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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject Re: running pipeline from command line
Date Wed, 29 Jun 2016 13:16:59 GMT
Hi Peter,

This helps, thank you.

I also found a way to get the full command-line that Eclipse uses to run a class. (I believe
Tim Miller discovered this a while ago too, but I had to re-discover this now).

http://stackoverflow.com/questions/2276219/can-i-run-from-command-line-program-created-by-eclipse

"Go to the Debug perspective, and select the program you just run (where it says Termintated,
exit value... in the Debug tab) Right click, and choose Properties, there you can see the
whole command line command that was launched by eclipse.”

It would still be nice to figure out how to run using maven (i.e. without having to specify
the classpath manually).

Thank you everybody who helped with this issue.

Dima

> On Jun 28, 2016, at 13:32, Abramowitsch, Peter <pabramowitsch@hearst.com> wrote:
> 
> Hi Dima
> 
> Personally I hate Maven because of how it obscures classpaths and
> dependencies (even though it purports to make that easier).   My use case
> is a little different than yours, but when I launch a little pipeline from
> the command line, it looks as simple as this:
> 
> Cd into the top of my application directory
> export MSPK=$PWD
> 
> /usr/bin/java -cp 
> "${MSPK}/classes":"${MSPK}/desc/":"${MSPK}/resources/":"${MSPK}/lib/*"
> -Dlog4j.configuration=file:${MSPK}/config/log4j.xml
> -Dctakes.umlsuser=xxxxx  -Dctakes.umlspw=xxxx  -Xms512M -Xmx3g
> com.hbm.Main
> 
> 
> ** Desc being a tree where I have recursively copied all the descs from
> individual ctakes packages
> ** Resources being a tree where I have recursively copied all the resource
> from individual ctakes packages
> ** Lib contaning the complete set of Ctakes jars plus their supporting
> jars.
> 
> My main starts up a REST server that loads a pipeline and connects
> external requests to it.
> 
> 
> Hope this helps
> Peter
> 
> 
> 
> On 6/28/16, 11:22 AM, "Dligach, Dmitriy" <ddligach@luc.edu> wrote:
> 
>> 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=³org.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/d
>> ictionary/lookup/fast/cTakesHsql.xml
>> 
>> ./ctakes-dictionary-lookup-fast-res/target/classes/org/apache/ctakes/dicti
>> onary/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 it¹s doing that ‹
>> shouldn¹t 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(DelegatingMethodAccessorIm
>> pl.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.initiali
>> zeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>> 
>> 	at 
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initiali
>> ze(PrimitiveAnalysisEngine_impl.java:156)
>> 
>> 	at 
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEn
>> gineFactory_impl.java:94)
>> 
>> 	at 
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Composi
>> teResourceFactory_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.initiali
>> zeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> 
>> 	at 
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initiali
>> ze(AggregateAnalysisEngine_impl.java:185)
>> 
>> 	at 
>> org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEng
>> ineFactory.java:711)
>> 
>> 	at 
>> org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuil
>> der.java:207)
>> 
>> 	at 
>> org.apache.ctakes.examples.pipelines.BasicAnnotations.main(BasicAnnotation
>> s.java:69)
>> 
>> 	... 6 more
>> 
>> Caused by: org.apache.uima.resource.ResourceInitializationException
>> 
>> 	at 
>> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initiali
>> ze(AbstractJCasTermAnnotator.java:117)
>> 
>> 	at 
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initiali
>> zeAnalysisComponent(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:6
>> 1)
>> 
>> 	at 
>> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initiali
>> ze(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] 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confl
>> uence_display_MAVEN_MojoExecutionException&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCn
>> tw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=ixrQpER8b5VvscuhN0yquuo
>> ogfKG8tgJlDNU03kOwA4&s=VLcUCqZV24XNMC6542XwuaGC8QXo-_x0nI1edoVpUvc&e=
>> 
>> 
>> 
>> Dima
>> 
>> 
>> 
> 


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