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

Richard Smith richard at flymine.org
Wed Oct 26 09:07:01 BST 2011


Thomas is exactly right :)  Ignore my last mail which was answering the
wrong question!

Richard.



> Hi JD,
> When different sources can define a piece of data (and are therefore
> conflicting), you have to define which one  has the priority. This is
> explained in the MalariaMine tutorial, section
> 9.4<http://intermine.org/wiki/GettingStarted#a9.4Dealingwithconflicts>
> .
> Hope this helps.
> Thomas
> --
> Thomas Triplet, Ph.D.
> http://www.thomastriplet.net
>
> Centre for Structural and Functional Genomics
> Concordia University
> 7141 West Sherbrooke St
> Montreal QC H4B 1R6
>
>
>
>
>
> On Tue, Oct 25, 2011 at 5:02 PM, JD Wong <jdmswong at gmail.com> wrote:
>
>> 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
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>




More information about the dev mailing list