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From Justin Zhang <justinzhang...@gmail.com>
Subject Re: smoking status - TypeSystem.xml could not be found
Date Thu, 23 Jul 2015 19:21:09 GMT
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 <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
> <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:justinzhang.xl@gmail.com]
> *Sent:* Wednesday, July 22, 2015 6:19 PM
> *To:* 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>
> 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]
> *Sent:* Wednesday, July 22, 2015 5:21 PM
> *To:* 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>
> 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]
> *Sent:* Wednesday, July 22, 2015 3:44 PM
> *To:* 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
> <justinzhang.xl@gmail.com>]
> *Sent:* Wednesday, July 22, 2015 10:54 AM
> *To:* 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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