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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: smoking status - TypeSystem.xml could not be found
Date Thu, 23 Jul 2015 19:37:33 GMT
Justin,
Compare
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
vs.
file:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml

From: Justin Zhang [mailto:justinzhang.xl@gmail.com]
Sent: Thursday, July 23, 2015 3:21 PM
To: user@ctakes.apache.org
Subject: Re: smoking status - TypeSystem.xml could not be found

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<https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_SimulatedProdSmokingTAE.xml&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=6unu4wtUrr68ito03x_fm5Il5HbinaeHxbt5lfa1XvA&s=rS_r2lnRzBU5ngPuJOt0TxXwZ7rBsW7XqJHPxz6hX4s&e=>

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<https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_SimulatedProdSmokingTAE.xml&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=6unu4wtUrr68ito03x_fm5Il5HbinaeHxbt5lfa1XvA&s=rS_r2lnRzBU5ngPuJOt0TxXwZ7rBsW7XqJHPxz6hX4s&e=>



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 <Pei.Chen@childrens.harvard.edu<mailto:Pei.Chen@childrens.harvard.edu>>
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<https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_SimulatedProdSmokingTAE.xml&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=6unu4wtUrr68ito03x_fm5Il5HbinaeHxbt5lfa1XvA&s=rS_r2lnRzBU5ngPuJOt0TxXwZ7rBsW7XqJHPxz6hX4s&e=>
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:justinzhang.xl@gmail.com<mailto:justinzhang.xl@gmail.com>]
Sent: Wednesday, July 22, 2015 6:19 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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 <Pei.Chen@childrens.harvard.edu<mailto:Pei.Chen@childrens.harvard.edu>>
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:justinzhang.xl@gmail.com<mailto:justinzhang.xl@gmail.com>]
Sent: Wednesday, July 22, 2015 5:21 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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 <Pei.Chen@childrens.harvard.edu<mailto:Pei.Chen@childrens.harvard.edu>>
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:fbraun@fredhutch.org<mailto:fbraun@fredhutch.org>]
Sent: Wednesday, July 22, 2015 3:44 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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:justinzhang.xl@gmail.com]
Sent: Wednesday, July 22, 2015 10:54 AM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
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
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