RE: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Gandhi Rajan Natarajan 
Matthew,

Looking forward to hear from you. Please let me know if there are any changes 
required to make the rest service more superior and performance effective. 
Cheers.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Sunday, October 29, 2017 9:30 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Sean,

Ghandi and I have met and we both agreed that his solution is superior to the 
one I was working on. Therefore, I will be helping to see this project through 
to the end so we can get it into the codebase!

Here are the remaining work items that I will be spending time on:

   1. Get it running (I'm using Linux Mint)
   2. Test it out (including stress tests)
   3. Automate it to run in Docker (just need UMLS credentials)
   4. Make a call to
   https://github.com/GoTeamEpsilon/cTAKES-Concept-Mention-Parser to get a
   nice JSON payload that is easy to traverse (this can be an optional switch,
   of course - I believe it may be best to rewrite this in Java should this be
   included with the solution)
   5. Test the output in my web viewer:
   https://github.com/GoTeamEpsilon/cTAKES-Friendly-Web-UI
   6. Work on preparing the solution for the cTAKES core codebase. I will
   prepare it with a very rich README.

I will provide my updates over the coming days.

Thanks,

Matthew Vita
www.matthewvita.com

On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> Hi Gandhi,
>
> Thank you for the additional information.  Having a reliable rest
> service included with ctakes would be a boon for everybody interested
> in web access.  I look forward to checking out the info in github as
> soon as I am able.
>
> Thanks to you and Mathew both!
>
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Sunday, October 29, 2017 5:44 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I feel it's better to upgrade cTAKES Spring version to 4x so that
> exposing it as rest service becomes seamless. Please find the github
> link that contains the proposed changes for Spring upgrade in cTAKES,
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> 2DSVN-2Dsrc=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=cedfmyhdY7P3qZdiVB-
> gp0T0WinfllT61pLMqbP_Jyw=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s
> =
>
> I have not tested the changes in ytex modules as I'm not sure how to
> go about that.
>
> Matthew Vita will be reviewing the changes. He is also reviewing and
> testing my rest service changes. He will provide more info to us once
> we are done with our testing. So that we can discuss about
> productizing the same.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Friday, October 27, 2017 12:53 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> That sounds really great!  Thank you for sharing the process!
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, October 26, 2017 3:02 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my
> sandbox. As you have mentioned, it is used by uima fit for firing some
> queries.
>
> To brief it, I did the following changes:
>
> 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
> 2) Changing Spring version in cTAKES root pom.xml
> 3) Adding Spring versions in ctakes type system, ctakes assertion,
> ctakes ytex and ctakes ytex web modules.
>
> Now I'm able to expose cTAKES as a rest service which takes the
> clinical text as Input and outputs the result.
>
>  Hope it helps someone.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Wednesday, October 25, 2017 7:33 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> Thanks for the instant response. Will try to upgrade to Spring 4 and
> keep you posted about the progress.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday, October 25, 2017 7:28 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> You can always build ctakes in your sandbox with spring 4 and see if
> it works.  This may require some "maven magic"(overrides) on your
> part.  If it does seem to work please create a jira item to upgrade the 
> spring version.
> Then hopefully before the next release somebody will thoroughly test
> an update.
>
> Offhand I don't know

Re: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Miller, Timothy 
Sounds great, Matthew and Gandhi, thanks for sharing your solution.
Tim


From: Matthew Vita 
Sent: Sunday, October 29, 2017 11:59 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Sean,

Ghandi and I have met and we both agreed that his solution is superior to
the one I was working on. Therefore, I will be helping to see this project
through to the end so we can get it into the codebase!

Here are the remaining work items that I will be spending time on:

   1. Get it running (I'm using Linux Mint)
   2. Test it out (including stress tests)
   3. Automate it to run in Docker (just need UMLS credentials)
   4. Make a call to
   
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_cTAKES-2DConcept-2DMention-2DParser=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=RsnpR4AiLXd_qcFBYZG7T4_ExzPAkin8TsudEMLyPo8=YwuDivFqbAlEMTdeK-uxI2c01mLaq-4TfNwqDnVWUW4=
 to get a
   nice JSON payload that is easy to traverse (this can be an optional switch,
   of course - I believe it may be best to rewrite this in Java should this be
   included with the solution)
   5. Test the output in my web viewer:
   
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-2DUI=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=RsnpR4AiLXd_qcFBYZG7T4_ExzPAkin8TsudEMLyPo8=NjO4o8D_b6137joWwzPbit21dfg58a0_BXTikkpMFm8=
   6. Work on preparing the solution for the cTAKES core codebase. I will
   prepare it with a very rich README.

I will provide my updates over the coming days.

