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From Robert Spurrier <robert.spurr...@explorys.com>
Subject Re: Creating Runnable .JARs From A Subset of cTAKES Maven Modules
Date Mon, 09 Sep 2013 15:02:54 GMT
Hello Pei,

My plan is to use cTAKES source and expand upon it with additional custom
annotator modules.

So I would like a build process where I can selectively define what parts
I want to use, and then compile a jar from source with just those items
(and all their dependencies of course). In the program that runs the
pipelines, I am thinking I will use uimaFit to instantiate the objects I
need which are located in the jar, and then pass text into those objects
for processing.

Essentially I would like to have Maven build files for each of my custom
pipelines. Here's an example. My end goal is to be able to compile my LVEF
pipeline, my Discharge Summary pipeline, and my Lab Results pipeline, all
from the same set of source modules, but generate 3 different jars that
contain only the resources I need for each respective pipeline.

It seems that the general cTAKES object model is completely based around
creating the 'ctakes-clinical-pipeline'. So maybe it doesn't make sense
for me to try to shimmy my custom build files in with the cTAKES project.
What do you think?


On 9/9/13 10:38 AM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

>Hi Robert,
>Are you planning to a process to build everything from source?
>Or were you planning to have a build process that combines the ctakes-***
>jars with your custom application jars?
>> -----Original Message-----
>> From: Robert Spurrier [mailto:robert.spurrier@explorys.com]
>> Sent: Monday, September 09, 2013 9:27 AM
>> To: dev@ctakes.apache.org
>> Subject: Creating Runnable .JARs From A Subset of cTAKES Maven Modules
>> Good Morning!
>> I am trying to use cTAKES tools on a distributed computing platform. I
>> rather not ship the entire compiled cTAKES package (~1.5 Gb) out to the
>> shared cache when I only need a few annotators and their resources at a
>> time.
>> I should first mention that I am not very familiar with Maven. I
>> upgraded cTAKES from v 2.5.0, where I was configuring smaller pipelines
>> using ant build files. This process was cumbersome however, and I can
>> appreciate the new modular Maven project layout.  I just do not know how
>> to effectively utilize it in a way that is flexible.
>> Does anyone have any advice on how I can package subsets of cTAKES
>> annotator modules and their dependencies/resources, so  I can create
>> 'thinner' custom pipelines that are geared towards specific tasks?
>> For example, I might ultimately want a pipeline .JAR that contains the
>>tools to
>> RegEx Left Ventricular Ejection Fraction measurements from free text. In
>> such a .JAR I would not need any of the dictionary resources or negation
>> annotators, so they could be excluded.
>> It looks like I could create Maven assembly plugin descriptors to
>> these custom .JARs, but I would like to see if anyone here has any
>> advice/caveats before I pursue this route.
>> Thanks,
>> Robert Spurrier

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