[InterMine Dev] go-annotation source throws error

Kalpana Karra kkarra at stanford.edu
Wed Oct 31 16:16:00 GMT 2012


Must have to do with storing non-PMID references and the change in the model..

load:
     [echo] 
     [echo]       Loading go-annotation (go-annotation) tgt items into production DB
     [echo]     
[integrate] Creating index: CREATE INDEX Publication__key_pubmed ON Publication (pubMedId)
[integrate] Creating index: CREATE INDEX DataSet__key_title ON DataSet (name)
[integrate] Creating index: CREATE INDEX Gene__key_secondaryidentifier ON Gene (secondaryIdentifier, organismid)
[integrate] Creating index: CREATE INDEX Gene__key_symbol_org ON Gene (symbol, organismid)
[integrate] Creating index: CREATE INDEX Gene__key_primaryidentifier ON Gene (primaryIdentifier)
[integrate] Creating index: CREATE INDEX GOEvidenceCode__key_code ON GOEvidenceCode (code)
[integrate] Creating index: CREATE INDEX DataSource__key_name ON DataSource (name)
[integrate] Creating index: CREATE INDEX OntologyTerm__key_name_ontology ON OntologyTerm (name, ontologyid)
[integrate] Creating index: CREATE INDEX OntologyTerm__key_identifier ON OntologyTerm (identifier)
[integrate] Creating index: CREATE INDEX Ontology__key_title ON Ontology (name)
[integrate] Creating index: CREATE INDEX Organism__key_taxonid ON Organism (taxonId)
     [null] Exiting /Users/kkarra/Dev/intermine/bio/sources/go-annotation/build.xml.

BUILD FAILED
/Users/kkarra/Dev/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/kkarra/Dev/intermine/imbuild/source.xml:330: java.lang.NullPointerException
	at java.util.TreeMap.put(TreeMap.java:541)
	at java.util.TreeSet.add(TreeSet.java:238)
	at org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.execute(ObjectStoreFastCollectionsForTranslatorImpl.java:257)
	at org.intermine.dataloader.BatchingFetcher$NoseyObjectStore.execute(BatchingFetcher.java:559)
	at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:192)
	at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:240)
	at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:235)
	at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:145)
	at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
	at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
	at org.intermine.objectstore.query.Results.range(Results.java:196)
	at org.intermine.objectstore.query.SingletonResults.range(SingletonResults.java:65)
	at org.intermine.objectstore.query.Results.get(Results.java:225)
	at org.intermine.objectstore.query.Results$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:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	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:392)
	at org.apache.tools.ant.Target.performTasks(Target.java:413)
	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:811)
	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)

Total time: 9 minutes 38 seconds




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