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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Getting ctakes smoking-status component to run in Eclipse
Date Thu, 07 Jan 2016 20:11:49 GMT
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

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