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From: "Chen, Pei" <Pei.Chen@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: scala and groovy
Thread-Topic: scala and groovy
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Date: Fri, 13 Dec 2013 19:19:25 +0000
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James,
I wonder why the transitive dependencies didn't resolve that automatically =
(I think scala is in maven central) just like the other jars...
i.e. why do we need to have it manually added to the classpath?

> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Friday, December 13, 2013 2:02 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: scala and groovy
>=20
>=20
> Sort of good news on the scala front -- after I added the complete filena=
me
> for the jars to the rootLoader statements (I had left out the "version" p=
art of
> the jar names),  using scala now works.
>=20
> jarName =3D "scala-library-2.9.0.jar";
> this.class.classLoader.rootLoader.addURL( new URL(libLocation + jarName) =
);
> jarName =3D "sbinary_2.9.0-0.4.0.jar";
> this.class.classLoader.rootLoader.addURL( new URL(libLocation + jarName) =
);
>=20
> (not ready to post a full solution yet - pipeline did not run to completi=
on, but
> at least I'm on to the next issue now)
>=20
> -- James
>=20
> -----Original Message-----
> From: dev-return-2314-Masanz.James=3Dmayo.edu@ctakes.apache.org
> [mailto:dev-return-2314-Masanz.James=3Dmayo.edu@ctakes.apache.org] On
> Behalf Of Masanz, James J.
> Sent: Friday, December 13, 2013 10:59 AM
> To: 'dev@ctakes.apache.org'
> Subject: RE: scala and groovy
>=20
> That would be great if you could try to replicate.
> Check out  ctakes/sandbox/groovy/cTAKES-with-resources.groovy
> Download the two zips from ctakes/sandbox/groovy-temp-resources/
> Extract them so that the directory containing  cTAKES-with-resources.groo=
vy
> also now contains a desc subdirectory and an org subdirectory.
> mkdir inputDir
> groovy cTAKES-with-resources.groovy  inputDir
>=20
> Thanks Pei!
>=20
> -----Original Message-----
> From: dev-return-2313-Masanz.James=3Dmayo.edu@ctakes.apache.org
> [mailto:dev-return-2313-Masanz.James=3Dmayo.edu@ctakes.apache.org] On
> Behalf Of Chen, Pei
> Sent: Friday, December 13, 2013 10:48 AM
> To: dev@ctakes.apache.org
> Subject: RE: scala and groovy
>=20
> James,
> Would it be possible to also attach your script?  I can try to replicate =
it here...
> --Pei
>=20
> > -----Original Message-----
> > From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > Sent: Friday, December 13, 2013 11:34 AM
> > To: 'dev@ctakes.apache.org'
> > Subject: scala and groovy
> >
> >
> > I'm still working on getting the clinical-pipeline
> > (AggregatePlaintextUMLSProcessor) to run from groovy, using the
> > parser.groovy as a starting point
> >
> > A side issue to the main point of this post:
> > The first  issue is already marked as a TODO in parser.groovy -- about
> > downloading models. I am working around that for now by
> > programmatically downloading all models needed and the
> > LookupDesc_Db.xml from SVN in the same way parser.groovy downloads
> the
> > sentence detector model, because things within the ctakes-*-res jars
> > aren't being found by
> > org.apache.ctakes.core.resource.FileLocator#getAsStream
> >
> > Another issue is some of the jars that are used by the assertion
> component:
> > med-facts-i2b2-1.2-SNAPSHOT.jar
> > med-facts-zoner-1.1.jar
> > jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
> > jcarafe-core_2.9.1-0.9.8.3.RC4.jar
> >
> > I download those also separately from SVN and add them using
> > statements like this:
> > this.class.classLoader.rootLoader.addURL( new URL(libLocation +
> > jarName) );
> >
> > The bigger issue is the following
> > I was getting an error about scala, so I added the following to the
> > Grapes annotation in my groovy script @Grab(group=3D'org.scala-lang',
> > module=3D'scala- library', version=3D'2.9.0'),
> > @Grab(group=3D'org.scala-tools.sbinary',
> > module=3D'sbinary_2.9.0', version=3D'0.4.0'),
> >
> > Those grapes now appear in my grapes repo. But I am getting the
> > following error, and I don't know why ScopeParser cannot "see"
> > scala.ScalaObject which I believe is defined in one of the scala jars
> > that I added to the rootLoader as I described above.
> >
> > scope model: /C:/usr/meTAKES/using-
> > groovy/org/apache/ctakes/assertion/models/scope.model
> > Caught: java.lang.NoClassDefFoundError: scala/ScalaObject
> > java.lang.NoClassDefFoundError: scala/ScalaObject
> >         at
> >
> org.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParser.java:22=
)
> >         at
> > org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initializ
> > e(Ass
> > ertionAnalysisEngine.java:121)
> >         at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> > ialize
> > AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >         at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> > ialize
> > (PrimitiveAnalysisEngine_impl.java:156)
> >         at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > i
> > sEngineFactory_impl.java:94)
> >         at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > ompositeResourceFactory_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:
> > 25
> > 4)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > AS
> > B(AggregateAnalysisEngine_impl.java:431)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > e(AggregateAnalysisEngine_impl.java:185)
> >         at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > i
> > sEngineFactory_impl.java:94)
> >         at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > ompositeResourceFactory_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:
> > 25
> > 4)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > AS
> > B(AggregateAnalysisEngine_impl.java:431)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > e(AggregateAnalysisEngine_impl.java:185)
> >         at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > i
> > sEngineFactory_impl.java:94)
> >         at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > ompositeResourceFactory_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:
> > 25
> > 4)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > AS
> > B(AggregateAnalysisEngine_impl.java:431)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >         at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > e(AggregateAnalysisEngine_impl.java:185)
> >         at
> > org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngi
> > neFa
> > ctory.java:505)
> >         at
> > org.uimafit.factory.AggregateBuilder.createAggregate(AggregateBuilder.
> > java
> > :200)
> >         at
> > org.uimafit.factory.AggregateBuilder$createAggregate.call(Unknown
> > Source)
> >         at cTAKES-with-resources.run(cTAKES-with-resources.groovy:365)
> > Caused by: java.lang.ClassNotFoundException: scala.ScalaObject
> >         ... 32 more