Re: cTAKES user interface

2013-10-30 Thread Andrew McMurry
James: EXCELLENT suggestion. Last time I checked CTAKES was way out of date. Makes sense that one of us should play "red rover" and keep cTakes up to date. I just this moment sent a message to iDASH to start the update conversation. --Andy On Oct 30, 2013, at 8:04 AM, "Masanz, James J.

apache maven errors

2013-10-30 Thread Chen, Pei
Anyone else getting maven central errors recently? I was trying a fresh checkout and build of ctakes trunk... If using the apache parent pom 13: [INFO] Scanning for projects... Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/13/apache-13.pom [ERROR] The build could not read 1 p

Re: cTAKES user interface

2013-10-30 Thread Wu, Stephen T., Ph.D.
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,

RE: cTAKES user interface

2013-10-30 Thread Finan, Sean
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 h

RE: cTAKES user interface

2013-10-30 Thread Finan, Sean
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 fol

RE: cTAKES user interface

2013-10-30 Thread Lingren, Todd
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-parallelizati

RE: cTAKES user interface

2013-10-30 Thread Finan, Sean
> 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

Re: cTAKES user interface

2013-10-30 Thread Pan Teng
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 On Wed, Oct 30, 2013 at 11:02 AM, Pan Teng wrote: > Hi all, > > Thank you so much for your reply. Yes I was trying to st

RE: cTAKES user interface

2013-10-30 Thread Masanz, James J.
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-2

RE: cTAKES user interface

2013-10-30 Thread Masanz, James J.
Andy, You might want to talk with the folks at iDASH. They have an image with a number of NLP tools installed, but it doesn't have the latest version of cTAKES. http://idash.ucsd.edu/nlp/natural-language-processing-nlp-ecosystem Perhaps they would be open to your help with upgrading to a later

RE: cTAKES user interface

2013-10-30 Thread Masanz, James J.
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

Re: Sundry

2013-10-30 Thread Tim Miller
Thanks for bumping this Pei, it reminds me I meant to respond to it. The OPQRST does sound like a great ML project. At a glance I might think a sequence model over sentences (like a CRF) would be a good model. But I'm wondering what the end use case is? Is it for teaching OPQRST to new clinicia

RE: Sundry

2013-10-30 Thread Chen, Pei
Hi John, I was away for a little bit and finally got a chance to catch up on emails... > 2) I work for the DoD and have latched on to several IRB approved projects > within that community where Ill be using cTakes, though minimally at first. > This is just a statement, a bug in the ear of the comm

RE: cTAKES user interface

2013-10-30 Thread Lingren, Todd
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