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Posted to dev@ctakes.apache.org by Patrick Eads <Pa...@dartmouth.edu> on 2016/01/07 21:00:11 UTC
Getting ctakes smoking-status component to run in Eclipse
Hello all,
We are trying to get the ctakes smoking-status component to run after getting the code from SVN and successfully compiling it. Following all of the steps here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Developer+Install+Guide, we are able to successful test the clinical-pipeline by processing the testpatient_plaintext_1.txt from the User Install Guide. However, when we attempt to load the SimulatedProdSmokingTAE.xml after running the smoking-status project, the following exception is thrown (sorry for the long stack trace):
1/7/16 2:45:14 PM - 17: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:943)
at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:586)
at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:483)
at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:429)
at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:329)
at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupMenuUI.java:870)
at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2425)
at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2317)
at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2275)
at java.awt.Component.dispatchEventImpl(Component.java:4787)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWrapper.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 59 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:164)
... 60 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 66 more
Please let me know if you have any advice. Thank you.
Regards,
Patrick Eads
RE: Getting ctakes smoking-status component to run in Eclipse
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Patrick,
That is very strange. If I can find some time later I'll try to run the workflow myself and see what happens.
Sean
-----Original Message-----
From: Patrick Eads [mailto:Patrick.Eads@dartmouth.edu]
Sent: Thursday, January 07, 2016 3:48 PM
To: dev@ctakes.apache.org
Subject: RE: Getting ctakes smoking-status component to run in Eclipse
Hi Sean,
I'm pulling the head from https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=I2RDR92crNxCMkNkHohpBpc_wMG1FJ2xFSfWwgVIxW8&s=v3FlCkQgYLzmZHBhHASLna5gkLUIQ0LqwPrjavSIuew&e= .
Regards,
Patrick
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Thursday, January 07, 2016 3:12 PM
To: dev@ctakes.apache.org
Subject: RE: Getting ctakes smoking-status component to run in Eclipse
Hi Patrick,
What version of ctakes are you running? The stack trace looks a little strange.
The Tokenizer used by the smoking status module was changed from TokenizerAnnotator to tokenizerAnnotatorPTB in version 2.3 on 5/11/2012. But in your trace it looks like the TokenizerAnnotator class is being called. Also, it looks like it is being called directly instead of indirectly through an .xml
Sean
-----Original Message-----
From: Patrick Eads [mailto:Patrick.Eads@dartmouth.edu]
Sent: Thursday, January 07, 2016 3:00 PM
To: dev@ctakes.apache.org
Subject: Getting ctakes smoking-status component to run in Eclipse
Hello all,
We are trying to get the ctakes smoking-status component to run after getting the code from SVN and successfully compiling it. Following all of the steps here: https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=WVWuRCArUkT-KephujkeDXUIxpgJLSFpIcMwJKwfMp8&s=sU7N53JIbhAO_vfUc8O13mDkTzLCh1anfWuASe3tV5c&e= , we are able to successful test the clinical-pipeline by processing the testpatient_plaintext_1.txt from the User Install Guide. However, when we attempt to load the SimulatedProdSmokingTAE.xml after running the smoking-status project, the following exception is thrown (sorry for the long stack trace):
1/7/16 2:45:14 PM - 17: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:943)
at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:586)
at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:483)
at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:429)
at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:329)
at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupMenuUI.java:870)
at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2425)
at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2317)
at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2275)
at java.awt.Component.dispatchEventImpl(Component.java:4787)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWrapper.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 59 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:164)
... 60 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 66 more
Please let me know if you have any advice. Thank you.
Regards,
Patrick Eads
RE: Getting ctakes smoking-status component to run in Eclipse
Posted by Patrick Eads <Pa...@dartmouth.edu>.
Hi Sean,
I'm pulling the head from https://svn.apache.org/repos/asf/ctakes/trunk.
Regards,
Patrick
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Thursday, January 07, 2016 3:12 PM
To: dev@ctakes.apache.org
Subject: RE: Getting ctakes smoking-status component to run in Eclipse
Hi Patrick,
What version of ctakes are you running? The stack trace looks a little strange.
The Tokenizer used by the smoking status module was changed from TokenizerAnnotator to tokenizerAnnotatorPTB in version 2.3 on 5/11/2012. But in your trace it looks like the TokenizerAnnotator class is being called. Also, it looks like it is being called directly instead of indirectly through an .xml
Sean
-----Original Message-----
From: Patrick Eads [mailto:Patrick.Eads@dartmouth.edu]
Sent: Thursday, January 07, 2016 3:00 PM
To: dev@ctakes.apache.org
Subject: Getting ctakes smoking-status component to run in Eclipse
Hello all,
We are trying to get the ctakes smoking-status component to run after getting the code from SVN and successfully compiling it. Following all of the steps here: https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=WVWuRCArUkT-KephujkeDXUIxpgJLSFpIcMwJKwfMp8&s=sU7N53JIbhAO_vfUc8O13mDkTzLCh1anfWuASe3tV5c&e= , we are able to successful test the clinical-pipeline by processing the testpatient_plaintext_1.txt from the User Install Guide. However, when we attempt to load the SimulatedProdSmokingTAE.xml after running the smoking-status project, the following exception is thrown (sorry for the long stack trace):
1/7/16 2:45:14 PM - 17: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:943)
at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:586)
at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:483)
at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:429)
at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:329)
at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupMenuUI.java:870)
at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2425)
at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2317)
at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2275)
at java.awt.Component.dispatchEventImpl(Component.java:4787)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWrapper.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 59 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:164)
... 60 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 66 more
Please let me know if you have any advice. Thank you.
Regards,
Patrick Eads
RE: Getting ctakes smoking-status component to run in Eclipse
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Patrick,
What version of ctakes are you running? The stack trace looks a little strange.
The Tokenizer used by the smoking status module was changed from TokenizerAnnotator to tokenizerAnnotatorPTB in version 2.3 on 5/11/2012. But in your trace it looks like the TokenizerAnnotator class is being called. Also, it looks like it is being called directly instead of indirectly through an .xml
Sean
-----Original Message-----
From: Patrick Eads [mailto:Patrick.Eads@dartmouth.edu]
Sent: Thursday, January 07, 2016 3:00 PM
To: dev@ctakes.apache.org
Subject: Getting ctakes smoking-status component to run in Eclipse
Hello all,
We are trying to get the ctakes smoking-status component to run after getting the code from SVN and successfully compiling it. Following all of the steps here: https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=WVWuRCArUkT-KephujkeDXUIxpgJLSFpIcMwJKwfMp8&s=sU7N53JIbhAO_vfUc8O13mDkTzLCh1anfWuASe3tV5c&e= , we are able to successful test the clinical-pipeline by processing the testpatient_plaintext_1.txt from the User Install Guide. However, when we attempt to load the SimulatedProdSmokingTAE.xml after running the smoking-status project, the following exception is thrown (sorry for the long stack trace):
1/7/16 2:45:14 PM - 17: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:943)
at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:586)
at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:483)
at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:429)
at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:329)
at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupMenuUI.java:870)
at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2425)
at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2317)
at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2275)
at java.awt.Component.dispatchEventImpl(Component.java:4787)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWrapper.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 59 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:164)
... 60 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in the class path or data path. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 66 more
Please let me know if you have any advice. Thank you.
Regards,
Patrick Eads