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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: ctakes-web-rest changes [EXTERNAL]
Date Wed, 23 Jan 2019 21:51:55 GMT
I checked in some code to wrap the REST server in a docker container. The good news is, it
lets you run a ctakes rest server with a pretty simple build command that should be system
independent! The bad news is, the image is 16Gb, and it has a hard time running on a machine
with 8Gb. So this is a work in progress, but if anyone wants to try it I'd be happy to hear
how it works for you. It is in ctakes-web-rest/docker.
Just run:
docker build -t ctakes-web-rest .
from that directory, then run:
start_rest.sh
It will take a while for the server to start up because it needs to unpack the .war file and
initialize all the UIMA modules. If you run:
docker logs <container id>
you will be able to see how much progress it has made.
Once it's started you can navigate in a web browser to localhost:8080/ctakes-web-rest and
you should see it. Or from a REST client api the url will be localhost:8080/ctakes-web-rest/service/analyze

Thanks
Tim


-----Original Message-----
From: gandhi rajan <gandhirajan.n@gmail.com<mailto:gandhi%20rajan%20%3cgandhirajan.n@gmail.com%3e>>
Reply-to: <dev@ctakes.apache.org>
To: dev@ctakes.apache.org <dev@ctakes.apache.org<mailto:%22dev@ctakes.apache.org%22%20%3cdev@ctakes.apache.org%3e>>
Subject: Re: ctakes-web-rest changes [EXTERNAL]
Date: Sat, 22 Dec 2018 08:40:20 +0530


Thanks Tim. Great work.

On Friday, December 21, 2018, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.edu>>
wrote:



There is certainly no need to apologize! It's 100x easier for me to change
an existing version that runs than to write it from scratch since I don't
really know REST that well, so thanks for contributing that code. That's
the beauty of open source teams with different expertise!
Tim

________________________________________
From: Gandhi Rajan Natarajan <Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal.com>>
Sent: Friday, December 21, 2018 3:13 AM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: RE: ctakes-web-rest changes [EXTERNAL]

Hi Tim,

Thanks for taking your time out and checking this. Have left my comments
in the JIRA issue. Sorry that I could not improvise on the REST module
which is more suitable for our business needs due to lack of domain
expertise.

Regards,
Gandhi

-----Original Message-----
From: Miller, Timothy <Timothy.Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.edu>>
Sent: Friday, December 21, 2018 1:54 AM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: ctakes-web-rest changes

Hello all,
I've been trying out the ctakes-web-rest module for a project that uses
python where I wanted an easy way to send a sentence and get back some CUI
annotations. There was an issue where the returned json map was keyed by
the string of the concept, so it would only return one discovered concept
if more than one had the same string. In the course of fixing that I
noticed the code was writing the CAS to xmi, then manually parsing that
file, rather than just interrogating the JCas object, so I rewrote that as
well to use uimafit. Finally, I commented out the "full" pipeline -- it is
just too resource heavy to try to run 2 independent pipelines in parallel
on the same machine. I think the state of the module right now is suitable
for people who want to try and would make their own changes if they want
different pipelines (i.e., it's not yet shrink-wrapped) so I would prefer
it in a state with a simple pipeline that runs well.

Please take a look at the following issue with the attached patch and let
me know if there are any obvious problems.
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.
apache.org_jira_browse_CTAKES-2D529&d=DwIGaQ&c=qS4goWBT7poplM69zy_
3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=k-ebO4GxtYSuyXd6BYi7jXvTFAafL_
nm1IIPeVzHdKA&s=yHIpAw72nyKeovPpQpuIFW1AxiENG54X5iOIKTtxtto&e=

Overall, it's in nice shape and I'm excited to get it into a usable shape,
I think this is a use case that would satisfy a lot of users.

Tim

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