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

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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 java.lang.Object\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 java.lang.Object<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>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
 121 <A NAME="constructor_summary"><!-- --></A>\r
 122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 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/AsyncJobRunner.html#AsyncJobRunner()">AsyncJobRunner</A></B>()</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
 136 \r
 137 <A NAME="method_summary"><!-- --></A>\r
 138 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 139 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 140 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 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/AsyncJobRunner.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop 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/AsyncJobRunner.html#cleanup(java.lang.String)">cleanup</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</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;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 162 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 166  engine cancelled job is the same as failed.</TD>\r
 167 </TR>\r
 168 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 170 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 171 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
 175 </TR>\r
 176 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 178 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 179 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 187 <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
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
 191  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
 192 </TR>\r
 193 </TABLE>\r
 194 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 197 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 201 </TR>\r
 202 </TABLE>\r
 203 &nbsp;\r
 204 <P>\r
 205 \r
 206 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 207 \r
 208 <A NAME="constructor_detail"><!-- --></A>\r
 209 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 210 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 211 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 212 <B>Constructor Detail</B></FONT></TH>\r
 213 </TR>\r
 214 </TABLE>\r
 215 \r
 216 <A NAME="AsyncJobRunner()"><!-- --></A><H3>\r
 217 AsyncJobRunner</H3>\r
 218 <PRE>\r
 219 public <B>AsyncJobRunner</B>()</PRE>\r
 220 <DL>\r
 221 </DL>\r
 222 \r
 223 <!-- ============ METHOD DETAIL ========== -->\r
 224 \r
 225 <A NAME="method_detail"><!-- --></A>\r
 226 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 227 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 228 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 229 <B>Method Detail</B></FONT></TH>\r
 230 </TR>\r
 231 </TABLE>\r
 232 \r
 233 <A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 234 submitJob</H3>\r
 235 <PRE>\r
 236 public java.lang.String <B>submitJob</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)\r
 237                            throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 238 <DL>\r
 239 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>\r
 240 <DD>Submits job for the execution
 241  Immediate execution is not guaranteed, this method puts the job in the queue.
 242  All it guarantees that the job will be eventually executed.
 243  The start of execution will depend on the number of jobs in the queue.\r
 244 <P>\r
 245 <DD><DL>\r
 246 <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
 247 </DD>\r
 248 <DD><DL>\r
 249 \r
 250 <DT><B>Returns:</B><DD>unique job identifier\r
 251 <DT><B>Throws:</B>\r
 252 <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
 253 </DD>\r
 254 </DL>\r
 255 <HR>\r
 256 \r
 257 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 258 cancelJob</H3>\r
 259 <PRE>\r
 260 public boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
 261 <DL>\r
 262 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 263 <DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
 264 <P>\r
 265 <DD><DL>\r
 266 <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
 267 </DD>\r
 268 <DD><DL>\r
 269 \r
 270 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
 271 </DD>\r
 272 </DL>\r
 273 <HR>\r
 274 \r
 275 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
 276 getJobStatus</H3>\r
 277 <PRE>\r
 278 public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
 279 <DL>\r
 280 <DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 281  engine cancelled job is the same as failed. Cancelled jobs needs to be
 282  tracked manually!\r
 283 <P>\r
 284 <DD><DL>\r
 285 <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
 286 </DD>\r
 287 <DD><DL>\r
 288 \r
 289 <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
 290 </DD>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
 295 cleanup</H3>\r
 296 <PRE>\r
 297 public boolean <B>cleanup</B>(java.lang.String&nbsp;jobId)</PRE>\r
 298 <DL>\r
 299 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 300 <DD>Remove all files and a job directory for a jobid.\r
 301 <P>\r
 302 <DD><DL>\r
 303 <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
 304 </DD>\r
 305 <DD><DL>\r
 306 \r
 307 <DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>\r
 308 </DD>\r
 309 </DL>\r
 310 <HR>\r
 311 \r
 312 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 313 getResults</H3>\r
 314 <PRE>\r
 315 public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>getResults</B>(java.lang.String&nbsp;jobId)\r
 316                                    throws <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 317 <DL>\r
 318 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 319 <DD>Retrieve the results of the job. Please not that current implementations of this method
 320  blocks if the task is running until the end of the calculation.\r
 321 <P>\r
 322 <DD><DL>\r
 323 <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
 324 </DD>\r
 325 <DD><DL>\r
 326 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission\r
 327 <DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
 328 <DT><B>Throws:</B>\r
 329 <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.
 330  Could be due to execution failure, or due to the results being removed from the server at
 331  the time of request.</DL>\r
 332 </DD>\r
 333 </DL>\r
 334 <HR>\r
 335 \r
 336 <A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 337 getWorkDirectory</H3>\r
 338 <PRE>\r
 339 public java.lang.String <B>getWorkDirectory</B>(java.lang.String&nbsp;jobId)</PRE>\r
 340 <DL>\r
 341 <DD><DL>\r
 342 <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
 343 </DD>\r
 344 <DD><DL>\r
 345 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
 346 <DT><B>Returns:</B><DD>task working directory</DL>\r
 347 </DD>\r
 348 </DL>\r
 349 <!-- ========= END OF CLASS DATA ========= -->\r
 350 <HR>\r
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 362   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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