Re: ctakes gui [EXTERNAL]
Thanks Sean I am looking for a way to get cTAKES run for a dataset and get the ourput in a database. not sure if such interface exists ( even if it is a command lines ) or it requires new development. Thanks again for your help On Friday, 13 December 2019, 12:33:42 am AEDT, Finan, Sean wrote: Hi Akram, That was never released with ctakes. It is in ctakes sandbox as a "proof of concept" project. https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/ The original author Pei Chen might be able to say more. It has nothing to do with the released "ctakes-gui" module, which contains completely different tools and reusable ctakes-oriented gui components. If you are looking for a web solution, there is a ctakes-rest-server project that might be useful. Sean From: Akram Sent: Thursday, December 12, 2019 6:11 AM To: dev@ctakes.apache.org Subject: ctakes gui [EXTERNAL] Warning: Email originated outside Boston Children's. Don't click links/attachments unless you know sender & content seems safe. ** Hi I have been trying to get ctakes GUI working as the instructions in herehttps://community.i2b2.org/wiki/display/NLPCTAKES/NLP+cTakes+Home I could not find any website that has ctakesgui.war I thought it must be the same project in ctakes open source which is ctakes-gui but this project ctakes-gui does not have any .jsp or .html files. I wonder if there are update instructions of how to get ctakes gui running as indicated. Thanks
Re: ctakes gui [EXTERNAL]
Hi Akram, That was never released with ctakes. It is in ctakes sandbox as a "proof of concept" project. https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/ The original author Pei Chen might be able to say more. It has nothing to do with the released "ctakes-gui" module, which contains completely different tools and reusable ctakes-oriented gui components. If you are looking for a web solution, there is a ctakes-rest-server project that might be useful. Sean From: Akram Sent: Thursday, December 12, 2019 6:11 AM To: dev@ctakes.apache.org Subject: ctakes gui [EXTERNAL] Warning: Email originated outside Boston Children's. Don't click links/attachments unless you know sender & content seems safe. ** Hi I have been trying to get ctakes GUI working as the instructions in herehttps://community.i2b2.org/wiki/display/NLPCTAKES/NLP+cTakes+Home I could not find any website that has ctakesgui.war I thought it must be the same project in ctakes open source which is ctakes-gui but this project ctakes-gui does not have any .jsp or .html files. I wonder if there are update instructions of how to get ctakes gui running as indicated. Thanks
ctakes gui
Hi I have been trying to get ctakes GUI working as the instructions in herehttps://community.i2b2.org/wiki/display/NLPCTAKES/NLP+cTakes+Home I could not find any website that has ctakesgui.war I thought it must be the same project in ctakes open source which is ctakes-gui but this project ctakes-gui does not have any .jsp or .html files. I wonder if there are update instructions of how to get ctakes gui running as indicated. Thanks
Re: ctakes gui
Hi Ben, I think the ctakes-gui in the sandbox area is really outdated and hasn't been maintained in a long time (hence in sandbox). But there was a old thread [1] that you may find useful. [1] https://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3cCAPUoHuEj1aFC6PQG=jlkgsoquutq17l0mhmdpwvatd6uwqg...@mail.gmail.com%3e On Thu, Feb 18, 2016 at 12:56 PM, Ben Yu <ben...@pharm.utah.edu> wrote: > Hi ctakes group, > Is the ctakes gui actively maintained? I downloaded it and followed Pei's > installation guide (not entirely because some of the instructions don't seem > to apply), and after some maneuvering I had it up and running with tomcat7. > When I try to bring the app up http://localhost:8080/ctakesgui/, the > login.html page came back blank. I noticed that the login.jsp (which seems to > be the file Spring mvc mapped to for login.html) used some external > javascript files and one of them, i18n.js is missing. I have not used it at > all and not sure what it is. Is that the reason why I got the blank page? Am > I missing some other front end stuff? The body tag does not have any content > in it. > > Thanks, and appreciate any help. > > Ben Yu > Software Design Engineer > College of Pharmacy, University of Utah > 801-587-7751 >
RE: cTAKES GUI for I2B2
Hello Timothy - I have posted the screenshots here: https://drive.google.com/file/d/0B4sR85qs377yTThzWHM4YXlxOFE/view?usp=sharing Kindly advise as soon as possible. Many thanks, Sekhar H. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, August 04, 2015 4:14 PM To: dev@ctakes.apache.org Subject: RE: cTAKES GUI for I2B2 Can you post the screenshot somewhere it might be linked to? I don't know if we can post image attachments to the dev list. Thanks Tim From: Hari, Sekhar [sekhar.h...@cgi.com] Sent: Monday, August 03, 2015 10:35 PM To: chen...@apache.org; dev@ctakes.apache.org; u...@ctakes.apache.org Subject: RE: cTAKES GUI for I2B2 Hello there - Please, can somebody advise me on my question below? Thanks, Sekhar H. From: Hari, Sekhar Sent: 31 July 2015 15:02 To: chen...@apache.org Subject: cTAKES GUI for I2B2 Hello Pei - Can you please assist me. I am doing a few experiments using I2B2. There is a requirement for me to use cTAKES for reading clinical notes and to extract the key terminologies from the notes so it can be inserted into I2B2. I found cTAKES GUI for I2B2 and installed it. While trying to read a sample clinical note, though seemingly the pipelines run, I don't see any useful output in the Results section of the GUI. I have included a screenshot below. The Results page says language: x-unspecified. Not sure what is going wrong. Am I doing anything wrong or missing any configurations? Also, I have included the NLP processors that am using to do this read and extract. You can see this screenshot at the bottom of this email. Hope you can help. Many thanks, Sekhar H.
