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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: cTAKES user interface
Date Wed, 30 Oct 2013 16:13:30 GMT
Well, thanks to my not checking the utils pom (or building trunk since I'm currently still
in incubator), I made Jenkins angry.  Instead of adding uima as a dependency to ctakes-utils,
I moved the cpe cli to ctakes-core.  I hope that works.  My apologies to anybody that checked
out in the last hour.

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Wednesday, October 30, 2013 11:20 AM
To: Lingren, Todd; dev@ctakes.apache.org
Subject: RE: cTAKES user interface

> Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei
described.
I am in this group, and I have written a very simple cli cpe runner.  As Pei mentioned:

>>> The problem is that most of us who are already familiar with the nitty gritty
are probably doing this with some sort of custom scripts or solution.
The class that I have is probably not doing anything that others are not - in fact, I'm sure
that I used somebody else's code as a template as I am not that familiar with Senior Nitty
Gritty.

I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to ctakes-utils in package
...utils.cpe   It was so quick 'n dirty that there isn't any documentation, no logging, etc.
but it gets the job done.  It takes a path to a cpe.xml file as an argument and simply runs
the pipeline specified therein.  

I suggest that James has the correct startup approach:
> However you need to have a classpath set properly. To accomplish that, 
>you could try copying runctakesCPE.bat or runctakesCPE.sh and within 
>the script file, replacing org.apache.uima.tools.cpm.CpmFrame with 
>[CLASS TO CALL]

To the best of my knowledge the easiest way to create the cpe.xml file is probably to run
through the gui once, setting up the pipeline and saving the xml - but run through at least
once to make certain that the pipeline works.

Enjoy,
Sean

-----Original Message-----
From: Lingren, Todd [mailto:Todd.Lingren@cchmc.org]
Sent: Wednesday, October 30, 2013 9:52 AM
To: dev@ctakes.apache.org
Cc: Finan, Sean
Subject: RE: cTAKES user interface

Hi all,
Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described.
I've been using it and would be happy to provide some user guides if he provides the class,etc.


Todd Lingren
Biomedical Informatics
Cincinnati Children's Hospital
Todd.Lingren@cchmc.org
513-803-9032


-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, October 29, 2013 9:56 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES user interface

Thanks William and Richard, those are both really excellent pointers.
Tim

On 10/29/2013 07:58 PM, William Karl Thompson wrote:
> Nice! 
>
> +1 for Groovy. It's like being able to program in Python again.
>
> -----Original Message-----
> From: Richard Eckart de Castilho [mailto:rec@apache.org]
> Sent: Tuesday, October 29, 2013 5:49 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES user interface
>
> Maven allows to do marvelous things on the CLI, provided you throw in an additional component:
Groovy.
>
> We did some amazing self-contained Groovy scripts with uimaFIT and 
> DKPro Core which you might find interesting
>
>   http://code.google.com/p/dkpro-core-asl/wiki/DKProGroovyCookbook
>
> -- Richard
>
> On 29.10.2013, at 23:09, "Miller, Timothy" <Timothy.Miller@childrens.harvard.edu>
wrote:
>
>> I think this is also an area where Maven integration was a small step backwards (I
greatly appreciate the steps forward it allowed). I used to run stuff from the command line
and in scripts more often but it's slightly less straightforward setting up the classpath
with maven -- before you could put a simple java -cp lib/*.jar <class name> in a script,
now I'm not sure how to go about it using maven. I'm sure there's a way, but I am afraid of
falling down the maven rabbit hole.
>> Tim
>>
>>
>> On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote:
>>
>>> +1
>>> Pan, the short answer is yes- it can be done in CLI.  
>>> The problem is that most of us who are already familiar with the nitty gritty
are probably doing this with some sort of custom scripts or solution.
>>> Cc' the dev group to get a fresh perspective; not sure what the easiest would
be-- run the CPE via command line with default input/output directories or running a Driver
Main Class as part of examples.
>>>
>>> --Pei
>



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