Re: ctake web service [EXTERNAL]

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

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
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> 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
> > 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 !!!"

Re: ctake web service [EXTERNAL]

["Finan, Sean" <Se...@childrens.harvard.edu>]

I think that this might be for Tim
________________________________________
From: Kathy Ferro <he...@gmail.com>
Sent: Monday, March 4, 2019 10:57 PM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]

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> 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
> 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> 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
> > > 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
> !!!"
>

Re: ctake web service [EXTERNAL] [SUSPICIOUS]

[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
> !!!"
>
>
>
>

Re: ctake web service [EXTERNAL] [SUSPICIOUS]

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

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


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: ctake web service [EXTERNAL]

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

Ok Tim. Thanks for the response.

On Thursday, March 7, 2019, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> I basically took the lookup descriptor that is used by the fast aggregate
> pipeline in ctakes-clinical-pipeline/desc/
> 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: ctake web service [EXTERNAL]
> Date: Wed, 6 Mar 2019 20:36:05 +0530
>
>
> I guess this makes a big difference. Tim, are you using the other settings
> in custom dictionary xml as is?
>
> On Tuesday, March 5, 2019, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu<mailto:
> Timothy.Miller@childrens.harvard.edu>> wrote:
>
>
>
> 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<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<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
> ><mailto:gandhirajan.n@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><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><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
> !!!"
>
>
>
>
>
>
>
>

-- 
Regards,
Gandhi

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

Re: ctake web service [EXTERNAL]

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

I basically took the lookup descriptor that is used by the fast aggregate pipeline in ctakes-clinical-pipeline/desc/
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: ctake web service [EXTERNAL]
Date: Wed, 6 Mar 2019 20:36:05 +0530


I guess this makes a big difference. Tim, are you using the other settings
in custom dictionary xml as is?

On Tuesday, March 5, 2019, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu<ma...@childrens.harvard.edu>> wrote:



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<ma...@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><mailto:
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><mailto:gandhirajan.n@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><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<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><mailto:
healthcare1111@gmail.com<ma...@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


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: ctake web service [EXTERNAL]

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

I guess this makes a big difference. Tim, are you using the other settings
in custom dictionary xml as is?

On Tuesday, March 5, 2019, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> 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:
> 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<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
> >>
> 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 <healthcare1111@gmail.com<mailto:
> healthcare1111@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 <healthcare1111@gmail.com<mailto:
> healthcare1111@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
>
>
> 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
> !!!"
>
>
>

-- 
Regards,
Gandhi

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

Re: ctake web service [EXTERNAL]

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

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: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


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: ctake web service [EXTERNAL]

[Kathy Ferro <he...@gmail.com>]

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> 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
> 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> 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
> > > 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
> !!!"
>

Re: ctake web service [EXTERNAL]

[Jeffrey Miller <je...@gmail.com>]

Thank you Peter, that is helpful.

On Sat, Mar 9, 2019 at 3:46 PM Peter Abramowitsch <pa...@gmail.com>
wrote:

