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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[copy] added as is outdated.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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