website/full_javadoc/compbio/engine/local/AsyncLocalRunner.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.local</FONT>\r
  92 <BR>\r
  93 Class AsyncLocalRunner</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.AsyncLocalRunner</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 final class <B>AsyncLocalRunner</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 <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/AsyncLocalRunner.html#AsyncLocalRunner()">AsyncLocalRunner</A></B>()</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/AsyncLocalRunner.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
 139 \r
 140 <BR>\r
 141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop 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/AsyncLocalRunner.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
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</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;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 154 <TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.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
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of 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/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 162 <TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.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;taskId)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</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/AsyncLocalRunner.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
 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="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
 178 <TD><CODE><B><A HREF="../../../compbio/engine/local/AsyncLocalRunner.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
 179 \r
 180 <BR>\r
 181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
 182  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
 183 </TR>\r
 184 </TABLE>\r
 185 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 186 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 187 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 188 <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
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <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
 192 </TR>\r
 193 </TABLE>\r
 194 &nbsp;\r
 195 <P>\r
 196 \r
 197 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 198 \r
 199 <A NAME="constructor_detail"><!-- --></A>\r
 200 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 201 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 202 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 203 <B>Constructor Detail</B></FONT></TH>\r
 204 </TR>\r
 205 </TABLE>\r
 206 \r
 207 <A NAME="AsyncLocalRunner()"><!-- --></A><H3>\r
 208 AsyncLocalRunner</H3>\r
 209 <PRE>\r
 210 public <B>AsyncLocalRunner</B>()</PRE>\r
 211 <DL>\r
 212 </DL>\r
 213 \r
 214 <!-- ============ METHOD DETAIL ========== -->\r
 215 \r
 216 <A NAME="method_detail"><!-- --></A>\r
 217 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 218 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 219 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 220 <B>Method Detail</B></FONT></TH>\r
 221 </TR>\r
 222 </TABLE>\r
 223 \r
 224 <A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 225 getWorkDirectory</H3>\r
 226 <PRE>\r
 227 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
 228 <DL>\r
 229 <DD><DL>\r
 230 <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
 231 </DD>\r
 232 <DD><DL>\r
 233 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
 234 <DT><B>Returns:</B><DD>task working directory</DL>\r
 235 </DD>\r
 236 </DL>\r
 237 <HR>\r
 238 \r
 239 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 240 cancelJob</H3>\r
 241 <PRE>\r
 242 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
 243 <DL>\r
 244 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 245 <DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
 246 <P>\r
 247 <DD><DL>\r
 248 <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
 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(java.lang.String)"><!-- --></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>(<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
 261 <DL>\r
 262 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 263 <DD>Query the status of the job\r
 264 <P>\r
 265 <DD><DL>\r
 266 <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
 267 </DD>\r
 268 <DD><DL>\r
 269 \r
 270 <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
 271 </DD>\r
 272 </DL>\r
 273 <HR>\r
 274 \r
 275 <A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 276 submitJob</H3>\r
 277 <PRE>\r
 278 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
 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/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>\r
 282 <DD>Submits job for the execution
 283  Immediate execution is not guaranteed, this method puts the job in the queue.
 284  All it guarantees that the job will be eventually executed.
 285  The start of execution will depend on the number of jobs in the queue.\r
 286 <P>\r
 287 <DD><DL>\r
 288 <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
 289 </DD>\r
 290 <DD><DL>\r
 291 \r
 292 <DT><B>Returns:</B><DD>unique job identifier\r
 293 <DT><B>Throws:</B>\r
 294 <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
 295 </DD>\r
 296 </DL>\r
 297 <HR>\r
 298 \r
 299 <A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
 300 cleanup</H3>\r
 301 <PRE>\r
 302 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
 303 <DL>\r
 304 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 305 <DD>Remove all files and a job directory for a jobid.\r
 306 <P>\r
 307 <DD><DL>\r
 308 <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
 309 </DD>\r
 310 <DD><DL>\r
 311 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - \r
 312 <DT><B>Returns:</B><DD>true if all files were removed, false otherwise</DL>\r
 313 </DD>\r
 314 </DL>\r
 315 <HR>\r
 316 \r
 317 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 318 getResults</H3>\r
 319 <PRE>\r
 320 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;taskId)\r
 321                                    throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 322 <DL>\r
 323 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>\r
 324 <DD>Retrieve the results of the job. Please not that current implementations of this method
 325  blocks if the task is running until the end of the calculation.\r
 326 <P>\r
 327 <DD><DL>\r
 328 <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
 329 </DD>\r
 330 <DD><DL>\r
 331 <DT><B>Parameters:</B><DD><CODE>taskId</CODE> - job identifier obtained at the job submission\r
 332 <DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
 333 <DT><B>Throws:</B>\r
 334 <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.
 335  Could be due to execution failure, or due to the results being removed from the server at
 336  the time of request.</DL>\r
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