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

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