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(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.main(PiperFileRunner.java:27)
Can you please help me fix this!
-Ankit.
Best,
Ankit Anand
Graduate Assistant | Informatics Institute,
UAB<https://www.uab.edu/medicine/informatics/>
Department of Computer Science, UAB<https://www.uab.edu/cas/computerscience/>
University of Alabama at Birmingham
