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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->\r
+<TITLE>\r
+JobRunner\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JobRunner.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.engine.cluster.drmaa</FONT>\r
+<BR>\r
+Class JobRunner</H2>\r
+<PRE>\r
+<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
+ <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.JobRunner</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>JobRunner</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
+</PRE>\r
+\r
+<P>\r
+Single cluster job runner class\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExec)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()">cancelJob</A></B>()</CODE>\r
+\r
+<BR>\r
+ Stops running job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()">cleanup</A></B>()</CODE>\r
+\r
+<BR>\r
+ Clean up after the job</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()">deepClean</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>\r
+\r
+<BR>\r
+ Execute the job</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> org.ggf.drmaa.JobInfo</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()">getJobInfo</A></B>()</CODE>\r
+\r
+<BR>\r
+ This method will block before the calculation has completed and then
+ return the object containing a job execution statistics</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
+\r
+<BR>\r
+ Query the status of the job by its id.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <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
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
+\r
+<BR>\r
+ Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<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
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<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
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="JobRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
+JobRunner</H3>\r
+<PRE>\r
+public <B>JobRunner</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExec)\r
+ throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="deepClean()"><!-- --></A><H3>\r
+deepClean</H3>\r
+<PRE>\r
+public boolean <B>deepClean</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cleanup()"><!-- --></A><H3>\r
+cleanup</H3>\r
+<PRE>\r
+public boolean <B>cleanup</B>()</PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>\r
+<DD>Clean up after the job\r
+<P>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cancelJob()"><!-- --></A><H3>\r
+cancelJob</H3>\r
+<PRE>\r
+public boolean <B>cancelJob</B>()</PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>\r
+<DD>Stops running job.
+ Clean up is not performed.\r
+<P>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
+getWorkDirectory</H3>\r
+<PRE>\r
+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
+<DL>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>working directory if the task</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="executeJob()"><!-- --></A><H3>\r
+executeJob</H3>\r
+<PRE>\r
+public void <B>executeJob</B>()\r
+ throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>\r
+<DD>Execute the job\r
+<P>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getJobInfo()"><!-- --></A><H3>\r
+getJobInfo</H3>\r
+<PRE>\r
+public org.ggf.drmaa.JobInfo <B>getJobInfo</B>()\r
+ throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
+<DL>\r
+<DD>This method will block before the calculation has completed and then
+ return the object containing a job execution statistics\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="waitForResult()"><!-- --></A><H3>\r
+waitForResult</H3>\r
+<PRE>\r
+public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>waitForResult</B>()\r
+ throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>\r
+<DD>Call to this method block for as long as it is required for an executable to finish its job.
+ If the calculation has been completed already, the this method returns results immediately.
+ This could return the result directly, but that would be type unsafe\r
+<P>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>object from wich the result can be obtained\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getJobStatus()"><!-- --></A><H3>\r
+getJobStatus</H3>\r
+<PRE>\r
+public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>\r
+<DD>Query the status of the job by its id.\r
+<P>\r
+<DD><DL>\r
+<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
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>- JobStatus</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getInstance(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
+getInstance</H3>\r
+<PRE>\r
+public static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A> <B>getInstance</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)\r
+ throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
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