[InterMine Dev] Intermine relationships and database IDs

JD Wong jdmswong at gmail.com
Tue Sep 20 21:08:55 BST 2011


Regarding my error, I needed to chance "Location" to "chromosomeLocation" :)

-JD

On Tue, Sep 20, 2011 at 3:13 PM, JD Wong <jdmswong at gmail.com> wrote:

> Hi,
>
> I'm trying to map locations to genes, but I'm getting this error:
>
> /home/jdmswong/intermine_0_97/imbuild/integrate.xml:54: The following error
> occurred while executing this line:
> /home/jdmswong/intermine_0_97/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:134)
>  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.GeneratedMethodAccessor88.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: org.intermine.objectstore.ObjectStoreException:
> org.intermine.metadata.MetaDataException: Reference not found in class:
> Gene.Location while translating Item with identifier 2_0
>  at
> org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute(ObjectStoreTranslatingImpl.java:168)
>  at
> org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.execute(ObjectStoreFastCollectionsForTranslatorImpl.java:197)
>  at
> org.intermine.dataloader.BatchingFetcher$NoseyObjectStore.execute(BatchingFetcher.java:559)
>  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:235)
>  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:196)
>  at
> org.intermine.objectstore.query.SingletonResults.range(SingletonResults.java:65)
>  at org.intermine.objectstore.query.Results.get(Results.java:225)
> ... 35 more
> Caused by: org.intermine.metadata.MetaDataException: Reference not found in
> class: Gene.Location while translating Item with identifier 2_0
>  at
> org.intermine.dataconversion.ItemToObjectTranslator.translateFromDbObject(ItemToObjectTranslator.java:372)
>  at
> org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute(ObjectStoreTranslatingImpl.java:155)
>  ... 46 more
>
> Total time: 45 seconds
> Tue Sep 20 14:43:24 EDT 2011
>
> finished
>
>
> ERROR: 256
> failed with exit code 0: ant -v -Dsource=fb-genes
>
> Looks like, I need to reverse-reference, but my items XML looks like this:
>
>           <item id="2_0" class="Gene">
>       <attribute name="primaryIdentifier" value="CG42703"/>
>       <attribute name="symbol" value="CG42703"/>
>       <attribute name="FlyBaseFeatureType" value="protein_coding_gene"/>
>       <attribute name="FlyBaseAnnotationSymbol" value="CG42703"/>
>       <attribute name="FlyBaseID" value="FBgn0261614"/>
>       <attribute name="FlyBaseCytogenicMap" value="59C4-59C4"/>
>       <reference name="Organism" ref_id="0_6"/>
>       <reference name="Chromosome" ref_id="0_19"/>
>       <reference name="Location" ref_id="7_0"/>
>    </item>
>    <item id="7_0" class="Location">
>       <attribute name="start" value="18988754"/>
>       <attribute name="end" value="18989224"/>
>       <attribute name="strand" value="-1"/>
>       <reference name="feature" ref_id="2_0"/>
>    </item>
>
> Looking at the location table in the database, I'm not sure what
> "featureid" maps to either.  I remember mentioning adopting a global id
> naming convention for the database (the id for the gene table would be
> "gene_id" everywhere it was referenced), is there any way this can make it's
> way into 0.98? :)
>
> Also, is there a comprehensive resource on the database relationships and
> Items XML class specifications so I don't have to mail the list so often? :P
>
> Thanks!
> -JD
>
>
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