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@deepakunni3 deepakunni3/stackTrace Secret
Created Nov 27, 2014

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-init-task-xml:
-init-deps:
[copy] noncoding-gff_keys.properties omitted as /Users/Deepak/Intermine/intermine/bio/sources/noncoding-gff/build/main/noncoding-gff_keys.properties is up to date.
[copy] added as is outdated.
-init-flags:
Property "have.file.custom.direct" has not been set
Property "have.file.custom.direct" has not been set
-pre-load:
load:
[echo]
[echo] Loading ador-noncoding-gff (noncoding-gff) tgt items into production DB
[echo]
[integrate] Creating index: CREATE INDEX Gene__key_primaryIdentifier ON Gene (primaryIdentifier)
[integrate] Creating index: CREATE INDEX SOTerm__key ON SOTerm (name, ontologyid)
[integrate] Creating index: CREATE INDEX Chromosome__key ON Chromosome (primaryIdentifier)
[integrate] Creating index: CREATE INDEX Ontology__key ON Ontology (name)
[integrate] Creating index: CREATE INDEX DataSource__key ON DataSource (name)
[integrate] Creating index: CREATE INDEX DataSet__key ON DataSet (name)
[integrate] Creating index: CREATE INDEX Organism__key ON Organism (taxonId)
[integrate] [102606533]
[null] Exiting /Users/Deepak/Intermine/intermine/bio/sources/noncoding-gff/build.xml.
BUILD FAILED
/Users/Deepak/Intermine/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/Deepak/Intermine/intermine/imbuild/source.xml:330: java.lang.RuntimeException: ObjectStore error has occurred (in get)
at org.intermine.objectstore.query.Results.get(Results.java:233)
at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:135)
at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)
at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:136)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.Main.runBuild(Main.java:851)
at org.apache.tools.ant.Main.startAnt(Main.java:235)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.objectstore.ObjectStoreException: Error in worker thread
at org.intermine.dataloader.ParallelBatchingFetcher.doPks(ParallelBatchingFetcher.java:99)
at org.intermine.dataloader.BatchingFetcher.getEquivalentsFor(BatchingFetcher.java:240)
at org.intermine.dataloader.BatchingFetcher$NoseyObjectStore.execute(BatchingFetcher.java:563)
at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:192)
at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:240)
at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:145)
at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
at org.intermine.objectstore.query.Results.range(Results.java:197)
at org.intermine.objectstore.query.SingletonResults.range(SingletonResults.java:65)
at org.intermine.objectstore.query.Results.get(Results.java:226)
... 35 more
Caused by: org.intermine.objectstore.ObjectStoreException: Duplicate objects found for pk org.intermine.model.bio.Gene.key_primaryIdentifier: Gene [briefDescription="null", chromosome=172, chromosomeLocation=2580, description="null", downstreamIntergenicRegion=null, id="616", length="73", name="null", organism=1, primaryIdentifier="102606533", score="null", scoreType="null", secondaryIdentifier="null", sequence=null, sequenceOntologyTerm=551, symbol="Trnaf-gaa", upstreamIntergenicRegion=null]
at org.intermine.dataloader.BatchingFetcher.doPk(BatchingFetcher.java:425)
at org.intermine.dataloader.ParallelBatchingFetcher$WorkUnit.fetch(ParallelBatchingFetcher.java:142)
at org.intermine.dataloader.ParallelBatchingFetcher$Worker.run(ParallelBatchingFetcher.java:163)
at java.lang.Thread.run(Thread.java:744)
Total time: 19 seconds
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