Hi Badeep,
Thank you for your feedback.Answers for your questions are highlighted
within yellow color brackets.
1) Which cTakes version are you installing ?? ( I'm using cTakes 3.1.0 ) If
its cTakes 3.2.2 , i would
recommend go for cTakes SNAPSHOT 3.2.3 , since a lot of bugs are fixed in it.
2) Also, When you put everything in a JAR (Same issue i had couple of days
back), the code should treat file as a resource inside a JAR. Pleas make
sure the piece of code that reads AggregatePlaintextUMLSProcessor should
read it as a resource and not as a file. (Do you see any "URI is
not hierarchical" error anywhere in the error logs? No )
I got some idea to resolve this from your feedback. but don't know whether
it'll works.
But anyway thanks & appreciate your help.
Thanks
Roshan
On Wed, Sep 21, 2016 at 10:30 PM, Bandeep Singh <bsi...@phemi.com> wrote:
> Hi Roshan,
>
> Couple of things here to notice.
>
> 1) Which cTakes version are you installing ?? If its cTakes 3.2.2 , i would
> recommend go for cTakes SNAPSHOT 3.2.3 , since a lot of bugs are fixed in
> it.
> 2) Also, When you put everything in a JAR (Same issue i had couple of days
> back), the code should treat file as a resource inside a JAR. Pleas make
> sure the piece of code that reads AggregatePlaintextUMLSProcessor should
> read it as a resource and not as a file. (Do you see any "URI is
> not hierarchical" error anywhere in the error logs?)
>
> The reason why its works in eclipse is because the
> AggregatePlaintextUMLSProcessor.xml file exists on the file system and not
> inside the JAR.
>
> Hope that helps!
>
> Bandeep
>
> On Wed, Sep 21, 2016 at 12:12 AM, WP Roshan <suno...@gmail.com> wrote:
>
> > Hi All,
> >
> > I made a cTakes command line application using "ctakes\ctakes-clinical-
> > pipeline\src\main\java\org\apache\ctakes\clinicalpipelineClinicalPipeli
> > neWithUmls.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
> >
>
--
SunONE
