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 [a...@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.ja...@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:a...@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
