James, Would it be possible to also attach your script? I can try to replicate it here... --Pei
> -----Original Message----- > From: Masanz, James J. [mailto:masanz.ja...@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='org.scala-lang', module='scala- > library', version='2.9.0'), @Grab(group='org.scala-tools.sbinary', > module='sbinary_2.9.0', version='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.initialize(Ass > ertionAnalysisEngine.java:121) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize > AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize > (PrimitiveAnalysisEngine_impl.java:156) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi > 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.initAS > B(AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > e(AggregateAnalysisEngine_impl.java:185) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi > 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.initAS > B(AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > e(AggregateAnalysisEngine_impl.java:185) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi > 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.initAS > B(AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > e(AggregateAnalysisEngine_impl.java:185) > at > org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFa > 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
