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Posted to dev@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2019/03/05 16:11:46 UTC
Re: ctake web service [EXTERNAL] [SUSPICIOUS]
The custom dictionary lookup descriptor I use is the one I checked into the svn repo:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml?view=markup
for this to work you need to have the snomed/rxnorm dictionary somewhere that the dictionary module looks for dictionaries (like in $CTAKES_HOME/resources/)
You can also check out the Docker build file for a step-by-step of setting up and building the war file with that setup.
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/Dockerfile?view=markup
Tim
-----Original Message-----
From: "Miller, Timothy" <Timothy.Miller@childrens.harvard.edu<mailto:%22Miller,%20Timothy%22%20%3cTimothy.Miller@childrens.harvard.edu%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: ctake web service [EXTERNAL] [SUSPICIOUS]
Date: Tue, 5 Mar 2019 15:34:18 +0000
Assuming you meant me, I'm hosting on an ubuntu linux machine, and I'm using the hsql dictionary instead of the mysql dictionary.
Tim
-----Original Message-----
From: Kathy Ferro <he...@gmail.com><mailto:Kathy%20Ferro%20%3chealthcare1111@gmail.com%3e>>
Reply-to: <de...@ctakes.apache.org>>
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: ctake web service [EXTERNAL]
Date: Mon, 4 Mar 2019 22:57:22 -0500
Sean,
What machine do you hosting the WS and mysql on? I am on window 10
server. mySQL ini file looks fine. I'm wondering window and mysql are not
being friend.
Thanks
Kathy
On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu<ma...@childrens.harvard.edu>> wrote:
I don't know what the solution was, but I leave my ctakes REST server
running basically full time and haven't seen time outs yet.
Tim
________________________________________
From: gandhi rajan <ga...@gmail.com>>
Sent: Monday, March 4, 2019 10:43 AM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: ctake web service [EXTERNAL]
Hi Kathy, Sean did respond that there is no timeout happening from cTAKES
end. You might probably have to look at database settings for this closed
connection issue.
Does someone have any clue on this?
On Monday, March 4, 2019, Kathy Ferro <he...@gmail.com>> wrote:
Gandhi,
Do you get any response to this issue? Does it try to keep the
connection
open while WS is up? Or does it open and close after it's done?
We are still getting this error.
"ERROR JdbcRareWordDictionary - No operations allowed after statement
closed."
Thanks
Kathy
On Fri, Aug 17, 2018 at 9:43 AM Gandhi Rajan Natarajan <
Gandhi.Natarajan@arisglobal.com<ma...@arisglobal.com>> wrote:
Hi Kathy,
Sometime back we encountered this issue and the problem seems to be DB
connections getting timed out.
Currently we are using the following implementations:
"org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary"
and "org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory"
Does anybody aware of any timeout settings that needs to be done in
these
implementations to avoid DB connection timeout issue?
-----Original Message-----
From: Kathy Ferro <he...@gmail.com>>
Sent: Thursday, August 16, 2018 11:07 PM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: ctake web service
Hi,
Just want to see if anybody has experience this issue.
If the web service had been up for a day or two, it will drop the
dictionary lookup. The only result it returns are ConllDependencyNode
tag
in the xmi file; no mention, no concept, etc...
I haven't have a chance to investigate it, yet.
Kathy
This email and any files transmitted with it are confidential and
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If you are not the named addressee you should not disseminate,
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against the law.
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others
!!!"
Re: ctake web service [EXTERNAL] [SUSPICIOUS]
Posted by Kathy Ferro <he...@gmail.com>.
Thank you, Tim.
I don't know where I get Sean from.
On Tue, Mar 5, 2019 at 11:11 AM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> The custom dictionary lookup descriptor I use is the one I checked into
> the svn repo:
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/customDictionary.xml?view=markup
>
> for this to work you need to have the snomed/rxnorm dictionary somewhere
> that the dictionary module looks for dictionaries (like in
> $CTAKES_HOME/resources/)
>
> You can also check out the Docker build file for a step-by-step of setting
> up and building the war file with that setup.
