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

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   7 ClusterSession\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.engine.cluster.drmaa</FONT>\r
  92 <BR>\r
  93 Class ClusterSession</H2>\r
  94 <PRE>\r
  95 java.lang.Object\r
  96   <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.ClusterSession</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>ClusterSession</B><DT>extends java.lang.Object</DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 <!-- =========== FIELD SUMMARY =========== -->\r
 108 \r
 109 <A NAME="field_summary"><!-- --></A>\r
 110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 113 <B>Field Summary</B></FONT></TH>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 117 <CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 118 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</A></B></CODE>\r
 119 \r
 120 <BR>\r
 121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 122 </TR>\r
 123 </TABLE>\r
 124 &nbsp;\r
 125 <!-- ========== METHOD SUMMARY =========== -->\r
 126 \r
 127 <A NAME="method_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>Method Summary</B></FONT></TH>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 135 <CODE>&nbsp;void</CODE></FONT></TD>\r
 136 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#close()">close</A></B>()</CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 143 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A></CODE></FONT></TD>\r
 144 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)">getClusterJobId</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
 145 \r
 146 <BR>\r
 147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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;int</CODE></FONT></TD>\r
 152 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)">getJobStatus</A></B>(<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>&nbsp;jobId)</CODE>\r
 153 \r
 154 <BR>\r
 155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Apparently completed jobs cannot be found! If this happened most likely
 156  that the job is not running any more and Most likely it has been
 157  cancelled, finished or failed.</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>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 162 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)">getJobStatus</A></B>(int&nbsp;status)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 170 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>&nbsp;org.ggf.drmaa.Session</CODE></FONT></TD>\r
 178 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()">getSession</A></B>()</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>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A></CODE></FONT></TD>\r
 186 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)">getStatistics</A></B>(org.ggf.drmaa.JobInfo&nbsp;status)</CODE>\r
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 190 </TR>\r
 191 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 192 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 193 <CODE>&nbsp;void</CODE></FONT></TD>\r
 194 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#removeJob(java.lang.String)">removeJob</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 201 <CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
 202 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String)">waitForJob</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 209 <CODE>&nbsp;org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
 210 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#waitForJob(java.lang.String, long)">waitForJob</A></B>(java.lang.String&nbsp;jobId,\r
 211            long&nbsp;waitingTime)</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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.Object</B></TH>\r
 221 </TR>\r
 222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 223 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 224 </TR>\r
 225 </TABLE>\r
 226 &nbsp;\r
 227 <P>\r
 228 \r
 229 <!-- ============ FIELD DETAIL =========== -->\r
 230 \r
 231 <A NAME="field_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>Field Detail</B></FONT></TH>\r
 236 </TR>\r
 237 </TABLE>\r
 238 \r
 239 <A NAME="JOBID"><!-- --></A><H3>\r
 240 JOBID</H3>\r
 241 <PRE>\r
 242 public static final java.lang.String <B>JOBID</B></PRE>\r
 243 <DL>\r
 244 <DL>\r
 245 <DT><B>See Also:</B><DD><A HREF="../../../../constant-values.html#compbio.engine.cluster.drmaa.ClusterSession.JOBID">Constant Field Values</A></DL>\r
 246 </DL>\r
 247 \r
 248 <!-- ============ METHOD DETAIL ========== -->\r
 249 \r
 250 <A NAME="method_detail"><!-- --></A>\r
 251 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 252 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 253 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 254 <B>Method Detail</B></FONT></TH>\r
 255 </TR>\r
 256 </TABLE>\r
 257 \r
 258 <A NAME="getSession()"><!-- --></A><H3>\r
 259 getSession</H3>\r
 260 <PRE>\r
 261 public org.ggf.drmaa.Session <B>getSession</B>()</PRE>\r
 262 <DL>\r
 263 <DD><DL>\r
 264 </DL>\r
 265 </DD>\r
 266 </DL>\r
 267 <HR>\r
 268 \r
 269 <A NAME="close()"><!-- --></A><H3>\r
 270 close</H3>\r
 271 <PRE>\r
 272 public void <B>close</B>()</PRE>\r