> I haven't made our code available, Sorry.  Not sure if I can.  But from my
> description, you should find it pretty easy.  I started by extending a
> GenericObjectPool and going from there. As each instance is instantiated, I
> re-read the piper file - creating a new engine which is assigned to a Pool
> member.
>
> Peter
>
> On Sat, Mar 9, 2019 at 9:20 AM Jeffrey Miller <je...@gmail.com> wrote:
>
> > Thanks for your response Sean- we are still working on this (and have
> some
> > things to look into given your last response), but I will share details
> > when we have it working. We are still deciding on whether to use Spark or
> > Apache Beam.
> >
> > Just to clarify my previous confusion, I assumed the TS wrappers were so
> > you could avoid creating multiple pipelines and just run one instance of
> > the pipeline with a separate JCAS per thread. I thought the main
> motivation
> > behind that would be to avoid loading >1 dictionaries into memory, for
> > example. But it sounds like I was mistaken. With respect to sharing
> > resources, are static variables the main concern? Do you know if this is
> a
> > problem for any of the annotators in the default clinical pipeline (the
> > regular components, not the thread safe ones)? From Peter's response (I
> am
> > not sure if that split off into another forum thread because the subject
> > changed), it sounds like it may not be a problem? I'd like to really
> > understand thread-safe with respect to core cTAKES components (with the
> > caveat that community-created annotators could be implemented in any
> number
> > of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy
> > to contribute documentation back to the wiki once I feel I have a solid
> > grasp on it.
> >
> > Peter- have you made your pipeline pool code available anywhere?
> >
> > On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > Hi all,
> > >
> > > >Is there any known reason that you can't create a pipeline pool, but
> > keep
> > > everything in the same process?
> > > -- No, but ...
> > > > Is it safe to load multiple pipelines in
> > > the same process as long as only one thread can access each one at a
> time
> > > (we plan to use this in a Spark pipeline).
> > > -- If you are talking about oob ctakes being the process, only a single
> > > pipeline will run on multiple threads.  The threads will share
> resources,
> > > static variables, etc. and the  pipeline will give you terrible results
> > and
> > > very quickly crash.  That is why I wrote the thread-safe wrappers.
> > > -- That being said, supposedly you can configure spark to handle this
> by
> > > keeping everything contained in a unique copy per thread.  Sort of like
> > > ThreadLocal (I think), but more effective on a full-pipeline level.
> > >
> > > > it must have reduced the DefaultJCasTermAnnotator to a singleton
> object
> > > in memory.
> > > -- Yes.  The thread-safe pipeline is not meant to have siblings in the
> > > same process - the wrappers can only do so much.  That being said, I am
> > > pretty sure that the Default... is thread-safe so it doesn't actually
> > need
> > > the wrapper.  Regardless, the rest of the pipeline would crash.
> > >
> > > Jeff, can you share information about your efforts on spark?  If we
> could
> > > get that working and in standard ctakes it would be fantastic.
> > >
> > > I hope that this information is useful.
> > >
> > > Sean
> > >
> > >
> > >
> > > ________________________________________
> > > From: Jeffrey Miller <je...@gmail.com>
> > > Sent: Friday, March 8, 2019 11:23 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: ctake web service [EXTERNAL]
> > >
> > > Is there any known reason that you can't create a pipeline pool, but
> keep
> > > everything in the same process? Is it safe to load multiple pipelines
> in
> > > the same process as long as only one thread can access each one at a
> time
> > > (we plan to use this in a Spark pipeline). One caveat I have noticed-
> it
> > > seems like if I use the thread safe components to build a pipeline
> pool,
> > > only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> > > process. For example, I was trying to take advantage of the ability to
> > > switch pipelines via a query parameter that is suggested at in the code
> > for
> > > the rest service. The two pipelines used different ontology
> dictionaries,
> > > but it seemed like with the thread safe components it must have reduced
> > > the DefaultJCasTermAnnotator to a singleton object in memory, because
> it
> > > only used the first dictionary instantiated. Either way, given how Sean
> > > described how the thread safe components worked above, you probably
> > > wouldn't want to use them in a pipeline pool, assuming that the
> problems
> > > with threading was limited to multiple threads access the same pipeline
> > at
> > > the same time, and not having multiple pipelines loaded into memory
> each
> > > accessed by only a single thread.
> > >
> > > On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> > > wrote:
> > >
> > > > I thought about creating a queue that acts as traffic cop.  Only the
> > > > traffic cop calls the WS.  I also want to test multiple WS running on
> > > > different port.  Traffic cop calls which every WS is available and
> keep
> > > > track of WS statuses.  With all this processing going, it might kill
> > the
> > > > power for blocks.
> > > >
> > > > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> > > > Sean.Finan@childrens.harvard.edu> wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I guess that a quick test could be run with a multi-threaded
> > pipeline.
> > > > > Tim, for some reason I recall you checking in one with a
> dockerfile.
> > > > Maybe
> > > > > not, and it might not be the default in the service.  Anyway, you
> > could
> > > > set
> > > > > the procs to something like 50 and throw 50 users at it.  It
> > definitely
> > > > > does not scale anything close to linearly.  ctakes aes aren't build
> > for
> > > > > thread-safety, so they are all wrapped with locks and there is a
> lot
> > of
> > > > > thread contention.  However, running such a test might indicate the
> > > > source
> > > > > of the problem.
> > > > >
> > > > > The other option is to create a queue that collects post calls and
> > > doles
> > > > > them out serially to a single pipeline.  User #50 would probably
> not
> > > > > appreciate it though ...
> > > > > ________________________________________
> > > > > From: gandhi rajan <ga...@gmail.com>
> > > > > Sent: Friday, March 8, 2019 10:02 AM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > >
> > > > > Hi Kathy,
> > > > >
> > > > > I guess the initializations happens in post construct method. So if
> > we
> > > > > could synchronize that I feel we can get away from the problem.
> > > > > Unfortunately I m not able to tet this as my setup is gone with my
> > old
> > > > job.
> > > > > Try it out.
> > > > >
> > > > > Regards,
> > > > > Gandhi.
> > > > >
> > > > > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com>
> > > wrote:
> > > > >
> > > > > > Tim,
> > > > > >
> > > > > > Thanks for reply.  I'm continuing the research.  With all the
> > layers
> > > > that
> > > > > > wrap around this, you would think we can handle this suggestion.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > > > >
> > > > > > > That's a good question that I've also heard from others, and
> > > > > > unfortunately
> > > > > > > I don't know the answer. My use cases are typically a single
> job
> > > at a
> > > > > > time
> > > > > > > making sequential calls, so I wasn't stressing it with multiple
> > > > > > > asynchronous calls. I would've thought that the Tomcat
> container
> > > > would
> > > > > > have
> > > > > > > some ability to manage that though!
> > > > > > > Tim
> > > > > > >
> > > > > > > ________________________________________
> > > > > > > From: Kathy Ferro <he...@gmail.com>
> > > > > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > > > > To: dev@ctakes.apache.org
> > > > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > > > >
> > > > > > > Tim,
> > > > > > >
> > > > > > > Does docker solution handle multiple instances?  I tested the
> > Rest
> > > > Web
> > > > > > > Service with 2 requests at the same time, it errors out.  I
> > removed
> > > > the
> > > > > > > part that write the result xml file to the disc; it still error
> > > out.
> > > > > > >
> > > > > > > Best,
> > > > > > > Kathy
> > > > > > >
> > > > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > > > > 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 <ga...@gmail.com>
> > > > > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > > > > To: 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>
> > > > > > 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> 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
> > > > > > > > > > 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
> > > > > > > > !!!"
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Regards,
> > > > > Gandhi
> > > > >
> > > > > "The best way to find urself is to lose urself in the service of
> > others
> > > > > !!!"
> > > > >
> > > >
> > >
> >
>

