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From Steven Bethard <steven.beth...@Colorado.EDU>
Subject Re: relation-extractor - how to include it as a dependency?
Date Thu, 14 Mar 2013 15:38:55 GMT
Yeah, I never saw a conclusion to the discussion of where the relation-extractor models should
go. My last impression was that they can't be in the Apache SVN at all, and they need to be
in the Sourceforge ctakesresources project. Is that right?

If that's the case, we need to update RelationExtractorTrain to deploy the models to that
project rather than src/main/resources (where it currently deploys them), and delete all the
models in the cTAKES SVN.

And then where would the descriptors go? In the Sourceforge project? Or in the cTAKES SVN?
Seems weird to have them in the cTAKES SVN if they can't refer to their models.

And if we move the descriptors to Sourceforge, I guess that also means moving the tests to
Sourceforge?

Steve

P.S. In the meantime, you may be able to get things working by making a copy of EntityMentionPairRelationExtractorAnnotator.xml
that looks in org/apache/ctakes/relationextractor/models/em_pair instead of  resources/models/em_pair,
since there are currently still models in src/main/resources.


On Mar 14, 2013, at 4:11 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

> Hi Vinod,
> I think that looks like a bug.  Feel free to open a Jira.  
> 
> Sent from my iPhone
> 
> Sent from my iPhone
> 
> On Mar 14, 2013, at 10:46 AM, "Kaggal, Vinod C." <Kaggal.Vinod@mayo.edu> wrote:
> 
>> Hello!
>> 
>> Quick Background: We have been working on integrating CTAKES with DataNormalization
pipeline (as part of SHARPN effort). I have added relation-extractor as a dependency to our
Normalization project as the template-filling module/project uses it.
>> 
>> Question: What is the is a recommended way of adding the relation-extraction's resource
directory to a project that uses this project? Just adding the project (relation-extractor)
to the build-path (projects) results in the following error:
>> 
>> 
>> Caused by: org.apache.uima.resource.ResourceInitializationException
>>         at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:115)
>>         at org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.initialize(RelationExtractorAnnotator.java:121)
>>         at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>>         ... 71 more
>> Caused by: java.io.FileNotFoundException: resources/models/em_pair/model.jar (No
such file or directory)
>>         at java.io.FileInputStream.open(Native Method)
>>         at java.io.FileInputStream.<init>(FileInputStream.java:120)
>>         at java.io.FileInputStream.<init>(FileInputStream.java:79)
>>         at org.cleartk.classifier.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:67)
>>         at org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
>>         at org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.java:113)
>> 
>> 
>> Looks like copying the resources directory to the target project (Normalization project
in this case) seems to take care of this issue. However, I wanted to see a cleaner way of
doing this instead of duplicating the jar (and other resources).
>> 
>> 
>> Vinod


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