website/full_javadoc/compbio/engine/local/LocalRunner.html

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   7 LocalRunner\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="LocalRunner";\r
  19     }\r
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  58 &nbsp;<A HREF="../../../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>PREV CLASS</B></A>&nbsp;\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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  89 <H2>\r
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  91 compbio.engine.local</FONT>\r
  92 <BR>\r
  93 Class LocalRunner</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.local.LocalRunner</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 final class <B>LocalRunner</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 <HR>\r
 108 \r
 109 <P>\r
 110 \r
 111 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 112 \r
 113 <A NAME="constructor_summary"><!-- --></A>\r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 117 <B>Constructor Summary</B></FONT></TH>\r
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)">LocalRunner</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
 121 \r
 122 <BR>\r
 123 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 124 </TR>\r
 125 </TABLE>\r
 126 &nbsp;\r
 127 <!-- ========== METHOD SUMMARY =========== -->\r
 128 \r
 129 <A NAME="method_summary"><!-- --></A>\r
 130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 132 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 133 <B>Method Summary</B></FONT></TH>\r
 134 </TR>\r
 135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 137 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 138 <TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#cancelJob()">cancelJob</A></B>()</CODE>\r
 139 \r
 140 <BR>\r
 141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops running job.</TD>\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/local/LocalRunner.html#cleanup()">cleanup</A></B>()</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Clean up after the 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;void</CODE></FONT></TD>\r
 154 <TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Execute 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;<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/local/LocalRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job by its id.</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="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
 170 <TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</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;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 178 <TD><CODE><B><A HREF="../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
 179 \r
 180 <BR>\r
 181 &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
 182 </TR>\r
 183 </TABLE>\r
 184 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 185 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 186 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 187 <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
 188 </TR>\r
 189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 190 <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
 191 </TR>\r
 192 </TABLE>\r
 193 &nbsp;\r
 194 <P>\r
 195 \r
 196 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 197 \r
 198 <A NAME="constructor_detail"><!-- --></A>\r
 199 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 200 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 201 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 202 <B>Constructor Detail</B></FONT></TH>\r
 203 </TR>\r
 204 </TABLE>\r
 205 \r
 206 <A NAME="LocalRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 207 LocalRunner</H3>\r
 208 <PRE>\r
 209 public <B>LocalRunner</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</PRE>\r
 210 <DL>\r
 211 </DL>\r
 212 \r
 213 <!-- ============ METHOD DETAIL ========== -->\r
 214 \r
 215 <A NAME="method_detail"><!-- --></A>\r
 216 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 217 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 218 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 219 <B>Method Detail</B></FONT></TH>\r
 220 </TR>\r
 221 </TABLE>\r
 222 \r
 223 <A NAME="getWorkDirectory()"><!-- --></A><H3>\r
 224 getWorkDirectory</H3>\r
 225 <PRE>\r
 226 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
 227 <DL>\r
 228 <DD><DL>\r
 229 <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
 230 </DD>\r
 231 <DD><DL>\r
 232 \r
 233 <DT><B>Returns:</B><DD>working directory if the task</DL>\r
 234 </DD>\r
 235 </DL>\r
 236 <HR>\r
 237 \r
 238 <A NAME="cancelJob()"><!-- --></A><H3>\r
 239 cancelJob</H3>\r
 240 <PRE>\r
 241 public boolean <B>cancelJob</B>()</PRE>\r
 242 <DL>\r
 243 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>\r
 244 <DD>Stops running job.
 245  Clean up is not performed.\r
 246 <P>\r
 247 <DD><DL>\r
 248 <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
 249 </DD>\r
 250 <DD><DL>\r
 251 \r
 252 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
 253 </DD>\r
 254 </DL>\r
 255 <HR>\r
 256 \r
 257 <A NAME="getJobStatus()"><!-- --></A><H3>\r
 258 getJobStatus</H3>\r
 259 <PRE>\r
 260 public <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
 261 <DL>\r
 262 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>\r
 263 <DD>Query the status of the job by its id.\r
 264 <P>\r
 265 <DD><DL>\r
 266 <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
 267 </DD>\r
 268 <DD><DL>\r
 269 \r
 270 <DT><B>Returns:</B><DD>- JobStatus</DL>\r
 271 </DD>\r
 272 </DL>\r
 273 <HR>\r
 274 \r
 275 <A NAME="executeJob()"><!-- --></A><H3>\r
 276 executeJob</H3>\r
 277 <PRE>\r
 278 public void <B>executeJob</B>()\r
 279                 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 280 <DL>\r
 281 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>\r
 282 <DD>Execute the job\r
 283 <P>\r
 284 <DD><DL>\r
 285 <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
 286 </DD>\r
 287 <DD><DL>\r
 288 \r
 289 <DT><B>Throws:</B>\r
 290 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
 291 </DD>\r
 292 </DL>\r
 293 <HR>\r
 294 \r
 295 <A NAME="waitForResult()"><!-- --></A><H3>\r
 296 waitForResult</H3>\r
 297 <PRE>\r
 298 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>waitForResult</B>()\r
 299                                       throws <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
 300 <DL>\r
 301 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>\r
 302 <DD>Call to this method block for as long as it is required for an executable to finish its job.
 303  If the calculation has been completed already, the this method returns results immediately.
 304  This could return the result directly, but that would be type unsafe\r
 305 <P>\r
 306 <DD><DL>\r
 307 <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
 308 </DD>\r
 309 <DD><DL>\r
 310 \r
 311 <DT><B>Returns:</B><DD>object from wich the result can be obtained\r
 312 <DT><B>Throws:</B>\r
 313 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/CancellationException.html?is-external=true" title="class or interface in java.util.concurrent">CancellationException</A></CODE>\r
 314 <DD><CODE><A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
 315 </DD>\r
 316 </DL>\r
 317 <HR>\r
 318 \r
 319 <A NAME="cleanup()"><!-- --></A><H3>\r
 320 cleanup</H3>\r
 321 <PRE>\r
 322 public boolean <B>cleanup</B>()</PRE>\r
 323 <DL>\r
 324 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>\r
 325 <DD>Clean up after the job\r
 326 <P>\r
 327 <DD><DL>\r
 328 <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
 329 </DD>\r
 330 <DD><DL>\r
 331 \r
 332 <DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
 333 </DD>\r
 334 </DL>\r
 335 <!-- ========= END OF CLASS DATA ========= -->\r
 336 <HR>\r
 337 \r
 338 \r
 339 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 340 <A NAME="navbar_bottom"><!-- --></A>\r
 341 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 342 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 343 <TR>\r
 344 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 345 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 346 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 347   <TR ALIGN="center" VALIGN="top">\r
 348   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 349   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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