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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: Command line invocation
Date Tue, 15 Apr 2014 11:06:13 GMT
It does look like that class has hardcoded paths. There may be another pipeline that is appropriate
-- what kind of output are you looking to get from your documents?

Tim

________________________________________
From: Abraham Tom [atom@practicefusion.com]
Sent: Tuesday, April 15, 2014 12:08 AM
To: dev@ctakes.apache.org
Subject: RE: Command line invocation

Update
java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml
-Xms512M -Xmx1024M org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls /opt/cTAKES-3.1.1/data/test01.txt
/opt/cTAKES-3.1.1/data_out/

Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
        at org.cleartk.util.cr.FilesCollectionReader.initialize(FilesCollectionReader.java:251)
        at org.uimafit.component.JCasCollectionReader_ImplBase.initialize(JCasCollectionReader_ImplBase.java:57)
        at org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:71)
        at org.apache.uima.impl.CollectionReaderFactory_impl.produceResource(CollectionReaderFactory_impl.java:103)
        at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
        at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
        at org.apache.uima.UIMAFramework.produceCollectionReader(UIMAFramework.java:711)
        at org.uimafit.factory.CollectionReaderFactory.createCollectionReader(CollectionReaderFactory.java:171)
        at org.cleartk.util.cr.FilesCollectionReader.getCollectionReader(FilesCollectionReader.java:88)
        at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:56)
Caused by: java.io.IOException: file or directory /sharp-home/assertion/data/ActiveLearning/plaintext
does not exist
        ... 10 more
file or directory /sharp-home/assertion/data/ActiveLearning/plaintext

does this mean I cannot pass a directory and file in and I have to use the expected directory?

Best regards,

Abraham Tom
____________________________
Abraham Tom

-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Sunday, April 13, 2014 5:32 AM
To: 'dev@ctakes.apache.org'
Subject: RE: Command line invocation


Yes, that's possible.

You need more things on your classpath - you can take a look at the classpath within runctakesCVD.bat

Or if you are open to using groovy, take a look at the scripts directory within ctakes-core

-----Original Message-----
From: Abraham Tom [mailto:atom@practicefusion.com]
Sent: Saturday, April 12, 2014 10:55 AM
To: dev@ctakes.apache.org
Subject: Command line invocation

I am not a core java developer, I am a Hadoop data guy We are experimenting with using cTakes
and we have no Java developers in house

I am trying to invoke ClinicalPipelineWithUmls on a server where I installed the developer
cTakes.   This invocation is done via the following command line

java -verbose -cp "/opt/cTAKES-3.1.1/ctakes-clinical-pipeline/target/classes;/home/mapr/.m2/repository/org/cleartk/cleartk-util/0.9.2/cleartk-util-0.9.2.jar"
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls

but I am getting a Class not found error

I would like to invoke via command line so that I can wrap a shell script around it and automate
the processing of various docs.

This should be possible shouldn't it?


Best regards,

Abraham Tom


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