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Semantic Software Lab
Concordia University
Montréal, Canada

Organism Tagger and GATE 7.1 error

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Hi all,

I get the following error while loading the Organism Tagger. I installed gate-7.1-build4485-installer.jar and installed OrganismTagger through CREOLE plugin manager.

Thanks
John

GATE 7.1 build 4485 started at Thu Mar 07 13:05:51 GMT 2013
and using Java 1.6.0_16 Sun Microsystems Inc. on Linux amd64 2.6.32-220.el6.x86_64.
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/gate/plugins/TextNormalizer/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/JAPE_Plus/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/Learning/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/gate/plugins/OrganismNormalizer/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/Gazetteer_LKB/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/gate/plugins/ANNIE/
CREOLE plugin loaded: file:/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/Ontology_Tools/
Logger com.ontotext.kim level set to INFO, overriding the default effective level of DEBUG. Set the level of com.ontotext.kim explictly if required.
Logger org.openrdf.sesame level set to INFO, overriding the default effective level of DEBUG. Set the level of org.openrdf.sesame explictly if required.
Logger httpclient level set to INFO, overriding the default effective level of DEBUG. Set the level of httpclient explictly if required.
Logger org.apache.commons.httpclient level set to INFO, overriding the default effective level of DEBUG. Set the level of org.apache.commons.httpclient explictly if required.
Query loaded from /bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/gate/application-resources/commonNames/query.txt
Looking for changes in configuration ...
Aliases in IGNORE list:0
Loading of trusted entities from Sesame
ruleSet=owl-horst-optimized, partialRdfs=false
ERROR: could not add '/bmm/home/if03/programs/gate/gate_developer_7.1/plugins/OrganismTagger/gate/application-resources/commonNames/kb/owl/commonnames.owl' into repostiory. Exception found:A worker thread exception catch!
Loading failed.
com.ontotext.kim.client.query.KIMQueryException: Error in repository connection.
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:106)
at com.ontotext.kim.model.AliasCacheImpl.loadTrustedMaps(AliasCacheImpl.java:364)
at com.ontotext.kim.model.AliasCacheImpl.initCache(AliasCacheImpl.java:278)
at com.ontotext.kim.model.AliasCacheImpl.createInstance(AliasCacheImpl.java:151)
at com.ontotext.kim.model.AliasCacheImpl.getInstance(AliasCacheImpl.java:107)
at com.ontotext.kim.gate.KimGazetteer.init(KimGazetteer.java:87)
at gate.Factory.createResource(Factory.java:432)
at gate.util.persistence.ResourcePersistence.createObject(ResourcePersistence.java:83)
at gate.util.persistence.PRPersistence.createObject(PRPersistence.java:76)
at gate.util.persistence.LanguageAnalyserPersistence.createObject(LanguageAnalyserPersistence.java:51)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.CollectionPersistence.createObject(CollectionPersistence.java:74)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.ControllerPersistence.createObject(ControllerPersistence.java:58)
at gate.util.persistence.SerialAnalyserControllerPersistence.createObject(SerialAnalyserControllerPersistence.java:53)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.PersistenceManager.loadObjectFromUrl(PersistenceManager.java:913)
at gate.gui.MainFrame$LoadApplicationAction$1.run(MainFrame.java:2772)
at java.lang.Thread.run(Thread.java:619)
Caused by: org.openrdf.repository.RepositoryException: java.lang.RuntimeException: A worker thread exception catch!
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:95)
at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:26)
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:93)
... 18 more
Caused by: org.openrdf.sail.SailException: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.SailImpl.if(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.initialize(Unknown Source)
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:86)
... 20 more
Caused by: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.r.a(Unknown Source)
at com.ontotext.trree.owlim_ext.SailConnectionImpl.commit(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.addThisOntology(Unknown Source)
... 23 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 100
at com.ontotext.trree.owlim_ext.b.if(Unknown Source)
at com.ontotext.trree.owlim_ext.Repository.putStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.g.addStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.r$a.if(Unknown Source)
at com.ontotext.trree.owlim_ext.m$a.run(Unknown Source)
The loading from Sesame finished
There was an error when loading the OrganismTagger System application.
gate.persist.PersistenceException: com.ontotext.kim.client.KIMRuntimeException: The loading failed.
at gate.util.persistence.PersistenceManager.loadObjectFromUrl(PersistenceManager.java:933)
at gate.gui.MainFrame$LoadApplicationAction$1.run(MainFrame.java:2772)
at java.lang.Thread.run(Thread.java:619)
Caused by: com.ontotext.kim.client.KIMRuntimeException: The loading failed.
at com.ontotext.kim.model.AliasCacheImpl.loadTrustedMaps(AliasCacheImpl.java:367)
at com.ontotext.kim.model.AliasCacheImpl.initCache(AliasCacheImpl.java:278)
at com.ontotext.kim.model.AliasCacheImpl.createInstance(AliasCacheImpl.java:151)
at com.ontotext.kim.model.AliasCacheImpl.getInstance(AliasCacheImpl.java:107)
