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Reverting old commits that made error handling better because ultimately they made things worse.

This commit is contained in:
Eric Banks 2012-07-25 12:37:59 -04:00
parent 66b409921a
commit e0c07f5567
4 changed files with 49 additions and 55 deletions
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86
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -11,13 +11,17 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.Queue;
import java.util.concurrent.*;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.FutureTask;
/**
* A microscheduler that schedules shards according to a tree-like structure.
@ -40,6 +44,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
private final Queue<TreeReduceTask> reduceTasks = new LinkedList<TreeReduceTask>();
/**
* An exception that's occurred in this traversal. If null, no exception has occurred.
*/
private RuntimeException error = null;
/**
* Queue of incoming shards.
*/
@ -90,13 +99,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
ReduceTree reduceTree = new ReduceTree(this);
initializeWalker(walker);
//
// exception handling here is a bit complex. We used to catch and rethrow exceptions all over
// the place, but that just didn't work well. Now we have a specific execution exception (inner class)
// to use for multi-threading specific exceptions. All RuntimeExceptions that occur within the threads are rethrown
// up the stack as their underlying causes
//
while (isShardTraversePending() || isTreeReducePending()) {
// Check for errors during execution.
if(hasTraversalErrorOccurred())
throw getTraversalError();
// Too many files sitting around taking up space? Merge them.
if (isMergeLimitExceeded())
mergeExistingOutput(false);
@ -123,8 +130,12 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
result = reduceTree.getResult().get();
notifyTraversalDone(walker,result);
}
catch( InterruptedException ex ) { handleException(ex); }
catch( ExecutionException ex ) { handleException(ex); }
catch (ReviewedStingException ex) {
throw ex;
}
catch (Exception ex) {
throw new ReviewedStingException("Unable to retrieve result", ex);
}
// do final cleanup operations
outputTracker.close();
@ -255,8 +266,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
// Specifically catch Tribble I/O exceptions and rethrow them as Reviewed. We don't expect
// any issues here because we created the Tribble output file mere moments ago and expect it to
// be completely valid.
final String reason = ex.getMessage();
throw new ReviewedStingException("Unable to merge temporary Tribble output file" + (reason == null ? "." : (" (" + reason + ").")), ex);
throw new ReviewedStingException("Unable to merge temporary Tribble output file.",ex);
}
}
}
@ -328,39 +338,30 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
}
/**
* Handle an exception that occurred in a worker thread as needed by this scheduler.
*
* The way to use this function in a worker is:
*
* try { doSomeWork();
* catch ( InterruptedException ex ) { hms.handleException(ex); }
* catch ( ExecutionException ex ) { hms.handleException(ex); }
*
* @param ex the exception that occurred in the worker thread
* Detects whether an execution error has occurred.
* @return True if an error has occurred. False otherwise.
*/
protected final void handleException(InterruptedException ex) {
throw new HierarchicalMicroScheduler.ExecutionFailure("Hierarchical reduce interrupted", ex);
private synchronized boolean hasTraversalErrorOccurred() {
return error != null;
}
private synchronized RuntimeException getTraversalError() {
if(!hasTraversalErrorOccurred())
throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
return error;
}
/**
* Handle an exception that occurred in a worker thread as needed by this scheduler.
*
* The way to use this function in a worker is:
*
* try { doSomeWork();
* catch ( InterruptedException ex ) { hms.handleException(ex); }
* catch ( ExecutionException ex ) { hms.handleException(ex); }
*
* @param ex the exception that occurred in the worker thread
* Allows other threads to notify of an error during traversal.
*/
protected final void handleException(ExecutionException ex) {
if ( ex.getCause() instanceof RuntimeException )
// if the cause was a runtime exception that's what we want to send up the stack
throw (RuntimeException )ex.getCause();
protected synchronized void notifyOfTraversalError(Throwable error) {
// If the error is already a Runtime, pass it along as is. Otherwise, wrap it.
if (error instanceof RuntimeException)
this.error = (RuntimeException)error;
else
throw new HierarchicalMicroScheduler.ExecutionFailure("Hierarchical reduce failed", ex);
}
this.error = new ReviewedStingException("An error occurred during the traversal.", error);
}
/** A small wrapper class that provides the TreeReducer interface along with the FutureTask semantics. */
@ -381,17 +382,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
}
}
/**
* A specific exception class for HMS-specific failures such as
* Interrupted or ExecutionFailures that aren't clearly the fault
* of the underlying walker code
*/
public static class ExecutionFailure extends ReviewedStingException {
public ExecutionFailure(final String s, final Throwable throwable) {
super(s, throwable);
}
}
/**
* Used by the ShardTraverser to report time consumed traversing a given shard.
*

4
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -80,8 +80,8 @@ public class ShardTraverser implements Callable {
return accumulator;
} catch(Throwable t) {
// Notify that an exception has occurred
microScheduler.handleException(new ExecutionException(t));
// Notify that an exception has occurred and rethrow it.
microScheduler.notifyOfTraversalError(t);
throw new RuntimeException(t);
} finally {
synchronized(this) {

10
public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
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@ -79,8 +79,14 @@ public class TreeReducer implements Callable {
else
result = walker.treeReduce( lhs.get(), rhs.get() );
}
catch( InterruptedException ex ) { microScheduler.handleException(ex); }
catch( ExecutionException ex ) { microScheduler.handleException(ex); }
catch( InterruptedException ex ) {
microScheduler.notifyOfTraversalError(ex);
throw new ReviewedStingException("Hierarchical reduce interrupted", ex);
}
catch( ExecutionException ex ) {
microScheduler.notifyOfTraversalError(ex);
throw new ReviewedStingException("Hierarchical reduce failed", ex);
}
final long endTime = System.currentTimeMillis();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -58,13 +58,11 @@ import java.util.ArrayList;
* of poor base quality. This walker generates tables based on various user-specified covariates (such as read group,
* reported quality score, cycle, and dinucleotide). Since there is a large amount of data one can then calculate an empirical
* probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations.
* The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score).
* The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score).
* <p>
* Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified.
*
* <p>
* See the GATK wiki for a tutorial and example recalibration accuracy plots.
* http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration
*
* <h2>Input</h2>
* <p>