[InterMine Dev] obo file

Richard Smith richard at flymine.org
Tue Mar 13 18:08:50 GMT 2012


Hi Ivan,
I just ran than that step on the intermine_0_98 branch and it works fine
for me.  The code that has gone wrong comes from two jars we use from
OBO-Edit we use for parsing ontologies - obo.jar and bbop.jar.  Is it
possibly you have other versions of these jars on you system and in
your classpath?

Did you run ant with the -v option to get the error message you sent?
If not 'ant -v clean build-db' it should provide a more complete stack
trace.

Regards,
Richard.


On 13/03/2012 15:46, Ivan Merelli wrote:
> 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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