Thanks,

Matthew Vita
www.matthewvita.com

On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> Hi Gandhi,
>
> Thank you for the additional information.  Having a reliable rest service
> included with ctakes would be a boon for everybody interested in web
> access.  I look forward to checking out the info in github as soon as I am
> able.
>
> Thanks to you and Mathew both!
>
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Sunday, October 29, 2017 5:44 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I feel it's better to upgrade cTAKES Spring version to 4x so that exposing
> it as rest service becomes seamless. Please find the github link that
> contains the proposed changes for Spring upgrade in cTAKES,
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> 2DSVN-2Dsrc=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=cedfmyhdY7P3qZdiVB-
> gp0T0WinfllT61pLMqbP_Jyw=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s=
>
> I have not tested the changes in ytex modules as I'm not sure how to go
> about that.
>
> Matthew Vita will be reviewing the changes. He is also reviewing and
> testing my rest service changes. He will provide more info to us once we
> are done with our testing. So that we can discuss about productizing the
> same.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Friday, October 27, 2017 12:53 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> That sounds really great!  Thank you for sharing the process!
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, October 26, 2017 3:02 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my
> sandbox. As you have mentioned, it is used by uima fit for firing some
> queries.
>
> To brief it, I did the following changes:
>
> 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
> 2) Changing Spring version in cTAKES root pom.xml
> 3) Adding Spring versions in ctakes type system, ctakes assertion, ctakes
> ytex and ctakes ytex web modules.
>
> Now I'm able to expose cTAKES as a rest service which takes the clinical
> text as Input and outputs the result.
>
>  Hope it helps someone.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Wednesday, October 25, 2017 7:33 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> Thanks for the instant response. Will try to upgrade to Spring 4 and keep
> you posted about the progress.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday, October 25, 2017 7:28 PM
> To: dev@ctakes.apache.org
>

RE: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Finan, Sean 
Cheers

-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com] 
Sent: Sunday, October 29, 2017 12:00 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Sean,

Ghandi and I have met and we both agreed that his solution is superior to the 
one I was working on. Therefore, I will be helping to see this project through 
to the end so we can get it into the codebase!

Here are the remaining work items that I will be spending time on:

   1. Get it running (I'm using Linux Mint)
   2. Test it out (including stress tests)
   3. Automate it to run in Docker (just need UMLS credentials)
   4. Make a call to
   
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_cTAKES-2DConcept-2DMention-2DParser=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=Oq31Y4PRf5muS_U0cyd_auCRZh4ktFD3cK4a6tMk9uU=XtFa_asPcbX2365X0ILtKW726QSmmi_PDfUoDLMkKCQ=
 to get a
   nice JSON payload that is easy to traverse (this can be an optional switch,
   of course - I believe it may be best to rewrite this in Java should this be
   included with the solution)
   5. Test the output in my web viewer:
   
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-2DUI=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=Oq31Y4PRf5muS_U0cyd_auCRZh4ktFD3cK4a6tMk9uU=hKBU6HEMwwZgk1UCPAitjL1thyV9inbHjed9rT_ObUI=
   6. Work on preparing the solution for the cTAKES core codebase. I will
   prepare it with a very rich README.

I will provide my updates over the coming days.

Thanks,

Matthew Vita
www.matthewvita.com

On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> Hi Gandhi,
>
> Thank you for the additional information.  Having a reliable rest 
> service included with ctakes would be a boon for everybody interested 
> in web access.  I look forward to checking out the info in github as 
> soon as I am able.
>
> Thanks to you and Mathew both!
>
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Sunday, October 29, 2017 5:44 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I feel it's better to upgrade cTAKES Spring version to 4x so that 
> exposing it as rest service becomes seamless. Please find the github 
> link that contains the proposed changes for Spring upgrade in cTAKES,
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> 2DSVN-2Dsrc=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=cedfmyhdY7P3qZdiVB-
> gp0T0WinfllT61pLMqbP_Jyw=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s
> =
>
> I have not tested the changes in ytex modules as I'm not sure how to 
> go about that.
>
> Matthew Vita will be reviewing the changes. He is also reviewing and 
> testing my rest service changes. He will provide more info to us once 
> we are done with our testing. So that we can discuss about 
> productizing the same.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Friday, October 27, 2017 12:53 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> That sounds really great!  Thank you for sharing the process!
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, October 26, 2017 3:02 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my 
> sandbox. As you have mentioned, it is used by uima fit for firing some 
> queries.
>
> To brief it, I did the following changes:
>
> 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
> 2) Changing Spring version in cTAKES root pom.xml
> 3) Adding Spring versions in ctakes type system, ctakes assertion, 
> ctakes ytex and ctakes ytex web modules.
>
> Now I'm able to expose cTAKES as a rest service which takes the 
> clinical text as Input and outputs the result.
>
>  Hope it helps someone.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Wednesday, October 25, 2017 7:33 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> Thanks for the instant response. Will try to upgrade to Spring 4 and 
> keep you posted about the progress.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday, October 25, 2017 7:28 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> You can always build ctakes in

Re: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Matthew Vita 
Sean,

Ghandi and I have met and we both agreed that his solution is superior to
the one I was working on. Therefore, I will be helping to see this project
through to the end so we can get it into the codebase!

