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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu.INVALID> on 2022/04/07 18:40:49 UTC
Re: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline [EXTERNAL]
Hi Ankit,
Did you add CuiListFileWriter to your pipeline? I don't think that it is in the default pipeline.
As long as you are running the latest code it should be present.
It is in ctakes-core org/apache/ctakes/core/cc/CuiListFileWriter.java
It was added to ctakes on 02/14/2018.
Sean
________________________________________
From: Anand, Ankit (Campus) <an...@uab.edu>
Sent: Thursday, April 7, 2022 2:29 PM
To: dev@ctakes.apache.org
Subject: RE: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline [EXTERNAL]
* External Email - Caution *
Thank you, the Issue below is resolved, but I am getting this error message. Is this something related with my setup.
I have setup ctakes on server which basically runs on linux. Since the build did not give any error and was successful, I think the setup should be fine.
[ankitk@login004 trunk]$ bin/runClinicalPipeline.sh -i ./inputdir --xmiOut ./outputdir
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].
07 Apr 2022 10:19:20 ERROR PiperFileRunner - MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for CuiListFileWriter
Thanks.
-Ankit
Best,
Ankit Anand
Graduate Assistant | Informatics Institute, UAB
Department of Computer Science, UAB
University of Alabama at Birmingham
Contact - (205) 585-7029
-----Original Message-----
From: Anand, Ankit (Campus)
Sent: Thursday, April 7, 2022 11:37 AM
To: pabramowitsch@gmail.com
Cc: dev@ctakes.apache.org
Subject: RE: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline
Thank you so much Peter :)
My Issue is resolved. I was giving -xmiOut in my command line instead of --xmiOut which was causing the problem.
Best,
Ankit Anand
Graduate Assistant | Informatics Institute, UAB Department of Computer Science, UAB University of Alabama at Birmingham Contact - (205) 585-7029
-----Original Message-----
From: Peter Abramowitsch <pa...@gmail.com>
Sent: Thursday, April 7, 2022 1:30 AM
To: dev@ctakes.apache.org
Subject: Re: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline
Hi Ankit,
One normally doesn't put the input and output folders in the trunk area, but I just tried it and works fin ....
r 2022 08:15:53 INFO FinishedLogger - Run Start Time: Thu
Apr 07 08:14:53 CEST 2022
07 Apr 2022 08:15:53 INFO FinishedLogger - Processing Start Time:
Thu Apr 07 08:15:18 CEST 2022
07 Apr 2022 08:15:53 INFO FinishedLogger - Processing End Time:
Thu Apr 07 08:15:53 CEST 2022
07 Apr 2022 08:15:53 INFO FinishedLogger - Initialization Time Elapsed:
24 seconds
07 Apr 2022 08:15:53 INFO FinishedLogger - Processing Time Elapsed:
35 seconds
07 Apr 2022 08:15:53 INFO FinishedLogger - Total Run Time Elapsed: 1
minutes, 0 seconds
.....
Your error message is complaining about your *command line option for the input folder.* That it is missing and that other args it's finding are unexpected.
So my guess is that your command line is not exactly as you have written.
For instance, the input folder has a space and a hyphen its name
Having a argument of -i input -folder instead of -i input-folder would
cause an error like yours. I tried that and I get your error
Option must have a value: [--option_u -u value] Option must have a value: [--option_t -t value] at
com.lexicalscope.jewel.cli.ValidationErrorBuilderImpl.validate(ValidationErrorBuilderImpl.java:64)
at
com.lexicalscope.jewel.cli.validation.ArgumentValidatorImpl.finishedProcessing(ArgumentValidatorImpl.java:104)
at
com.lexicalscope.jewel.cli.ArgumentCollectionBuilder.processArguments(ArgumentCollectionBuilder.java:129)
at
com.lexicalscope.jewel.cli.AbstractCliImpl.parseArguments(AbstractCliImpl.java:42)
at com.lexicalscope.jewel.cli.CliFactory.parseArguments(CliFactory.java:67)
at
org.apache.ctakes.core.pipeline.PiperFileRunner.run(PiperFileRunner.java:39)
at
org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:30)
Peter
On Thu, Apr 7, 2022 at 1:46 AM Anand, Ankit (Campus) <an...@uab.edu> wrote:
> Hi,
>
> I installed developer’s version of ctakes and I was able to build it
> successfully.
>
> Now, when I try to run the the default Clinical pipeline using command
> –
>
> bin/runClinicalPipeline.sh -i input --xmiOut output --user ankitk
> --key umlsAPIKey
>
> I am inside trunk directory which have bin, input where I have stored
> the file to process and output directories
>
> I am getting an error message –
>
> 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 INFOlog4j: 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 INFOlog4j: 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 INFOlog4j: 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].Exception
> in thread "main" com.lexicalscope.jewel.cli.ArgumentValidationException:
> Option must have a value: [--inputDir -i value] : path to the
> directory containing the clinical notes to be processed.Option must have a value:
> [--option_x -x value]Option must have a value: [--option_m -m
> value]Unexpected Option: OOption must have a value: [--option_u -u
> value] at
> com.lexicalscope.jewel.cli.ValidationErrorBuilderImpl.validate(Validat
> ionErrorBuilderImpl.java:64)
> at
> com.lexicalscope.jewel.cli.validation.ArgumentValidatorImpl.finishedPr
> ocessing(ArgumentValidatorImpl.java:104)
> at
> com.lexicalscope.jewel.cli.ArgumentCollectionBuilder.processArguments(
> ArgumentCollectionBuilder.java:129)
> at
> com.lexicalscope.jewel.cli.AbstractCliImpl.parseArguments(AbstractCliI
> mpl.java:42) at
> com.lexicalscope.jewel.cli.CliFactory.parseArguments(CliFactory.java:6
> 7)
> at
> org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.j
> ava:27)
>
> Can you please help me fix this!
>
> -Ankit.
>
> Best,
>
> Ankit Anand
> Graduate Assistant | Informatics Institute, UAB<
> https://urldefense.com/v3/__https://www.uab.edu/medicine/informatics/__;!!NZvER7FxgEiBAiR_!6DfFybCftuc_Yfnyx9IPjHyD0eKcLPqzaoADyG5S3HI1fIQmbKzW1akK1j8R9N9jFmoOgGlJ4L8$ >
> Department of Computer Science, UAB<
> https://urldefense.com/v3/__https://www.uab.edu/cas/computerscience/__;!!NZvER7FxgEiBAiR_!6DfFybCftuc_Yfnyx9IPjHyD0eKcLPqzaoADyG5S3HI1fIQmbKzW1akK1j8R9N9jFmoOYs_hzhs$ >
> University of Alabama at Birmingham
>
>