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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 19:59:40 GMT
On Mar 14, 2013, at 8:52 PM, "Masanz, James J." <Masanz.James@mayo.edu> wrote:
> If we end up unable to keep the (real) models in the apache SVN, I'm imagining not having
the tests that rely on the real models run automatically.
> 
> We can create some dummy models just for testing and only run those tests automatically.
> And to run the tests using the real models, someone would need to check out the project,
get the real resources, and run the real tests.

And the descriptors in SVN would also point to the dummy models?

Steve

> 
> 
> Regards, 
> James Masanz
> 
> 
>> -----Original Message-----
>> From: ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org
>> [mailto:ctakes-dev-return-1369-Masanz.James=mayo.edu@incubator.apache.org]
>> On Behalf Of Steven Bethard
>> Sent: Thursday, March 14, 2013 2:46 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: relation-extractor - how to include it as a dependency?
>> 
>> On Mar 14, 2013, at 8:43 PM, "Masanz, James J." <Masanz.James@mayo.edu>
>> wrote:
>>> I just posted a comment on LEGAL-157 asking for some movement.
>>> 
>>> No matter what the answer there about the models, I suggest leaving the
>> descriptors and the tests in Apache cTAKES SVN.
>> 
>> But if the tests require the models, won't they always fail if they're in
>> cTAKES SVN?
>> 
>> Or are you imagining that ctakes-relation-extractor will depend on ctakes-
>> resources-relationextractor?
>> 
>> Steve
>> 
>>> 
>>> -- James
>>> 
>>>> -----Original Message-----
>>>> From:
>>>> ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache.org
>>>> [mailto:ctakes-dev-return-1364-Masanz.James=mayo.edu@incubator.apache
>>>> .org]
>>>> On Behalf Of Steven Bethard
>>>> Sent: Thursday, March 14, 2013 10:39 AM
>>>> To: ctakes-dev@incubator.apache.org
>>>> Subject: Re: relation-extractor - how to include it as a dependency?
>>>> 
>>>> 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.j
>>>> ava:1
>>>> 15)
>>>>>>       at
>>>> org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnota
>>>> tor.i
>>>> nitialize(RelationExtractorAnnotator.java:121)
>>>>>>       at
>>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
>>>> tiali
>>>> zeAnalysisComponent(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.createClassifi
>>>> er(Ge
>>>> nericJarClassifierFactory.java:67)
>>>>>>       at
>>>> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(JarC
>>>> lassi
>>>> fierFactory.java:35)
>>>>>>       at
>>>> org.cleartk.classifier.CleartkAnnotator.initialize(CleartkAnnotator.j
>>>> ava:1
>>>> 13)
>>>>>> 
>>>>>> 
>>>>>> 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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