Re: ctakes-web-rest changes [EXTERNAL]

["Miller, Timothy" <Ti...@childrens.harvard.edu>]

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 <Ga...@arisglobal.com>
Sent: Friday, December 21, 2018 3:13 AM
To: 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 <Ti...@childrens.harvard.edu>
Sent: Friday, December 21, 2018 1:54 AM
To: 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

This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.

Re: ctakes-web-rest changes [EXTERNAL]

[gandhi rajan <ga...@gmail.com>]

This should be really handy Tim. Will have a look on this once my setup is
ready. I m still awaiting for my new personal PC to up and running.

Thanks again.

Regards,
Gandhi

On Thursday, January 24, 2019, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> 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: <de...@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<ma...@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<ma...@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
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> If you are not the named addressee you should not disseminate, distribute
> or copy this e-mail. Please notify the sender or system manager by email
> immediately if you have received this e-mail by mistake and delete this
> e-mail from your system. If you are not the intended recipient you are
> notified that disclosing, copying, distributing or taking any action in
> reliance on the contents of this information is strictly prohibited and
> against the law.
>
>
>
>
>
>
>

-- 
Regards,
Gandhi

"The best way to find urself is to lose urself in the service of others !!!"

Re: ctakes-web-rest changes [EXTERNAL]

["Miller, Timothy" <Ti...@childrens.harvard.edu>]

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: <de...@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<ma...@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 <Ga...@arisglobal.com>>
Sent: Friday, December 21, 2018 3:13 AM
To: dev@ctakes.apache.org<ma...@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 <Ti...@childrens.harvard.edu>>
Sent: Friday, December 21, 2018 1:54 AM
To: dev@ctakes.apache.org<ma...@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

This email and any files transmitted with it are confidential and intended
solely for the use of the individual or entity to whom they are addressed.
If you are not the named addressee you should not disseminate, distribute
or copy this e-mail. Please notify the sender or system manager by email
immediately if you have received this e-mail by mistake and delete this
e-mail from your system. If you are not the intended recipient you are
notified that disclosing, copying, distributing or taking any action in
reliance on the contents of this information is strictly prohibited and
against the law.

Re: ctakes-web-rest changes [EXTERNAL]

[gandhi rajan <ga...@gmail.com>]

Thanks Tim. Great work.

On Friday, December 21, 2018, Miller, Timothy <
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 <Ga...@arisglobal.com>
> Sent: Friday, December 21, 2018 3:13 AM
> To: 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 <Ti...@childrens.harvard.edu>
> Sent: Friday, December 21, 2018 1:54 AM
> To: 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
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> If you are not the named addressee you should not disseminate, distribute
> or copy this e-mail. Please notify the sender or system manager by email
> immediately if you have received this e-mail by mistake and delete this
> e-mail from your system. If you are not the intended recipient you are
> notified that disclosing, copying, distributing or taking any action in
> reliance on the contents of this information is strictly prohibited and
> against the law.
>


-- 
Regards,
Gandhi

"The best way to find urself is to lose urself in the service of others !!!"