 273 <DL>\r
 274 <DD><DL>\r
 275 </DL>\r
 276 </DD>\r
 277 </DL>\r
 278 <HR>\r
 279 \r
 280 <A NAME="removeJob(java.lang.String)"><!-- --></A><H3>\r
 281 removeJob</H3>\r
 282 <PRE>\r
 283 public void <B>removeJob</B>(java.lang.String&nbsp;taskId)</PRE>\r
 284 <DL>\r
 285 <DD><DL>\r
 286 </DL>\r
 287 </DD>\r
 288 </DL>\r
 289 <HR>\r
 290 \r
 291 <A NAME="waitForJob(java.lang.String)"><!-- --></A><H3>\r
 292 waitForJob</H3>\r
 293 <PRE>\r
 294 public org.ggf.drmaa.JobInfo <B>waitForJob</B>(java.lang.String&nbsp;taskId)\r
 295                                  throws org.ggf.drmaa.DrmaaException,\r
 296                                         java.io.IOException</PRE>\r
 297 <DL>\r
 298 <DD><DL>\r
 299 \r
 300 <DT><B>Throws:</B>\r
 301 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
 302 <DD><CODE>java.io.IOException</CODE></DL>\r
 303 </DD>\r
 304 </DL>\r
 305 <HR>\r
 306 \r
 307 <A NAME="getClusterJobId(java.lang.String)"><!-- --></A><H3>\r
 308 getClusterJobId</H3>\r
 309 <PRE>\r
 310 public static <A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A> <B>getClusterJobId</B>(java.lang.String&nbsp;taskId)\r
 311                                     throws java.io.IOException</PRE>\r
 312 <DL>\r
 313 <DD><DL>\r
 314 \r
 315 <DT><B>Throws:</B>\r
 316 <DD><CODE>java.io.IOException</CODE></DL>\r
 317 </DD>\r
 318 </DL>\r
 319 <HR>\r
 320 \r
 321 <A NAME="waitForJob(java.lang.String, long)"><!-- --></A><H3>\r
 322 waitForJob</H3>\r
 323 <PRE>\r
 324 public org.ggf.drmaa.JobInfo <B>waitForJob</B>(java.lang.String&nbsp;jobId,\r
 325                                         long&nbsp;waitingTime)\r
 326                                  throws org.ggf.drmaa.DrmaaException,\r
 327                                         java.io.IOException</PRE>\r
 328 <DL>\r
 329 <DD><DL>\r
 330 \r
 331 <DT><B>Throws:</B>\r
 332 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
 333 <DD><CODE>java.io.IOException</CODE></DL>\r
 334 </DD>\r
 335 </DL>\r
 336 <HR>\r
 337 \r
 338 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 339 getResults</H3>\r
 340 <PRE>\r
 341 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;taskId)\r
 342                                    throws org.ggf.drmaa.DrmaaException,\r
 343                                           <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 344 <DL>\r
 345 <DD><DL>\r
 346 \r
 347 <DT><B>Throws:</B>\r
 348 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE>\r
 349 <DD><CODE><A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 350 </DD>\r
 351 </DL>\r
 352 <HR>\r
 353 \r
 354 <A NAME="getStatistics(org.ggf.drmaa.JobInfo)"><!-- --></A><H3>\r
 355 getStatistics</H3>\r
 356 <PRE>\r
 357 public static <A HREF="../../../../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A> <B>getStatistics</B>(org.ggf.drmaa.JobInfo&nbsp;status)\r
 358                                       throws org.ggf.drmaa.DrmaaException</PRE>\r
 359 <DL>\r
 360 <DD><DL>\r
 361 \r
 362 <DT><B>Throws:</B>\r
 363 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
 364 </DD>\r
 365 </DL>\r
 366 <HR>\r
 367 \r
 368 <A NAME="getJobStatus(compbio.engine.ClusterJobId)"><!-- --></A><H3>\r
 369 getJobStatus</H3>\r
 370 <PRE>\r
 371 public int <B>getJobStatus</B>(<A HREF="../../../../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>&nbsp;jobId)\r
 372                  throws org.ggf.drmaa.DrmaaException,\r
 373                         org.ggf.drmaa.InvalidJobException</PRE>\r
 374 <DL>\r
 375 <DD>Apparently completed jobs cannot be found! If this happened most likely
 376  that the job is not running any more and Most likely it has been
 377  cancelled, finished or failed.\r
 378 <P>\r
 379 <DD><DL>\r
 380 \r
 381 <DT><B>Throws:</B>\r
 382 <DD><CODE>org.ggf.drmaa.InvalidJobException</CODE> - if the job is no longer in the queue or running. basically it
 383              will throw this exception for all finished or cancelled jobs\r
 384 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
 385 </DD>\r
 386 </DL>\r
 387 <HR>\r
 388 \r
 389 <A NAME="getJobStatus(int)"><!-- --></A><H3>\r
 390 getJobStatus</H3>\r
 391 <PRE>\r
 392 <FONT SIZE="-1">@Deprecated\r
 393 </FONT>public static java.lang.String <B>getJobStatus</B>(int&nbsp;status)\r
 394                                      throws org.ggf.drmaa.DrmaaException</PRE>\r
 395 <DL>\r
 396 <DD><B>Deprecated.</B>&nbsp;\r
 397 <P>\r
 398 <DD>Method for getting jobs status by quering the cluster, It returns status
 399  in therms of a Sessions, not a JobStatus Should only be used for testing!\r
 400 <P>\r
 401 <DD><DL>\r
 402 <DT><B>Parameters:</B><DD><CODE>status</CODE> - \r
 403 <DT><B>Returns:</B><DD>\r
 404 <DT><B>Throws:</B>\r
 405 <DD><CODE>org.ggf.drmaa.DrmaaException</CODE></DL>\r
 406 </DD>\r
 407 </DL>\r
 408 <!-- ========= END OF CLASS DATA ========= -->\r
 409 <HR>\r
 410 \r
 411 \r
 412 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 413 <A NAME="navbar_bottom"><!-- --></A>\r
 414 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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 418 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 419 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 420   <TR ALIGN="center" VALIGN="top">\r
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