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/docker/Dockerfile?view=markup
>
> Tim
>
>
> -----Original Message-----
> From: "Miller, Timothy" <Timothy.Miller@childrens.harvard.edu<mailto:
> %22Miller,%20Timothy%22%20%3cTimothy.Miller@childrens.harvard.edu%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: ctake web service [EXTERNAL] [SUSPICIOUS]
> Date: Tue, 5 Mar 2019 15:34:18 +0000
>
>
> Assuming you meant me, I'm hosting on an ubuntu linux machine, and I'm
> using the hsql dictionary instead of the mysql dictionary.
> Tim
>
>
> -----Original Message-----
> From: Kathy Ferro <healthcare1111@gmail.com<mailto:
> healthcare1111@gmail.com><mailto:
> Kathy%20Ferro%20%3chealthcare1111@gmail.com%3e>>
> Reply-to: <de...@ctakes.apache.org>>
> To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:
> dev@ctakes.apache.org>
> Subject: Re: ctake web service [EXTERNAL]
> Date: Mon, 4 Mar 2019 22:57:22 -0500
>
>
> Sean,
>
> What machine do you hosting the WS and mysql on? I am on window 10
> server. mySQL ini file looks fine. I'm wondering window and mysql are not
> being friend.
>
> Thanks
> Kathy
>
> On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu<mailto:
> Timothy.Miller@childrens.harvard.edu><mailto:
> Timothy.Miller@childrens.harvard.edu>> wrote:
>
>
>
> I don't know what the solution was, but I leave my ctakes REST server
> running basically full time and haven't seen time outs yet.
> Tim
>
> ________________________________________
> From: gandhi rajan <gandhirajan.n@gmail.com<mailto:gandhirajan.n@gmail.com
> ><ma...@gmail.com>>
> Sent: Monday, March 4, 2019 10:43 AM
> To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:
> dev@ctakes.apache.org>
> Subject: Re: ctake web service [EXTERNAL]
>
> Hi Kathy, Sean did respond that there is no timeout happening from cTAKES
> end. You might probably have to look at database settings for this closed
> connection issue.
>
> Does someone have any clue on this?
>
> On Monday, March 4, 2019, Kathy Ferro <healthcare1111@gmail.com<mailto:
> healthcare1111@gmail.com><ma...@gmail.com>> wrote:
>
>
>
> Gandhi,
>
> Do you get any response to this issue? Does it try to keep the
>
>
> connection
>
>
> open while WS is up? Or does it open and close after it's done?
>
> We are still getting this error.
> "ERROR JdbcRareWordDictionary - No operations allowed after statement
> closed."
>
> Thanks
> Kathy
>
>
>
> On Fri, Aug 17, 2018 at 9:43 AM Gandhi Rajan Natarajan <
> Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal.com
> ><ma...@arisglobal.com>> wrote:
>
>
>
> Hi Kathy,
>
> Sometime back we encountered this issue and the problem seems to be DB
> connections getting timed out.
>
> Currently we are using the following implementations:
>
>
>
>
>
> "org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary"
>
>
>
>
> and "org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory"
>
> Does anybody aware of any timeout settings that needs to be done in
>
>
>
>
> these
>
>
>
>
> implementations to avoid DB connection timeout issue?
>
> -----Original Message-----
> From: Kathy Ferro <healthcare1111@gmail.com<mailto:
> healthcare1111@gmail.com><ma...@gmail.com>>
> Sent: Thursday, August 16, 2018 11:07 PM
> To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:
> dev@ctakes.apache.org>
> Subject: ctake web service
>
> Hi,
>
> Just want to see if anybody has experience this issue.
>
> If the web service had been up for a day or two, it will drop the
> dictionary lookup. The only result it returns are ConllDependencyNode
>
>
> tag
>
>
> in the xmi file; no mention, no concept, etc...
>
> I haven't have a chance to investigate it, yet.
>
> Kathy
> 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
> !!!"
>
>
>
>