Here are the remaining work items that I will be spending time on:

   1. Get it running (I'm using Linux Mint)
   2. Test it out (including stress tests)
   3. Automate it to run in Docker (just need UMLS credentials)
   4. Make a call to
   https://github.com/GoTeamEpsilon/cTAKES-Concept-Mention-Parser to get a
   nice JSON payload that is easy to traverse (this can be an optional switch,
   of course - I believe it may be best to rewrite this in Java should this be
   included with the solution)
   5. Test the output in my web viewer:
   https://github.com/GoTeamEpsilon/cTAKES-Friendly-Web-UI
   6. Work on preparing the solution for the cTAKES core codebase. I will
   prepare it with a very rich README.

I will provide my updates over the coming days.

Thanks,

Matthew Vita
www.matthewvita.com

On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> Hi Gandhi,
>
> Thank you for the additional information.  Having a reliable rest service
> included with ctakes would be a boon for everybody interested in web
> access.  I look forward to checking out the info in github as soon as I am
> able.
>
> Thanks to you and Mathew both!
>
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Sunday, October 29, 2017 5:44 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I feel it's better to upgrade cTAKES Spring version to 4x so that exposing
> it as rest service becomes seamless. Please find the github link that
> contains the proposed changes for Spring upgrade in cTAKES,
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> 2DSVN-2Dsrc=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=cedfmyhdY7P3qZdiVB-
> gp0T0WinfllT61pLMqbP_Jyw=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s=
>
> I have not tested the changes in ytex modules as I'm not sure how to go
> about that.
>
> Matthew Vita will be reviewing the changes. He is also reviewing and
> testing my rest service changes. He will provide more info to us once we
> are done with our testing. So that we can discuss about productizing the
> same.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Friday, October 27, 2017 12:53 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> That sounds really great!  Thank you for sharing the process!
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, October 26, 2017 3:02 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my
> sandbox. As you have mentioned, it is used by uima fit for firing some
> queries.
>
> To brief it, I did the following changes:
>
> 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
> 2) Changing Spring version in cTAKES root pom.xml
> 3) Adding Spring versions in ctakes type system, ctakes assertion, ctakes
> ytex and ctakes ytex web modules.
>
> Now I'm able to expose cTAKES as a rest service which takes the clinical
> text as Input and outputs the result.
>
>  Hope it helps someone.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Wednesday, October 25, 2017 7:33 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
>
> Thanks for the instant response. Will try to upgrade to Spring 4 and keep
> you posted about the progress.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday, October 25, 2017 7:28 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Gandhi,
>
> You can always build ctakes in your sandbox with spring 4 and see if it
> works.  This may require some "maven magic"(overrides) on your part.  If it
> does seem to work please create a jira item to upgrade the spring version.
> Then hopefully before the next release somebody will thoroughly test an
> update.
>
> Offhand I don't know if or why spring is needed for ctakes itself.  At a
> quick search it looks like uimafit requires it.  Does anybody out there
> know what spring capabilities are used, directly or indirectly, by ctakes
> modules?
>
> Thanks,
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Wednesday, October 25, 2017 9:20 AM
> To:

RE: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Finan, Sean 
Hi Gandhi,

Thank you for the additional information.  Having a reliable rest service 
included with ctakes would be a boon for everybody interested in web access.  I 
look forward to checking out the info in github as soon as I am able.

Thanks to you and Mathew both!

Sean


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] 
Sent: Sunday, October 29, 2017 5:44 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean,

I feel it's better to upgrade cTAKES Spring version to 4x so that exposing it 
as rest service becomes seamless. Please find the github link that contains the 
proposed changes for Spring upgrade in cTAKES,

https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-2DSVN-2Dsrc=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=cedfmyhdY7P3qZdiVB-gp0T0WinfllT61pLMqbP_Jyw=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJcgd8s=

I have not tested the changes in ytex modules as I'm not sure how to go about 
that.

Matthew Vita will be reviewing the changes. He is also reviewing and testing my 
rest service changes. He will provide more info to us once we are done with our 
testing. So that we can discuss about productizing the same.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, October 27, 2017 12:53 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Gandhi,

That sounds really great!  Thank you for sharing the process!

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, October 26, 2017 3:02 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean,

I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my sandbox. 
As you have mentioned, it is used by uima fit for firing some queries.

