ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: cTAKES user interface
Date Wed, 30 Oct 2013 15:05:16 GMT
I'll paste Pan's reply to my email here so it shows within the same thread:

Hi all,

Thank you so much for your reply. Yes I was trying to start it faster when I run it repeatedly.
Your emails help me a lot. I really appreciate it. Thanks.

Best,
Pan

-----Original Message-----
From: dev-return-2158-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2158-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of Masanz, James J.
Sent: Wednesday, October 30, 2013 9:28 AM
To: 'dev@ctakes.apache.org'; Pan Teng
Subject: RE: cTAKES user interface


Hi Pan,

Is your interest in a command line because you are unable to open a GUI on your display, or
is it for other reason, such as able to start it faster when you run repeatedly? Understanding
why you are asking for a command line interface might help us make sure we address the root
of the question.

There is a class that will run one of the pipelines from the command line without a gui and
put the xml output into a directory. 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
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls

For now that might be a start. 


All, 
I don't think the class I mentioned above is documented anywhere other than some brief comments
at the start of the class. Maybe it could be a start of something simple that is command line
driven until we get something with groovy written.  Otherwise if a simpler interface (GUI)
is needed than the UIMA-provided CPE/CVD GUIs (rather than strictly command line), perhaps
our own GUI with some defaults would do a better job address new users.

-- James

-----Original Message-----
From: dev-return-2154-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2154-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of Miller, Timothy
Sent: Tuesday, October 29, 2013 8:56 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
>


Mime
View raw message