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Posted to dev@ctakes.apache.org by WP Roshan <su...@gmail.com> on 2016/09/21 07:12:13 UTC
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: )
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
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: )
Posted by Bandeep Singh <bs...@phemi.com>.
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 <su...@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 <bs...@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 <su...@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
>
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: )
Posted by WP Roshan <su...@gmail.com>.
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 <bs...@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 <su...@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
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: )
Posted by Bandeep Singh <bs...@phemi.com>.
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 <su...@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
>