To brief it, I did the following changes:

1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
2) Changing Spring version in cTAKES root pom.xml
3) Adding Spring versions in ctakes type system, ctakes assertion, ctakes ytex 
and ctakes ytex web modules.

Now I'm able to expose cTAKES as a rest service which takes the clinical text 
as Input and outputs the result.

 Hope it helps someone.

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 7:33 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean,

Thanks for the instant response. Will try to upgrade to Spring 4 and keep you 
posted about the progress.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 25, 2017 7:28 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Gandhi,

You can always build ctakes in your sandbox with spring 4 and see if it works.  
This may require some "maven magic"(overrides) on your part.  If it does seem 
to work please create a jira item to upgrade the spring version.  Then 
hopefully before the next release somebody will thoroughly test an update.

Offhand I don't know if or why spring is needed for ctakes itself.  At a quick 
search it looks like uimafit requires it.  Does anybody out there know what 
spring capabilities are used, directly or indirectly, by ctakes modules?

Thanks,
Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 9:20 AM
To: dev@ctakes.apache.org
Subject: cTAKES as REST service [EXTERNAL]

Hi All,

We have extended the cTAKES web application available under 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=e5GMRO_5OwQhQrkfpV5fwBp7uG07tZVd1u_xJRo9wDs=meOj7MzEliqIQEhU_FeQwEnsUrWFSzgk5ihSEzoGRCI=
 and added our custom annotator. We have tested the same and it works fine with 
CVD. But we are facing problems while trying to expose this as rest service.

cTAKES uses Spring 3.1.2 version internally which don't have out of the box 
support for rest controller. Can we go ahead and update the spring version to 
4x in cTAKES? Will it have any impact in the cTAKES behavior? Also is there a 
better way to expose cTAKES as rest service apart from spring?

Please advise.

Regards,
Gandhi

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 
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RE: cTAKES as REST service [EXTERNAL]

2017-10-29 Thread Gandhi Rajan Natarajan 
Hi Sean,

I feel it's better to upgrade cTAKES Spring version to 4x so that exposing it 
as rest service becomes seamless. Please find the github link that contains the 
proposed changes for Spring upgrade in cTAKES,

https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes-SVN-src

I have not tested the changes in ytex modules as I'm not sure how to go about 
that.

Matthew Vita will be reviewing the changes. He is also reviewing and testing my 
rest service changes. He will provide more info to us once we are done with our 
testing. So that we can discuss about productizing the same.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, October 27, 2017 12:53 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Gandhi,

That sounds really great!  Thank you for sharing the process!

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, October 26, 2017 3:02 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean,

I'm glad to inform that I was able to upgrade cTAKES to Spring 4 in my sandbox. 
As you have mentioned, it is used by uima fit for firing some queries.

To brief it, I did the following changes:

1) Changing SimpleJdbcTemplate to JdbcTemplate in uima modules
2) Changing Spring version in cTAKES root pom.xml
3) Adding Spring versions in ctakes type system, ctakes assertion, ctakes ytex 
and ctakes ytex web modules.

Now I'm able to expose cTAKES as a rest service which takes the clinical text 
as Input and outputs the result.

 Hope it helps someone.

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 7:33 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean,

Thanks for the instant response. Will try to upgrade to Spring 4 and keep you 
posted about the progress.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 25, 2017 7:28 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Gandhi,

You can always build ctakes in your sandbox with spring 4 and see if it works.  
This may require some "maven magic"(overrides) on your part.  If it does seem 
to work please create a jira item to upgrade the spring version.  Then 
hopefully before the next release somebody will thoroughly test an update.

Offhand I don't know if or why spring is needed for ctakes itself.  At a quick 
search it looks like uimafit requires it.  Does anybody out there know what 
spring capabilities are used, directly or indirectly, by ctakes modules?

Thanks,
Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 9:20 AM
To: dev@ctakes.apache.org
Subject: cTAKES as REST service [EXTERNAL]

Hi All,

We have extended the cTAKES web application available under 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=e5GMRO_5OwQhQrkfpV5fwBp7uG07tZVd1u_xJRo9wDs=meOj7MzEliqIQEhU_FeQwEnsUrWFSzgk5ihSEzoGRCI=
 and added our custom annotator. We have tested the same and it works fine with 
CVD. But we are facing problems while trying to expose this as rest service.

cTAKES uses Spring 3.1.2 version internally which don't have out of the box 
support for rest controller. Can we go ahead and update the spring version to 
4x in cTAKES? Will it have any impact in the cTAKES behavior? Also is there a 
better way to expose cTAKES as rest service apart from spring?

Please advise.

Regards,
Gandhi

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, 
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information is strictly prohibited and against the law.
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