[InterMine Dev] Intermine relationships and database IDs

JD Wong jdmswong at gmail.com
Tue Sep 20 20:13:05 BST 2011


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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