Dear cTAKES developers, I ran into new issues running a uimafit pipeline from command line. I am trying to get a basic pipeline to run using this command:
mvn exec:java -Dexec.mainClass=“org.apache.ctakes.examples.pipelines.BasicAnnotations" It runs fine in Eclipse, but it stumbles on dictionary lookup when I run from command line. The dictionary lookup is added as follows: aggregateBuilder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() ) The full error message is below, but basically it is unable to find org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml. Which does exist on my system in two places: ./ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml ./ctakes-dictionary-lookup-fast-res/target/classes/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml I noticed that when I execute the mvn exec:java command, maven downloads the jars into my maven repository. Not sure why it’s doing that — shouldn’t it be able to run everything from the project directories? Any thoughts will be greatly appreciated. Dima 28 Jun 2016 12:28:29 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml [WARNING] java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:294) at java.lang.Thread.run(Thread.java:745) Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) 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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at org.apache.ctakes.examples.pipelines.BasicAnnotations.main(BasicAnnotations.java:69) ... 6 more Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:117) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 18 more Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:114) ... 19 more [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 09:17 min [INFO] Finished at: 2016-06-28T12:28:29-05:00 [INFO] Final Memory: 104M/188M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:java (default-cli) on project ctakes-examples: An exception occured while executing the Java class. null: InvocationTargetException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>): ResourceInitializationException: org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml (No such file or directory) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException Dima