at com.ontotext.kim.gate.KimGazetteer.init(KimGazetteer.java:87)
at gate.Factory.createResource(Factory.java:432)
at gate.util.persistence.ResourcePersistence.createObject(ResourcePersistence.java:83)
at gate.util.persistence.PRPersistence.createObject(PRPersistence.java:76)
at gate.util.persistence.LanguageAnalyserPersistence.createObject(LanguageAnalyserPersistence.java:51)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.CollectionPersistence.createObject(CollectionPersistence.java:74)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.ControllerPersistence.createObject(ControllerPersistence.java:58)
at gate.util.persistence.SerialAnalyserControllerPersistence.createObject(SerialAnalyserControllerPersistence.java:53)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.PersistenceManager.loadObjectFromUrl(PersistenceManager.java:913)
... 2 more
Caused by: com.ontotext.kim.client.query.KIMQueryException: Error in repository connection.
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:106)
at com.ontotext.kim.model.AliasCacheImpl.loadTrustedMaps(AliasCacheImpl.java:364)
... 17 more
Caused by: org.openrdf.repository.RepositoryException: java.lang.RuntimeException: A worker thread exception catch!
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:95)
at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:26)
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:93)
... 18 more
Caused by: org.openrdf.sail.SailException: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.SailImpl.if(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.initialize(Unknown Source)
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:86)
... 20 more
Caused by: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.r.a(Unknown Source)
at com.ontotext.trree.owlim_ext.SailConnectionImpl.commit(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.addThisOntology(Unknown Source)
... 23 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 100
at com.ontotext.trree.owlim_ext.b.if(Unknown Source)
at com.ontotext.trree.owlim_ext.Repository.putStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.g.addStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.r$a.if(Unknown Source)
at com.ontotext.trree.owlim_ext.m$a.run(Unknown Source)
Caused by:
com.ontotext.kim.client.KIMRuntimeException: The loading failed.
at com.ontotext.kim.model.AliasCacheImpl.loadTrustedMaps(AliasCacheImpl.java:367)
at com.ontotext.kim.model.AliasCacheImpl.initCache(AliasCacheImpl.java:278)
at com.ontotext.kim.model.AliasCacheImpl.createInstance(AliasCacheImpl.java:151)
at com.ontotext.kim.model.AliasCacheImpl.getInstance(AliasCacheImpl.java:107)
at com.ontotext.kim.gate.KimGazetteer.init(KimGazetteer.java:87)
at gate.Factory.createResource(Factory.java:432)
at gate.util.persistence.ResourcePersistence.createObject(ResourcePersistence.java:83)
at gate.util.persistence.PRPersistence.createObject(PRPersistence.java:76)
at gate.util.persistence.LanguageAnalyserPersistence.createObject(LanguageAnalyserPersistence.java:51)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.CollectionPersistence.createObject(CollectionPersistence.java:74)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.ControllerPersistence.createObject(ControllerPersistence.java:58)
at gate.util.persistence.SerialAnalyserControllerPersistence.createObject(SerialAnalyserControllerPersistence.java:53)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:477)
at gate.util.persistence.PersistenceManager.loadObjectFromUrl(PersistenceManager.java:913)
at gate.gui.MainFrame$LoadApplicationAction$1.run(MainFrame.java:2772)
at java.lang.Thread.run(Thread.java:619)
Caused by: com.ontotext.kim.client.query.KIMQueryException: Error in repository connection.
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:106)
at com.ontotext.kim.model.AliasCacheImpl.loadTrustedMaps(AliasCacheImpl.java:364)
... 17 more
Caused by: org.openrdf.repository.RepositoryException: java.lang.RuntimeException: A worker thread exception catch!
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:95)
at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:26)
at org.openrdf.repository.http.PrivateRepositoryFeed.feedTo(PrivateRepositoryFeed.java:93)
... 18 more
Caused by: org.openrdf.sail.SailException: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.SailImpl.if(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.initialize(Unknown Source)
at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:86)
... 20 more
Caused by: java.lang.RuntimeException: A worker thread exception catch!
at com.ontotext.trree.owlim_ext.r.a(Unknown Source)
at com.ontotext.trree.owlim_ext.SailConnectionImpl.commit(Unknown Source)
at com.ontotext.trree.owlim_ext.SailImpl.addThisOntology(Unknown Source)
... 23 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 100
at com.ontotext.trree.owlim_ext.b.if(Unknown Source)
at com.ontotext.trree.owlim_ext.Repository.putStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.g.addStatement(Unknown Source)
at com.ontotext.trree.owlim_ext.r$a.if(Unknown Source)
at com.ontotext.trree.owlim_ext.m$a.run(Unknown Source)

rene's picture

seems to be a 7.0 vs. 7.1 issue

Hi John,

This is probably because the current OT release was built on 7.0; I'll have to check why exactly it is not upwards-compatible with 7.1.

We'll push out a 7.1 release in a couple of days; if you want to try it right now, you could use a 7.0 version of GATE.

Cheers, René

solved

Thanks Rene. It worked with GATE 7.0

Cheers,
John