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Fix concurrency issue that periodically kills VariantEvalIntegrationTest -- 

a member field of RMDTrackBuilder was getting rebuilt every time it was
called, creating concurrency issues.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5001 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-01-14 18:52:21 +00:00
parent 73acfa654a
commit af31d02a2d
3 changed files with 11 additions and 29 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -871,7 +871,7 @@ public class GenomeAnalysisEngine {
SAMSequenceDictionary sequenceDictionary,
GenomeLocParser genomeLocParser,
ValidationExclusion.TYPE validationExclusionType) {
RMDTrackBuilder builder = new RMDTrackBuilder(referenceMetaDataFiles,sequenceDictionary,genomeLocParser,validationExclusionType);
RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser,validationExclusionType);
// try and make the tracks given their requests
// create of live instances of the tracks
List<RMDTrack> tracks = new ArrayList<RMDTrack>();

36
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
View File

@ -73,9 +73,6 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
// a constant we use for marking sequence dictionary entries in the Tribble index property list
public static final String SequenceDictionaryPropertyPredicate = "DICT:";
// the input strings we use to create RODs from
private final Collection<RMDTriplet> inputs;
private Map<String, Class> classes = null;
// private sequence dictionary we use to set our tracks with
@ -91,24 +88,6 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
*/
private ValidationExclusion.TYPE validationExclusionType;
/**
* Create a new RMDTrackBuilder, predefined to use a given set of reference metadata.
* @param referenceMetaDataDescriptors file descriptors to build out during trackbuilder construction.
* @param dict Sequence dictionary to use.
* @param genomeLocParser Location parser to use.
* @param validationExclusionType Types of validations to exclude, for sequence dictionary verification.
*/
public RMDTrackBuilder(Collection<RMDTriplet> referenceMetaDataDescriptors,
SAMSequenceDictionary dict,
GenomeLocParser genomeLocParser,
ValidationExclusion.TYPE validationExclusionType) {
super(FeatureCodec.class, "Codecs", "Codec");
this.inputs = referenceMetaDataDescriptors;
this.dict = dict;
this.genomeLocParser = genomeLocParser;
this.validationExclusionType = validationExclusionType;
}
/**
* Construct an RMDTrackerBuilder, allowing the user to define tracks to build after-the-fact. This is generally
* used when walkers want to directly manage the ROD system for whatever reason. Before using this constructor,
@ -120,16 +99,19 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
public RMDTrackBuilder(SAMSequenceDictionary dict,
GenomeLocParser genomeLocParser,
ValidationExclusion.TYPE validationExclusionType) {
this(Collections.<RMDTriplet>emptyList(),dict,genomeLocParser,validationExclusionType);
}
super(FeatureCodec.class, "Codecs", "Codec");
this.dict = dict;
this.genomeLocParser = genomeLocParser;
this.validationExclusionType = validationExclusionType;
/** @return a list of all available track types we currently have access to create */
public Map<String, Class> getAvailableTrackNamesAndTypes() {
classes = new HashMap<String, Class>();
for (String name: this.getPluginsByName().keySet()) {
classes.put(name.toUpperCase(), getPluginsByName().get(name));
}
return classes;
} }
/** @return a list of all available track types we currently have access to create */
public Map<String, Class> getAvailableTrackNamesAndTypes() {
return Collections.unmodifiableMap(classes);
}
/** @return a list of all available track record types we currently have access to create */

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java
View File

@ -76,7 +76,7 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
if (indexFileName.exists()) indexFileName.delete();
triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE);
builder = new RMDTrackBuilder(Collections.singletonList(triplet),seq.getSequenceDictionary(),genomeLocParser,null);
builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null);
}
@Test