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91 compbio.engine.cluster.drmaa</FONT>
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93 Class AsyncJobRunner</H2>
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96 <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.AsyncJobRunner</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></DD>
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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>
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107 Single cluster job runner class
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112 <DT><B>Author:</B></DT>
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119 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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125 <B>Constructor Summary</B></FONT></TH>
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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#AsyncJobRunner()">AsyncJobRunner</A></B>()</CODE>
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131 </TD>
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141 <B>Method Summary</B></FONT></TH>
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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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145 <CODE> boolean</CODE></FONT></TD>
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146 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String jobId)</CODE>
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149 Stop running job.</TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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153 <CODE> boolean</CODE></FONT></TD>
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154 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)">cleanup</A></B>(java.lang.String jobId)</CODE>
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157 Remove all files and a job directory for a jobid.</TD>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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161 <CODE> <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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162 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String jobId)</CODE>
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165 This will never return clust.engine.JobStatus.CANCELLED as for sun grid
166 engine cancelled job is the same as failed.</TD>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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170 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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171 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String jobId)</CODE>
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174 Retrieve the results of the job.</TD>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <CODE> java.lang.String</CODE></FONT></TD>
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179 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)">getWorkDirectory</A></B>(java.lang.String jobId)</CODE>
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182 </TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> java.lang.String</CODE></FONT></TD>
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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><?> executable)</CODE>
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190 Submits job for the execution
191 Immediate execution is not guaranteed, this method puts the job in the queue.</TD>
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197 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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212 <B>Constructor Detail</B></FONT></TH>
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216 <A NAME="AsyncJobRunner()"><!-- --></A><H3>
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217 AsyncJobRunner</H3>
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219 public <B>AsyncJobRunner</B>()</PRE>
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229 <B>Method Detail</B></FONT></TH>
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233 <A NAME="submitJob(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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236 public java.lang.String <B>submitJob</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)
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237 throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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239 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">AsyncExecutor</A></CODE></B></DD>
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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.
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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>
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250 <DT><B>Returns:</B><DD>unique job identifier
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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>
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257 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
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260 public boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>
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262 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)">AsyncExecutor</A></CODE></B></DD>
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263 <DD>Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.
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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>
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270 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>
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275 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
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278 public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String jobId)</PRE>
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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
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>
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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>
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294 <A NAME="cleanup(java.lang.String)"><!-- --></A><H3>
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297 public boolean <B>cleanup</B>(java.lang.String jobId)</PRE>
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299 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)">AsyncExecutor</A></CODE></B></DD>
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300 <DD>Remove all files and a job directory for a jobid.
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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>
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307 <DT><B>Returns:</B><DD>true if job directory was successfully removed, false otherwise.</DL>
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312 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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315 public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>getResults</B>(java.lang.String jobId)
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316 throws <A HREF="../../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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318 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">AsyncExecutor</A></CODE></B></DD>
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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.
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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>
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326 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - job identifier obtained at the job submission
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327 <DT><B>Returns:</B><DD>ConfiguredExecutable object from which result can be obtained
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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>
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336 <A NAME="getWorkDirectory(java.lang.String)"><!-- --></A><H3>
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337 getWorkDirectory</H3>
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339 public java.lang.String <B>getWorkDirectory</B>(java.lang.String jobId)</PRE>
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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>
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345 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - unique job identifier
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346 <DT><B>Returns:</B><DD>task working directory</DL>
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