website/full_javadoc/compbio/engine/AsyncExecutor.html

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   7 AsyncExecutor\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  91 compbio.engine</FONT>\r
  92 <BR>\r
  93 Interface AsyncExecutor</H2>\r
  94 <DL>\r
  95 <DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>, <A HREF="../../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A></DD>\r
  96 </DL>\r
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  98 <DL>\r
  99 <DT><PRE>public interface <B>AsyncExecutor</B></DL>\r
 100 </PRE>\r
 101 \r
 102 <P>\r
 103 An asynchronous executor engine, capable of running, cancelling,
 104  obtaining results calculated by a native executable wrapper in Executable interface.
 105  Implementation agnostic. Executables can be run either locally to the JVM or on the cluster.\r
 106 <P>\r
 107 \r
 108 <P>\r
 109 <DL>\r
 110 <DT><B>Author:</B></DT>\r
 111   <DD>pvtroshin
 112                 Date October 2009</DD>\r
 113 </DL>\r
 114 <HR>\r
 115 \r
 116 <P>\r
 117 \r
 118 <!-- ========== METHOD SUMMARY =========== -->\r
 119 \r
 120 <A NAME="method_summary"><!-- --></A>\r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 124 <B>Method Summary</B></FONT></TH>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 128 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 129 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 130 \r
 131 <BR>\r
 132 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stop running job.</TD>\r
 133 </TR>\r
 134 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 135 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 136 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 137 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 138 \r
 139 <BR>\r
 140 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all files and a job directory for a jobid.</TD>\r
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 144 <CODE>&nbsp;<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 145 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 146 \r
 147 <BR>\r
 148 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Query the status of the job</TD>\r
 149 </TR>\r
 150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 152 <CODE>&nbsp;<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <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
 161 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <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
 169 <TD><CODE><B><A HREF="../../compbio/engine/AsyncExecutor.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
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
 173  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
 174 </TR>\r
 175 </TABLE>\r
 176 &nbsp;\r
 177 <P>\r
 178 \r
 179 <!-- ============ METHOD DETAIL ========== -->\r
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 185 <B>Method Detail</B></FONT></TH>\r
 186 </TR>\r
 187 </TABLE>\r
 188 \r
 189 <A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 190 submitJob</H3>\r
 191 <PRE>\r
 192 <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
 193                  throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 194 <DL>\r
 195 <DD>Submits job for the execution
 196  Immediate execution is not guaranteed, this method puts the job in the queue.
 197  All it guarantees that the job will be eventually executed.
 198  The start of execution will depend on the number of jobs in the queue.\r
 199 <P>\r
 200 <DD><DL>\r
 201 \r
 202 <DT><B>Returns:</B><DD>unique job identifier\r
 203 <DT><B>Throws:</B>\r
 204 <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
 205 </DD>\r
 206 </DL>\r
 207 <HR>\r
 208 \r
 209 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 210 getResults</H3>\r
 211 <PRE>\r
 212 <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
 213                                    throws <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 214 <DL>\r
 215 <DD>Retrieve the results of the job. Please not that current implementations of this method
 216  blocks if the task is running until the end of the calculation.\r
 217 <P>\r
 218 <DD><DL>\r
 219 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission\r
 220 <DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained\r
 221 <DT><B>Throws:</B>\r
 222 <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.
 223  Could be due to execution failure, or due to the results being removed from the server at
 224  the time of request.</DL>\r
 225 </DD>\r
 226 </DL>\r
 227 <HR>\r
 228 \r
 229 <A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 230 getWorkDirectory</H3>\r
 231 <PRE>\r
 232 <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
 233 <DL>\r
 234 <DD><DL>\r
 235 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier\r
 236 <DT><B>Returns:</B><DD>task working directory</DL>\r
 237 </DD>\r
 238 </DL>\r
 239 <HR>\r
 240 \r
 241 <A NAME="cleanup(java.lang.String)"><!-- --></A><H3>\r
 242 cleanup</H3>\r
 243 <PRE>\r
 244 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
 245 <DL>\r
 246 <DD>Remove all files and a job directory for a jobid.\r
 247 <P>\r
 248 <DD><DL>\r
 249 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - \r
 250 <DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>\r
 251 </DD>\r
 252 </DL>\r
 253 <HR>\r
 254 \r
 255 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 256 cancelJob</H3>\r
 257 <PRE>\r
 258 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
 259 <DL>\r
 260 <DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.\r
 261 <P>\r
 262 <DD><DL>\r
 263 \r
 264 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
 265 </DD>\r
 266 </DL>\r
 267 <HR>\r
 268 \r
 269 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
 270 getJobStatus</H3>\r
 271 <PRE>\r
 272 <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
 273 <DL>\r
 274 <DD>Query the status of the job\r
 275 <P>\r
 276 <DD><DL>\r
 277 <DT><B>Parameters:</B><DD><CODE>String</CODE> - jobId - unique job identifier\r
 278 <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
 279 </DD>\r
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