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Reply-To: dev@ctakes.apache.org
From: Patrick Eads <Patrick.Eads@dartmouth.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: Getting ctakes smoking-status component to run in Eclipse
Thread-Topic: Getting ctakes smoking-status component to run in Eclipse
Thread-Index: AdFJhJ5AKX1WvQY5Q8qdqk78XfLgfQ==
Date: Thu, 7 Jan 2016 20:00:11 +0000
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Hello all,

We are trying to get the ctakes smoking-status component to run after getti=
ng the code from SVN and successfully compiling it. Following all of the st=
eps here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Dev=
eloper+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 runn=
ing the smoking-status project, the following exception is thrown (sorry fo=
r 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.smoking=
status.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" f=
ailed.  (Descriptor: file:/home/.../ctakes/ctakes-smoking-status/desc/analy=
sis_engine/ClassifiableEntriesAnnotator.xml)
                at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEn=
gine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252=
)
                at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEn=
gine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
                at org.apache.uima.impl.AnalysisEngineFactory_impl.produceR=
esource(AnalysisEngineFactory_impl.java:94)
                at org.apache.uima.impl.CompositeResourceFactory_impl.produ=
ceResource(CompositeResourceFactory_impl.java:62)
                at org.apache.uima.UIMAFramework.produceResource(UIMAFramew=
ork.java:269)
                at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMA=
Framework.java:387)
                at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(=
ASB_impl.java:254)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn=
gine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn=
gine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.ja=
va:375)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn=
gine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
                at org.apache.uima.impl.AnalysisEngineFactory_impl.produceR=
esource(AnalysisEngineFactory_impl.java:94)
                at org.apache.uima.impl.CompositeResourceFactory_impl.produ=
ceResource(CompositeResourceFactory_impl.java:62)
                at org.apache.uima.UIMAFramework.produceResource(UIMAFramew=
ork.java:269)
                at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMA=
Framework.java:354)
                at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.ja=
va:1484)
                at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(Mai=
nFrame.java:476)
                at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHand=
ler.actionPerformed(AnnotatorOpenEventHandler.java:52)
                at javax.swing.AbstractButton.fireActionPerformed(AbstractB=
utton.java:2022)
                at javax.swing.AbstractButton$Handler.actionPerformed(Abstr=
actButton.java:2348)
                at javax.swing.DefaultButtonModel.fireActionPerformed(Defau=
ltButtonModel.java:402)
                at javax.swing.DefaultButtonModel.setPressed(DefaultButtonM=
odel.java:259)
                at javax.swing.AbstractButton.doClick(AbstractButton.java:3=
76)
                at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenu=
ItemUI.java:833)
                at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragM=
ouseReleased(BasicMenuItemUI.java:943)
                at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuIte=
m.java:586)
                at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuIte=
m.java:483)
                at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:4=
29)
                at javax.swing.MenuSelectionManager.processMouseEvent(MenuS=
electionManager.java:329)
                at javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eve=
ntDispatched(BasicPopupMenuUI.java:870)
                at java.awt.Toolkit$SelectiveAWTEventListener.eventDispatch=
ed(Toolkit.java:2425)
                at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched=
(Toolkit.java:2317)
                at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:22=
75)
                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(Contai=
ner.java:4888)
                at java.awt.LightweightDispatcher.processMouseEvent(Contain=
er.java:4525)
                at java.awt.LightweightDispatcher.dispatchEvent(Container.j=
ava: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:75=
8)
                at java.awt.EventQueue.access$500(EventQueue.java:97)
                at java.awt.EventQueue$3.run(EventQueue.java:709)
                at java.awt.EventQueue$3.run(EventQueue.java:703)
                at java.security.AccessController.doPrivileged(Native Metho=
d)
                at java.security.ProtectionDomain$JavaSecurityAccessImpl.do=
IntersectionPrivilege(ProtectionDomain.java:76)
                at java.security.ProtectionDomain$JavaSecurityAccessImpl.do=
IntersectionPrivilege(ProtectionDomain.java:86)
                at java.awt.EventQueue$4.run(EventQueue.java:731)
                at java.awt.EventQueue$4.run(EventQueue.java:729)
                at java.security.AccessController.doPrivileged(Native Metho=
d)
                at java.security.ProtectionDomain$JavaSecurityAccessImpl.do=
IntersectionPrivilege(ProtectionDomain.java:76)
                at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
                at org.GNOME.Accessibility.AtkWrapper$5.dispatchEvent(AtkWr=
apper.java:697)
                at java.awt.EventDispatchThread.pumpOneEventForFilters(Even=
tDispatchThread.java:201)
                at java.awt.EventDispatchThread.pumpEventsForFilter(EventDi=
spatchThread.java:116)
                at java.awt.EventDispatchThread.pumpEventsForHierarchy(Even=
tDispatchThread.java:105)
                at java.awt.EventDispatchThread.pumpEvents(EventDispatchThr=
ead.java:101)
                at java.awt.EventDispatchThread.pumpEvents(EventDispatchThr=
ead.java:93)
                at java.awt.EventDispatchThread.run(EventDispatchThread.jav=
a:82)
Caused by: org.apache.uima.resource.ResourceInitializationException: An imp=
ort could not be resolved.  No .xml file with name "org.apache.ctakes.core.=
analysis_engine.TokenizerAnnotator" was found in the class path or data pat=
h. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/clas=
ses/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceA=
ggregate_step1.xml)
                at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.i=
nitialize(ClassifiableEntries.java:178)
                at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEn=
gine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250=
)
                ... 59 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An imp=
ort could not be resolved.  No .xml file with name "org.apache.ctakes.core.=
analysis_engine.TokenizerAnnotator" was found in the class path or data pat=
h. (Descriptor: file:/home/.../ctakes/ctakes-smoking-status-res/target/clas=
ses/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceA=
ggregate_step1.xml)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn=
gine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
                at org.apache.uima.impl.AnalysisEngineFactory_impl.produceR=
esource(AnalysisEngineFactory_impl.java:94)
                at org.apache.uima.impl.CompositeResourceFactory_impl.produ=
ceResource(CompositeResourceFactory_impl.java:62)
                at org.apache.uima.UIMAFramework.produceResource(UIMAFramew=
ork.java:269)
                at org.apache.uima.UIMAFramework.produceResource(UIMAFramew=
ork.java:314)
                at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMA=
Framework.java:425)
                at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.i=
nitialize(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/c=
takes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.x=
ml)
                at org.apache.uima.resource.metadata.impl.Import_impl.findA=
bsoluteUrl(Import_impl.java:107)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr=
iption_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_=
impl.java:798)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr=
iption_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_=
impl.java:765)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr=
iption_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_i=
mpl.java:193)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn=
gine_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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