[InterMine Dev] obo file

Ivan Merelli ivan.merelli at itb.cnr.it
Tue Mar 13 15:46:44 GMT 2012


Dear Intermine developers,
I'm trying to follow the tutorial about malariamine,
but I have a problem the  "ant clean build-db" step.

The problem arise both with version 0.98 and 0.99
Any hits about the possible problem?
The obo files seem ok.
Best
I.



create-so-model:
  [so-model] Starting OboToModel conversion from 
/home/gmod/intermine_0_98/bio/sources/so/data/so_2_4_4.obo to 
/home/gmod/intermine_0_98/malariamine/dbmodel/build/model/so_additions.xml. 
  Filtering on 47 obo terms from 
/home/gmod/intermine_0_98/malariamine/dbmodel/resources/so_term_list.txt

BUILD FAILED
/home/gmod/intermine_0_98/malariamine/dbmodel/build.xml:12: 
java.lang.RuntimeException: Parsing obo file failed
	at 
org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:258)
	at 
org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.java:102)
	at org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68)
	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.bbop.dataadapter.DataAdapterException: Bad configuration
	at 
org.obo.dataadapter.SimpleLinkFileAdapter.doOperation(SimpleLinkFileAdapter.java:132)
	at 
org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:120)
	at 
org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:254)
	... 18 more





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