Cool -----Original Message----- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 11:50 AM To: dev@ctakes.apache.org Subject: RE: cTAKES user interface
I would add that in our environment we use this command line cpe runner in on a large cluster over many folders. I have a small shell script that I've written to write a new cpe.xml for each folder in a parent folder. In this method we are able to achieve a pretty efficient pseudo-parallelization of ctakes. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:15 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.ling...@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.ling...@cchmc.org 513-803-9032 -----Original Message----- From: Miller, Timothy [mailto:timothy.mil...@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:r...@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.mil...@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 >
