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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: relation-extractor - how to include it as a dependency?
Date Thu, 14 Mar 2013 20:02:19 GMT

In this theoretical version of things I would suggest we have 2 sets of descriptors and both
would live in the cTAKES SVN 
  - one set for all the real models
  - one set for the dummy models.

And 2 sets of tests, also both in cTAKES SVN

-- James

> -----Original Message-----
> From: ctakes-dev-return-1371-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1371-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Steven Bethard
> Sent: Thursday, March 14, 2013 3:00 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: relation-extractor - how to include it as a dependency?
> 
> 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.apac
> >>>> he
> >>>> .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.RelationExtractorAnno
> >>>> ta
> >>>> tor.i
> >>>> nitialize(RelationExtractorAnnotator.java:121)
> >>>>>>       at
> >>>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i
> >>>> ni
> >>>> 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.createClassi
> >>>> fi
> >>>> er(Ge
> >>>> nericJarClassifierFactory.java:67)
> >>>>>>       at
> >>>> org.cleartk.classifier.jar.JarClassifierFactory.createClassifier(Ja
> >>>> rC
> >>>> 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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