Hi Pei,
I got the following error when I load AE from "Clinical Document Pipeline" project in Eclipse AE: /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes / ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml <http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml> And there is no "SimulatedProdSmokingTAE.xml" in the following folder. ls /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ ArtificialSentenceAnnotator.xml KuRuleBasedClassifierAnnotator.xml PcsClassifierAnnotator_libsvm.xml ProductionPostSentenceAggregate_step1.xml ProductionPostSentenceAggregate_step2_libsvm.xml SentenceAdjuster.xml SmokingStatusDictionaryLookupAnnotator.xml ==== Error from /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes / ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml <http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml> 23/07/15 2:07:45 PM - 15: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed. (Descriptor: file:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486) 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$Handler.actionPerformed(AbstractButton.java:2346) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6525) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6290) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4703) 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$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.security.ProtectionDomain$1.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$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) 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:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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) ... 56 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:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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) ... 57 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:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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) ... 63 more On Thu, Jul 23, 2015 at 1:32 PM, Chen, Pei <[email protected]> wrote: > Justin, > > I meant, what is the error: > > When you use /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes > /ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml > <http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml> > > Instead of: > /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ > > > > > > *From:* Justin Zhang [mailto:[email protected]] > *Sent:* Wednesday, July 22, 2015 6:19 PM > *To:* [email protected] > *Subject:* Re: smoking status - TypeSystem.xml could not be found > > > > Hi Pei, > > > > I checked ProductionPostSentenceAggregate_step1.xml > <https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_ProductionPostSentenceAggregate-5Fstep1.xml-3Fview-3Dlog&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=NC8hDGtE8v99_f0CkYg4TWYDT5ga6tziR78hej5XtIM&e=> > and there is not redundant descriptors. For the bug, how to go proceed > to fix? > > > > Also, are there other ways to launch smoking pipeline besides > "takes-clinical-pipeline" project as document says. > > > > Thanks, > > > > Justin > > > > On Wed, Jul 22, 2015 at 4:48 PM, Chen, Pei <[email protected]> > wrote: > > Justin, > > There seems to be a bug or redundant descriptors. Check out: > > > https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=bDdwEocxxNTXXMVCZCk59PcW0DhiE53FzSoLiOAQCwM&e=> > > ProductionPostSentenceAggregate_step1.xml > <https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_ProductionPostSentenceAggregate-5Fstep1.xml-3Fview-3Dlog&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=NC8hDGtE8v99_f0CkYg4TWYDT5ga6tziR78hej5XtIM&e=> > > > > > > *From:* Justin Zhang [mailto:[email protected]] > *Sent:* Wednesday, July 22, 2015 5:21 PM > *To:* [email protected] > *Subject:* Re: smoking status - TypeSystem.xml could not be found > > > > Thanks Pei for the response. > > > > I launched it from cakes-clinical-pipeline project, and added > "smoking-status" dependency. The older error is gone, and got the new > error. > > > > 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:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/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) > > > > I checked "TokenizerAnnotator.xml" file, it is in the following folder. > > > > eclipse_mars/workspace_eclipse_mars/ctakes > > ctakes justin$ ls ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml > > ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml > > > > From file ProductionPostSentenceAggregate_step1.xml, it has the relevant > lines. > > <delegateAnalysisEngine key="TokenizerAnnotator"> > > <import > name="org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"/> > > </delegateAnalysisEngine> > > > > Where is the folder I should check > "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" xml file? > > > > Thanks, > > > > Justin > > > > On Wed, Jul 22, 2015 at 3:28 PM, Chen, Pei <[email protected]> > wrote: > > It should be able automatically resolved by using the Type System name > rather than absolute path. > > How is the pipeline being launched? If you’re using eclipse and launching > it from the ctakes-clinical-pipeline project, be sure to include the > smoking-status in the pom.xml as a dependency [I don’t think smoking-status > was part of the main pipeline]? Or ensure that that project is included > during runtime? > > Disclaimer: I didn’t try this myself yet- but let me know if that works > for you. > > > > > > *From:* Braun, Florian A [mailto:[email protected]] > *Sent:* Wednesday, July 22, 2015 3:44 PM > *To:* [email protected] > *Subject:* RE: smoking status - TypeSystem.xml could not be found > > > > Wow, was just about to send an email on this. I am getting the exact same > error. > > > > I found the xml file under <ctakes-home>\ctakes-smoking-status\src\main\ > *resources*\org\apache\ctakes\smokingstatus\types\ > > > > Looks like it has an issue being under resources and not under the java? > > > > Any info would be appreciated. > > > > Florian > > > > *From:* Justin Zhang [mailto:[email protected] > <[email protected]>] > *Sent:* Wednesday, July 22, 2015 10:54 AM > *To:* [email protected] > *Subject:* smoking status - TypeSystem.xml could not be found > > > > When I ran smoking pipeline from Eclipse, encountered the following error. > > > > Caused by: org.apache.uima.util.InvalidXMLException: An import could not > be resolved. No .xml file with name > "org.apache.ctakes.smokingstatus.types.TypeSystem" was found in the class > path or data path. (Descriptor: > file:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml) > > > > Everything looks fine. > > > > The file is there physically. > > The importing part from ClassifiableEntriesAnnotator.xml file is > > <typeSystemDescription> > > <imports> > > <import > name="org.apache.ctakes.smokingstatus.types.TypeSystem"/> > > </imports> > > </typeSystemDescription> > > > > Could any one help me some clues? > > > > Thanks, > > > > > > -- > > Justin > > > > > > -- > > Justin > > > > > > -- > > Justin > -- Justin
