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From Justin Zhang <justinzhang...@gmail.com>
Subject Re: smoking status - TypeSystem.xml could not be found
Date Wed, 22 Jul 2015 22:18:14 GMT
Hi Pei,

I checked ProductionPostSentenceAggregate_step1.xml
<https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml?view=log>
 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/
>
> ProductionPostSentenceAggregate_step1.xml
> <https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml?view=log>
>
>
>
>
>
> *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

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