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.fi...@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.e...@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
