[InterMine Dev] obo error

James Blackshaw jab250 at mrc-mbu.cam.ac.uk
Thu Mar 15 14:04:13 GMT 2012


Hi,
I just downloaded the 0.99 release, but when trying to work through the 
tutorial I get the following error when running 'ant clean build-db'. 
It's different from the other one recently reported.

-James

create-so-model:
  [so-model] Error: Expected :.
  [so-model] on line: 1 of 
file:/intermine/intermine_0_99/bio/sources/so/so.obo
  [so-model] charnum: 0
  [so-model] line: link data/so_2_4_4.obo
  [so-model]     at 
org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1431)
  [so-model]     at 
org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1423)
  [so-model]     at 
org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:325)
  [so-model]     at 
org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
  [so-model]     at 
org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72)
  [so-model]     at 
org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
  [so-model]     at 
org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:117)
  [so-model]     at 
org.intermine.bio.ontology.SequenceOntology.process(SequenceOntology.java:737)
  [so-model]     at 
org.intermine.bio.ontology.SequenceOntology.<init>(SequenceOntology.java:93)
  [so-model]     at 
org.intermine.bio.ontology.SequenceOntologyFactory.getSequenceOntology(SequenceOntologyFactory.java:91)
  [so-model]     at 
org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:75)
  [so-model]     at 
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
  [so-model]     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown 
Source)
  [so-model]     at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  [so-model]     at java.lang.reflect.Method.invoke(Method.java:616)
  [so-model]     at 
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
  [so-model]     at org.apache.tools.ant.Task.perform(Task.java:348)
  [so-model]     at org.apache.tools.ant.Target.execute(Target.java:390)
  [so-model]     at 
org.apache.tools.ant.Target.performTasks(Target.java:411)
  [so-model]     at 
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
  [so-model]     at 
org.apache.tools.ant.Project.executeTarget(Project.java:1329)
  [so-model]     at 
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
  [so-model]     at 
org.apache.tools.ant.Project.executeTargets(Project.java:1212)
  [so-model]     at org.apache.tools.ant.Main.runBuild(Main.java:801)
  [so-model]     at org.apache.tools.ant.Main.startAnt(Main.java:218)
  [so-model]     at 
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
  [so-model]     at 
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

BUILD FAILED
/intermine/intermine_0_99/malariamine/dbmodel/build.xml:12: 
java.lang.RuntimeException: Parsing obo file failed
     at 
org.intermine.bio.ontology.SequenceOntology.process(SequenceOntology.java:741)
     at 
org.intermine.bio.ontology.SequenceOntology.<init>(SequenceOntology.java:93)
     at 
org.intermine.bio.ontology.SequenceOntologyFactory.getSequenceOntology(SequenceOntologyFactory.java:91)
     at org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:75)
     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
     at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     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:1360)
     at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
     at 
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
     at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
     at org.apache.tools.ant.Main.runBuild(Main.java:801)
     at org.apache.tools.ant.Main.startAnt(Main.java:218)
     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: Load error, line 1
     at 
org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:285)
     at 
org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:117)
     at 
org.intermine.bio.ontology.SequenceOntology.process(SequenceOntology.java:737)
     ... 19 more
Caused by: Error: Expected :.
on line: 1 of file:/intermine/intermine_0_99/bio/sources/so/so.obo
charnum: 0
line: link data/so_2_4_4.obo
     at 
org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1431)
     at 
org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1423)
     at org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:325)
     at 
org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
     at 
org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72)
     at 
org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
     ... 21 more

Total time: 7 seconds
jab250 at bio4:/intermine/intermine_0_99/malariamine/dbmodel$




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