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From: "Masanz, James J." <Masanz.James@mayo.edu>
To: "'dev@ctakes.apache.org'" <dev@ctakes.apache.org>
Subject: scala and groovy
Thread-Topic: scala and groovy
Thread-Index: Ac74IOuNXdxjeltdSa2dureV5gBKnQ==
Date: Fri, 13 Dec 2013 16:32:44 +0000
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I'm still working on getting the clinical-pipeline (AggregatePlaintextUMLSP=
rocessor) 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 down=
loading models. I am working around that for now by programmatically downlo=
ading 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 lik=
e 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 e=
rror, 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 rootLoad=
er as I described above.

scope model: /C:/usr/meTAKES/using-groovy/org/apache/ctakes/assertion/model=
s/scope.model
Caught: java.lang.NoClassDefFoundError: scala/ScalaObject
java.lang.NoClassDefFoundError: scala/ScalaObject
        at org.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParse=
r.java:22)
        at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.ini=
tialize(AssertionAnalysisEngine.java:121)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_imp=
l.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_imp=
l.initialize(PrimitiveAnalysisEngine_impl.java:156)
        at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(=
AnalysisEngineFactory_impl.java:94)
        at org.apache.uima.impl.CompositeResourceFactory_impl.produceResour=
ce(CompositeResourceFactory_impl.java:62)
        at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java=
:269)
        at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramewor=
k.java:387)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl=
.java:254)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initASB(AggregateAnalysisEngine_impl.java:431)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initialize(AggregateAnalysisEngine_impl.java:185)
        at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(=
AnalysisEngineFactory_impl.java:94)
        at org.apache.uima.impl.CompositeResourceFactory_impl.produceResour=
ce(CompositeResourceFactory_impl.java:62)
        at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java=
:269)
        at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramewor=
k.java:387)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl=
.java:254)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initASB(AggregateAnalysisEngine_impl.java:431)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initialize(AggregateAnalysisEngine_impl.java:185)
        at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(=
AnalysisEngineFactory_impl.java:94)
        at org.apache.uima.impl.CompositeResourceFactory_impl.produceResour=
ce(CompositeResourceFactory_impl.java:62)
        at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java=
:269)
        at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramewor=
k.java:387)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl=
.java:254)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initASB(AggregateAnalysisEngine_impl.java:431)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_imp=
l.initialize(AggregateAnalysisEngine_impl.java:185)
        at org.uimafit.factory.AnalysisEngineFactory.createAggregate(Analys=
isEngineFactory.java:505)
        at org.uimafit.factory.AggregateBuilder.createAggregate(AggregateBu=
ilder.java:200)
        at org.uimafit.factory.AggregateBuilder$createAggregate.call(Unknow=
n Source)
        at cTAKES-with-resources.run(cTAKES-with-resources.groovy:365)
Caused by: java.lang.ClassNotFoundException: scala.ScalaObject
        ... 32 more

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