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From Abraham Tom <a...@practicefusion.com>
Subject RE: Command line invocation
Date Tue, 15 Apr 2014 02:56:16 GMT
Hi 
I have confirmed that the correct resources zip file was uncompressed and deployed to the
correct path


java -jar ./lib/ctakes-clinical-pipeline-3.1.0.jar -Dctakes.umlsuser=<hidden> -Dctakes.umlspw=<hidden>
-Xms512M -Xmx1024M /opt/cTAKES-3.1.1/data /opt/cTAKES-3.1.1/data_out
Failed to load Main-Class manifest attribute from
./lib/ctakes-clinical-pipeline-3.1.0.jar

Still resolving to the same error as if it cannot find appropriate dependancies
Can this jar (ctakes-clinical-pipeline-3.1.0.jar) not be called and used on its own with file
input and output parameters 

Again this is running on a server where I do wish process 1 file at a time in an automated
fashion 

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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