[InterMine Dev] Source loading order, does it matter?

JD Wong jdmswong at gmail.com
Tue Oct 25 22:02:24 BST 2011


Hi dev,

A little background, I generate the items xml for my fb-genes source
directly.

When I load my genes source before go-annotation, I get this stack trace.

BUILD FAILED
/home/jdmswong/intermine/imbuild/integrate.xml:54: The following error
occurred while executing this line:
/home/jdmswong/intermine/imbuild/source.xml:330: java.lang.RuntimeException:
Exception while dataloading - to allow multiple errors, set the property
"dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 3_1 because
Conflicting values for field Gene.organism between fb-genes (value "Organism
[commonName="null", genus="Drosophila", id="73000005", name="null",
shortName="Dmel", species="melanogaster", taxonId="null"]" in database with
ID 73122557) and go-annotation (value "Organism [commonName="null",
genus="null", id="74000002", name="null", shortName="null", species="null",
taxonId="7227"]" being stored). This field needs configuring in the
genomic_priorities.properties file
 at
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:164)
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.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.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: Conflicting values for field
Gene.organism between fb-genes (value "Organism [commonName="null",
genus="Drosophila", id="73000005", name="null", shortName="Dmel",
species="melanogaster", taxonId="null"]" in database with ID 73122557) and
go-annotation (value "Organism [commonName="null", genus="null",
id="74000002", name="null", shortName="null", species="null",
taxonId="7227"]" being stored). This field needs configuring in the
genomic_priorities.properties file
 at
org.intermine.dataloader.SourcePriorityComparator.compare(SourcePriorityComparator.java:268)
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.store(IntegrationWriterAbstractImpl.java:171)
 at
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:146)
... 33 more


It looks like the value for organism is conflicting, but not when the load
orders are reversed.

Can a developer shed some light on this?

Thanks!
-JD
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