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 218 <B>Constructor Detail</B></FONT></TH>\r
 219 </TR>\r
 220 </TABLE>\r
 221 \r
 222 <A NAME="AsyncJobRunner()"><!-- --></A><H3>\r
 223 AsyncJobRunner</H3>\r
 224 <PRE>\r
 225 public <B>AsyncJobRunner</B>()</PRE>\r
 226 <DL>\r
 227 </DL>\r
 228 \r
 229 <!-- ============ METHOD DETAIL ========== -->\r
 230 \r
 231 <A NAME="method_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>Method Detail</B></FONT></TH>\r
 236 </TR>\r
 237 </TABLE>\r
 238 \r
 239 <A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 240 submitJob</H3>\r
 241 <PRE>\r
 242 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>submitJob</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
 243                  throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 244 <DL>\r
 245 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>\r
 246 <DD>Submits job for the execution
 247  Immediate execution is not guaranteed, this method puts the job in the queue.
 248  All it guarantees that the job will be eventually executed.
 249  The start of execution will depend on the number of jobs in the queue.\r
 250 <P>\r
 251 <DD><DL>\r
 252 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 253 </DD>\r
 254 <DD><DL>\r
 255 \r
 256 <DT><B>Returns:</B><DD>unique job identifier\r
 257 <DT><B>Throws:</B>\r
 258 <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.</DL>\r
 259 </DD>\r
 260 </DL>\r
 261 <HR>\r
 262 \r
 263 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 264 cancelJob</H3>\r
 265 <PRE>\r
 266 public boolean <B>cancelJob</B>(<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>&nbsp;jobId)</PRE>\r
 267 <DL>\r
 268 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 269 <DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
 270 <P>\r
 271 <DD><DL>\r
 272 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 273 </DD>\r
 274 <DD><DL>\r
 275 \r
 276 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
 277 </DD>\r
 278 </DL>\r
 279 <HR>\r
 280 \r
 281 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
 282 getJobStatus</H3>\r
 283 <PRE>\r
 284 public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(<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>&nbsp;jobId)</PRE>\r
 285 <DL>\r
 286 <DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 287  engine cancelled job is the same as failed. Cancelled jobs needs to be
 288  tracked manually!\r
 289 <P>\r
 290 <DD><DL>\r
 291 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 292 </DD>\r
 293 <DD><DL>\r
 294 \r
 295 <DT><B>Returns:</B><DD>The JobStatus object representing the status of the job<DT><B>See Also:</B><DD><A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>\r
 296 </DD>\r
 297 </DL>\r
 298 <HR>\r
 299 \r
 300 <A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
 301 cleanup</H3>\r
 302 <PRE>\r
 303 public boolean <B>cleanup</B>(<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>&nbsp;jobId)</PRE>\r
 304 <DL>\r
 305 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 306 <DD>Remove all files and a job directory for a jobid.\r
 307 <P>\r
 308 <DD><DL>\r
 309 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">cleanup</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 310 </DD>\r
 311 <DD><DL>\r
 312 \r
 313 <DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>\r
 314 </DD>\r
 315 </DL>\r
 316 <HR>\r
 317 \r
 318 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 319 getResults</H3>\r
 320 <PRE>\r
 321 public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(<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>&nbsp;jobId)\r
 322                                    throws <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 323 <DL>\r
 324 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 325 <DD>Retrieve the results of the job. Please not that current implementations of this method
 326  blocks if the task is running until the end of the calculation.\r
 327 <P>\r
 328 <DD><DL>\r
 329 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 330 </DD>\r
 331 <DD><DL>\r
 332 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission\r
 333 <DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
 334 <DT><B>Throws:</B>\r
 335 <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.
 336  Could be due to execution failure, or due to the results being removed from the server at
 337  the time of request.</DL>\r
 338 </DD>\r
 339 </DL>\r
 340 <HR>\r
 341 \r
 342 <A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 343 getWorkDirectory</H3>\r
 344 <PRE>\r
 345 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>(<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>&nbsp;jobId)</PRE>\r
 346 <DL>\r
 347 <DD><DL>\r
 348 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></DL>\r
 349 </DD>\r
 350 <DD><DL>\r
 351 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
 352 <DT><B>Returns:</B><DD>task working directory</DL>\r
 353 </DD>\r
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