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

Thomas TRIPLET thomastriplet at gmail.com
Tue Oct 25 22:24:02 BST 2011


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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.intermine.org/pipermail/dev/attachments/20111025/039d01b3/attachment-0001.html>


More information about the dev mailing list