Hello all, I am reposting this on the advice of a developer. Below please find the comment thread already in progress.
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 From: Finan, Sean [mailto:[email protected]] Sent: Tuesday, January 12, 2016 5:24 PM To: Patrick Eads <[email protected]> Subject: RE: Getting ctakes smoking-status component to run in Eclipse Hi Patrick, My apologies for not getting back to you. I have had one task after another thrown onto my plate at work, and I haven’t dedicated any personal time to ctakes in the last couple of weeks. I don’t know if I’ll be able to pull together any time for this over the next week. Perhaps reposting on the listserv is the way to go. Sean From: Patrick Eads [mailto:[email protected]] Sent: Tuesday, January 12, 2016 3:12 PM To: Finan, Sean Subject: RE: Getting ctakes smoking-status component to run in Eclipse Hi Sean, I didn’t want to burden the mailserv with this and we can move any pertinent discussion back as needed, but have you had any time to look at the workflow? Regards, Patrick From: Finan, Sean<mailto:[email protected]> Sent: Thursday, January 7, 2016 3:50 PM To: [email protected]<mailto:[email protected]> Subject: RE: Getting ctakes smoking-status component to run in Eclipse 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:[email protected]] Sent: Thursday, January 07, 2016 3:48 PM To: [email protected]<mailto:[email protected]> 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:[email protected]] Sent: Thursday, January 07, 2016 3:12 PM To: [email protected]<mailto:[email protected]> 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:[email protected]] Sent: Thursday, January 07, 2016 3:00 PM To: [email protected]<mailto:[email protected]> 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
