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From "Wu, Stephen T., Ph.D." <Wu.Step...@mayo.edu>
Subject Re: cTAKES user interface
Date Wed, 30 Oct 2013 17:11:23 GMT
Fwiw, I've had trouble with runctakesCPE.sh classpath for projects that
are not ctakes-clinical-pipeline. The most reliable ways I know are to get
the runtime classpath are:
 1. Add it programmatically: System.getProperty("java.class.path")... Then
recompile and run.
 2. Run Eclipse in Debug mode, right click on running process, look under
Properties (don't remember exactly).
 3. Export an Ant buildfile.

Dunno if that's helpful to anyone.

stephen




On 10/30/13 11:13 AM, "Finan, Sean" <Sean.Finan@childrens.harvard.edu>
wrote:

>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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