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From Pei Chen <chen...@apache.org>
Subject Re: cTakes question
Date Wed, 21 Jan 2015 20:40:20 GMT
[+dev]
Yu,
Yes, you can run it from the command line in many ways.
1) You can write a Java class that does it for you.  Similar to
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java

2) Run the CPE (Collection Processing Engine) via command line.
I would suggest running it once via the CPE GUI first, then save the
configuration to be run via command line.
I would suggest using [CollectionReaderHere] [
*AggregatePlaintextFastUMLSProcessor*.xml] [CasConsumerHere] instead
of AggregateCdaUMLSProcessor
for your CPE configuration.

Example of running the CPE from command line: java <copyyourargumentshere>
org.apache.uima.examples.cpe.SimpleRunCPE <path_to_your_cpe.xml>




On Wed, Jan 21, 2015 at 1:25 PM, Liang, Yu <Yu.Liang@nyumc.org> wrote:

>  Dear Pei,
>
>  I have a question about cTakes. Our purpose is to use cTakes to
> identified UMLS concepts from our medical notes which are about 4000 notes
> in total and all are free-text.
>
>  In order to put cTakes into our final pipeline, we want to find a way to
> run the notes and get the output by command line not GUI. Is there any way
> we can do that? I am not Java person, it is very hard to me to play around
> myself. I am going to use the “AggregateCdaUMLSProcessor” analysis engine
> . So if you could give me a clue, really appreciate that. I guess the
> command line will contain many parameters, like .jar files to be run,
> right?
> I am very confused where to find them, and if I find them, how to decide
> which to be put in the command line in our case , for example, we use
> AggregateCDAUMLSProcessor?
>
>  Thanks again.
> Hope to hear from you very soon.
>
>
>
>
>  Yu Liang
>
>
>
>
>
>
>
>

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