Re: cTAKES GUI for I2B2
Sekhar, That application was done as a prototype/POC many years ago and hasn't been actively maintained (hence in sandbox). It seems from your screenshot that you have it up and running though. Would you mind attaching the log files as well? --Pei On Wed, Aug 5, 2015 at 4:41 AM, Hari, Sekhar sekhar.h...@cgi.com wrote: Hello Timothy - I have posted the screenshots here: https://drive.google.com/file/d/0B4sR85qs377yTThzWHM4YXlxOFE/view?usp=sharing Kindly advise as soon as possible. Many thanks, Sekhar H. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, August 04, 2015 4:14 PM To: dev@ctakes.apache.org Subject: RE: cTAKES GUI for I2B2 Can you post the screenshot somewhere it might be linked to? I don't know if we can post image attachments to the dev list. Thanks Tim From: Hari, Sekhar [sekhar.h...@cgi.com] Sent: Monday, August 03, 2015 10:35 PM To: chen...@apache.org; dev@ctakes.apache.org; u...@ctakes.apache.org Subject: RE: cTAKES GUI for I2B2 Hello there - Please, can somebody advise me on my question below? Thanks, Sekhar H. From: Hari, Sekhar Sent: 31 July 2015 15:02 To: chen...@apache.org Subject: cTAKES GUI for I2B2 Hello Pei - Can you please assist me. I am doing a few experiments using I2B2. There is a requirement for me to use cTAKES for reading clinical notes and to extract the key terminologies from the notes so it can be inserted into I2B2. I found cTAKES GUI for I2B2 and installed it. While trying to read a sample clinical note, though seemingly the pipelines run, I don't see any useful output in the Results section of the GUI. I have included a screenshot below. The Results page says language: x-unspecified. Not sure what is going wrong. Am I doing anything wrong or missing any configurations? Also, I have included the NLP processors that am using to do this read and extract. You can see this screenshot at the bottom of this email. Hope you can help. Many thanks, Sekhar H.
RE: cTAKES GUI for I2B2
Can you post the screenshot somewhere it might be linked to? I don't know if we can post image attachments to the dev list. Thanks Tim From: Hari, Sekhar [sekhar.h...@cgi.com] Sent: Monday, August 03, 2015 10:35 PM To: chen...@apache.org; dev@ctakes.apache.org; u...@ctakes.apache.org Subject: RE: cTAKES GUI for I2B2 Hello there - Please, can somebody advise me on my question below? Thanks, Sekhar H. From: Hari, Sekhar Sent: 31 July 2015 15:02 To: chen...@apache.org Subject: cTAKES GUI for I2B2 Hello Pei – Can you please assist me. I am doing a few experiments using I2B2. There is a requirement for me to use cTAKES for reading clinical notes and to extract the key terminologies from the notes so it can be inserted into I2B2. I found cTAKES GUI for I2B2 and installed it. While trying to read a sample clinical note, though seemingly the pipelines run, I don’t see any useful output in the “Results” section of the GUI. I have included a screenshot below. The “Results” page says language: “x-unspecified”. Not sure what is going wrong. Am I doing anything wrong or missing any configurations? Also, I have included the NLP processors that am using to do this read and extract. You can see this screenshot at the bottom of this email. Hope you can help. Many thanks, Sekhar H.
RE: cTAKES GUI for I2B2
Hello there - Please, can somebody advise me on my question below? Thanks, Sekhar H. From: Hari, Sekhar Sent: 31 July 2015 15:02 To: chen...@apache.org Subject: cTAKES GUI for I2B2 Hello Pei – Can you please assist me. I am doing a few experiments using I2B2. There is a requirement for me to use cTAKES for reading clinical notes and to extract the key terminologies from the notes so it can be inserted into I2B2. I found cTAKES GUI for I2B2 and installed it. While trying to read a sample clinical note, though seemingly the pipelines run, I don’t see any useful output in the “Results” section of the GUI. I have included a screenshot below. The “Results” page says language: “x-unspecified”. Not sure what is going wrong. Am I doing anything wrong or missing any configurations? Also, I have included the NLP processors that am using to do this read and extract. You can see this screenshot at the bottom of this email. Hope you can help. Many thanks, Sekhar H. [cid:image001.png@01D0CBA1.AF2F24E0] [cid:image002.png@01D0CBA1.F968C2F0]
ctakes gui shows a blank page (nothing)
Hi I am trying to establish the gui component, and to make it work out-of-box. I have disabled firewall, and did everything else (setting the JAVA paths etc). Running the bat and sh works (on windows and mac) once it is properly setup (note, I had to change the installation of JAVA to a C:\Java\ since Program Files folder-name gets truncated). All the environment variables are properly set. Adblocks were disabled , and the browser (Firefox) works with a javascript. I do get to a login page, and I do see the favicon in the browser. However, the whole web-page appears blank. I have also tried the Tomcat option and compiling the war file. I get exactly the same results. I assume that there is a problem with a javascript since the page source has nothing much than the scripts. Am I missing some additional setting ? Thank you! Damir
