[InterMine Dev] duplicate objects in the same datasource

Jayaraman, Pushkala pjayaraman at mcw.edu
Fri Aug 30 15:23:18 BST 2013


Hello im trying to load biogrid data and I get the following error. What am i doing wrong?:

Problem while loading item identifier 8_9389 because
Duplicate objects from the same data source; o1 = "Gene:5028978" (in database), o2 = "Gene:5028428" (in database), source1 = "<Source: name="human-gff", type="null", skeleton=false>", source2 = "<Source: name="human-gff", type="null", skeleton=false>"
        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:165)
        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:291)
        at sun.reflect.GeneratedMethodAccessor90.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        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:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
        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:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        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:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.Main.runBuild(Main.java:809)
        at org.apache.tools.ant.Main.startAnt(Main.java:217)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.IllegalArgumentException: Duplicate objects from the same data source; o1 = "Gene:5028978" (in database), o2 = "Gene:5028428" (in database), source1 = "<Source: name="human-gff", type="null", skeleton=false>", source2 = "<Source: name="human-gff", type="null", skeleton=false>"
        at org.intermine.dataloader.SourcePriorityComparator.compare(SourcePriorityComparator.java:144)
        at org.intermine.dataloader.SourcePriorityComparator.compare(SourcePriorityComparator.java:33)
        at java.util.TreeMap.put(TreeMap.java:530)
        at java.util.TreeSet.add(TreeSet.java:238)
        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:385)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(IntegrationWriterAbstractImpl.java:253)
        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:571)
        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:147)
        ... 33 more

Total time: 2 minutes 34 seconds
Fri Aug 30 09:20:22 CDT 2013

finished


ERROR: 256
failed with exit code 0: ant -v -Dsource=rat-biogrid

Pushkala Jayaraman
Programmer/Analyst - Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
414-955-2229
http://rgd.mcw.edu

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