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From Bandeep Singh <bsi...@phemi.com>
Subject Re: 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 Sat, 24 Sep 2016 00:11:47 GMT
cTakes 3.1.0 doesn't address the problem of using file as a resource inside
the JAR (which is what your are trying to do).
Try using 3.2.3-SNAPSHOT and see if it solves your problem (I have a
similar use case and 3.2.3-SNAPSHOT seems to be the answer)

-Bandeep

On Fri, Sep 23, 2016 at 2:42 AM, WP Roshan <sunone5@gmail.com> wrote:

> 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 <bsingh@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 <sunone5@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
>

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