Hi, Welcome to the cTAKES community.
I can at least help out with the "ArgumentValidationException: Unexpected trailing value" error. It indicates that you're missing the *-p* parameter. To run a piper from a command line using the batch file, you would use -p like this bin\runPiperFile.bat *-p* C:\Users\dwu\Documents\test\piper\mypiper.piper The following page lists the other parameters for runPiperFile.bat https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files Hope this helps, James On Thu, Nov 30, 2023 at 9:25 AM Wu, Dee H. (HSC) <[email protected]> wrote: > > Dear community > > This is my first email to this group. Hope you can help? What I’d like to > do is have a one pass approach to doing what I have to click through on > runctakesCVD.bat *I need *HELP with making analyzing text with > AggregatePlaintextUMLSProcessor.xml a script instead of manually clicking > lots of files using piper?] > > Here’s* what I do now (MANUALLY).* > > 1. > > From my base directory: C:\Users\dwu\Documents\apache-ctakes-4.0.0.1 > bin\runctakesCVD.bat > > desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml > > (this loads the engine from command line) > > 1. > > read in the text file (too bad that cant be command line implemented, > didn’t want to touch the java at this point) > 2. > > hit control-R (and/or run -> run > AggregatePlaintextUMLSProcessor.xml) from the men > 3. > > Then I write out the xmi file (see visuals) > > > > > > > > > > Wish this was Automated > > > > > > 1. > > Heres what I run > bin\runPiperFile.bat C:\Users\dwu\Documents\test\piper\mypiper.piper > > Ideally it should do what > > desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml > ‘ > > > > does > > *Here’s my piper:* > > // *** Piper File *** > > // Created by DWU > > // on November 19, 2023 > > // Text Files Reader > > // Reads document texts from text files specified in a provided list. > > # files The text files to be loaded > > reader > org.apache.ctakes.core.cr.TextReader > files=C:\Users\dwu\Documents\test\input_dir\inputsample.txt > > > > // Load a simple token processing pipeline from another pipeline file > > load DefaultTokenizerPipeline.piper > > > > // Add non-core annotators > > add ContextDependentTokenizerAnnotator > > addDescription POSTagger > > > > // Add Chunkers > > load ChunkerSubPipe.piper > > > > // Default fast dictionary lookup > > add DefaultJCasTermAnnotator > > > > // Add Cleartk Entity Attribute annotators > > load AttributeCleartkSubPipe.piper > > > > // XMI Writer > > // Writes XMI files with full representation of input text and all > extracted information. > > # OutputDirectory Output directory to write xmi files > > add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes > OutputDirectory=C:\Users\dwu\Documents\test\output_dir > > > > *Here’s the output:* > > 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]. > > Exception in thread "main" > com.lexicalscope.jewel.cli.ArgumentValidationException: Unexpected trailing > value (C:\Users\dwu\Documents\test\piper\mypiper.piper) > > 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) > > > > PROBLEM 1: > > It doesn’t run (broken > > > > Problem 2: its not doing what AggregatePlaintextUMLSProcessor > > > > Dee H. Wu, Ph.D. > > Professor & Chief, Technology Applications & Translational Research > > Department of Radiological Sciences > > Garrison Tower Room 3258 > > 940 NE 13th Street > > Stanton L. Young > > University of Oklahoma Health Sciences Center > > Oklahoma City, OK 73104 > > Ph: 405-271-8001 x 35405 (Lab) > > Ph: 405-596-2867 (Mobile - Best) > > > > Ph: 405-271-8001x46993 (Office) > > Fax: (405) 271-3462 > > Research Page: http://limes3.ouhsc.edu/deewu > > Direction Maps: (see footer above) > > email: [email protected] > >
