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(AssertionAnalysisEngine.java:121)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(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(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.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
