Sort of good news on the scala front -- after I added the complete filename for the jars to the rootLoader statements (I had left out the "version" part of the jar names), using scala now works.
jarName = "scala-library-2.9.0.jar"; this.class.classLoader.rootLoader.addURL( new URL(libLocation + jarName) ); jarName = "sbinary_2.9.0-0.4.0.jar"; this.class.classLoader.rootLoader.addURL( new URL(libLocation + jarName) ); (not ready to post a full solution yet - pipeline did not run to completion, but at least I'm on to the next issue now) -- James -----Original Message----- From: dev-return-2314-Masanz.James=mayo....@ctakes.apache.org [mailto:dev-return-2314-Masanz.James=mayo....@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 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.groovy also now contains a desc subdirectory and an org subdirectory. mkdir inputDir groovy cTAKES-with-resources.groovy inputDir Thanks Pei! -----Original Message----- From: dev-return-2313-Masanz.James=mayo....@ctakes.apache.org [mailto:dev-return-2313-Masanz.James=mayo....@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 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
