Mailing-List: contact dev-help@ctakes.apache.org; run by ezmlm
Precedence: bulk
Reply-To: dev@ctakes.apache.org
Received-SPF: pass (athena.apache.org: domain of atom@practicefusion.com
 designates 207.46.163.235 as permitted sender)
From: Abraham Tom <atom@practicefusion.com>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: Command line invocation
Thread-Topic: Command line invocation
Thread-Index: Ac9WZw8CdP6WNlhSRWy3wLi90Vjz5gArM+gwAAiX2vA=
Date: Sun, 13 Apr 2014 16:48:32 +0000
Message-ID: 
 <d4874b8f12f7414582928f7f84199063@DM2PR07MB463.namprd07.prod.outlook.com>
References: 
 <ec2e87449b5243f09722131575a61fdb@DM2PR07MB463.namprd07.prod.outlook.com>
 <6e55ab$8l34tf@ironport10.mayo.edu>
In-Reply-To: <6e55ab$8l34tf@ironport10.mayo.edu>
Accept-Language: en-US
Content-Language: en-US
received-spf: None (: practicefusion.com does not designate permitted sender
 hosts)
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable
MIME-Version: 1.0

Thanks for the information

I was on the developer version, but now I have reverted to the user version=
=20

I reinstalled cTakes, specifically apache-ctakes-3.1.0-bin.tar.gz and follo=
wed the instructions from https://cwiki.apache.org/confluence/display/CTAKE=
S/cTAKES+3.1+User+Install+Guide=20

Then I tried to execute the following=20
java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/  -Xm=
s512M -Xmx1024M org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls

and I got the following message
Exception in thread "main" org.apache.uima.resource.ResourceInitializationE=
xception

Then I tried to invoke the jar intself

java -jar  -Xms512M -Xmx1024M ./lib/ctakes-clinical-pipeline-3.1.0.jar=20

but I got the following error
Failed to load Main-Class manifest attribute from
./lib/ctakes-clinical-pipeline-3.1.0.jar


Groovy is an option if I there are instructions on how to use it
I would not mind helping to build those instructions to invoke specific cla=
sses

Best regards,

Abraham Tom
____________________________
Abraham Tom
Data Warehouse Engineer
=20
-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]=20
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 classpa=
th within runctakesCVD.bat

Or if you are open to using groovy, take a look at the scripts directory wi=
thin 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 installe=
d the developer cTakes.   This invocation is done via the following command=
 line

java -verbose -cp "/opt/cTAKES-3.1.1/ctakes-clinical-pipeline/target/classe=
s;/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 a=
round it and automate the processing of various docs.

This should be possible shouldn't it?


Best regards,

Abraham Tom