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From WP Roshan <suno...@gmail.com>
Subject Exception in thread "main" org.apache.uima.util.InvalidXMLException: An import could not be resolved. No .xml file with name "desc/analysis_engine/AggregatePlaintextUMLSProcessor" was found in the class path or data path. (Descriptor: <unknown>)
Date Wed, 21 Sep 2016 07:12:13 GMT
Hi All,

I made a cTakes command line application using
"ctakes\ctakes-clinical-pipeline\src\main\java\org\apache\ctakes\clinicalpipelineClinicalPipelineWithUmls.java".
It's perfectly running at the Eclipse environment with run-time argument*.
But when I deployed it as a jar with all the dependencies I got following
exception.

"Exception in thread "main" org.apache.uima.util.InvalidXMLException: An
import could not be resolved.  No .xml file with name
"desc/analysis_engine/AggregatePlaintextUMLSProcessor" was found in the
class path or data path. (Descriptor: <unknown>) "

Note : I changed pom.xml file inside "ctakes-clinical-pipeline" directory
so that it's able to build jar with all the dependencies.

mvn clean install was successful. complete "mvn clean install" log attached
herewith for anyone's reference.

jar ran at the command prompt with argument as follows

run-time arguments*
args[0] =
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\input\MS-pubmed-1.txt
args[1] = C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\output\xmi
args[2]
= C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\output\topics\MS-pubmed-1-topics.txt

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.
C:\Users\WPRoshan>cd
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\target

C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\target>java -classpath
%CTAKES_HOME%\desc;%CTAKES_HOME%\resources;%CTAKES_HOME%\lib\*
-Dlog4j.configuration=file:\

%CTAKES_HOME%\config\log4j.xml -Xms512M -Xmx3g -jar
ctakes-clinical-pipeline-3.2.0-SNAPSHOT-jar-with-dependencies.jar
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\input\MS-

pubmed-1.txt
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\output\xmi
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\output\topics\MS-pubmed-1-topics.txt
Started org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls at Wed
Sep 21 12:03:04 IST 2016
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is  [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
Reading from directory:
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\input\MS-pubmed-1.txt
Outputting to directory:
C:\EclipsProjects\ctakes\ctakes-clinical-pipeline\data\output\xmi
Exception in thread "main" org.apache.uima.util.InvalidXMLException: An
import could not be resolved.  No .xml file with name
"desc/analysis_engine/AggregatePlaintextUMLSProcessor" was found in the

class path or data path. (Descriptor: <unknown>)
        at
org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
        at
org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineDescription(AnalysisEngineFactory.java:109)
        at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:76)


Does anybody knows how to tackle this issue ?

Thanks
W.P.Roshan
-- 
SunONE

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