Re: ctake web service [EXTERNAL]

[Peter Abramowitsch <pa...@gmail.com>]

I haven't made our code available, Sorry.  Not sure if I can.  But from my
description, you should find it pretty easy.  I started by extending a
GenericObjectPool and going from there. As each instance is instantiated, I
re-read the piper file - creating a new engine which is assigned to a Pool
member.

Peter

On Sat, Mar 9, 2019 at 9:20 AM Jeffrey Miller <je...@gmail.com> wrote:

> Thanks for your response Sean- we are still working on this (and have some
> things to look into given your last response), but I will share details
> when we have it working. We are still deciding on whether to use Spark or
> Apache Beam.
>
> Just to clarify my previous confusion, I assumed the TS wrappers were so
> you could avoid creating multiple pipelines and just run one instance of
> the pipeline with a separate JCAS per thread. I thought the main motivation
> behind that would be to avoid loading >1 dictionaries into memory, for
> example. But it sounds like I was mistaken. With respect to sharing
> resources, are static variables the main concern? Do you know if this is a
> problem for any of the annotators in the default clinical pipeline (the
> regular components, not the thread safe ones)? From Peter's response (I am
> not sure if that split off into another forum thread because the subject
> changed), it sounds like it may not be a problem? I'd like to really
> understand thread-safe with respect to core cTAKES components (with the
> caveat that community-created annotators could be implemented in any number
> of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy
> to contribute documentation back to the wiki once I feel I have a solid
> grasp on it.
>
> Peter- have you made your pipeline pool code available anywhere?
>
> On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi all,
> >
> > >Is there any known reason that you can't create a pipeline pool, but
> keep
> > everything in the same process?
> > -- No, but ...
> > > Is it safe to load multiple pipelines in
> > the same process as long as only one thread can access each one at a time
> > (we plan to use this in a Spark pipeline).
> > -- If you are talking about oob ctakes being the process, only a single
> > pipeline will run on multiple threads.  The threads will share resources,
> > static variables, etc. and the  pipeline will give you terrible results
> and
> > very quickly crash.  That is why I wrote the thread-safe wrappers.
> > -- That being said, supposedly you can configure spark to handle this by
> > keeping everything contained in a unique copy per thread.  Sort of like
> > ThreadLocal (I think), but more effective on a full-pipeline level.
> >
> > > it must have reduced the DefaultJCasTermAnnotator to a singleton object
> > in memory.
> > -- Yes.  The thread-safe pipeline is not meant to have siblings in the
> > same process - the wrappers can only do so much.  That being said, I am
> > pretty sure that the Default... is thread-safe so it doesn't actually
> need
> > the wrapper.  Regardless, the rest of the pipeline would crash.
> >
> > Jeff, can you share information about your efforts on spark?  If we could
> > get that working and in standard ctakes it would be fantastic.
> >
> > I hope that this information is useful.
> >
> > Sean
> >
> >
> >
> > ________________________________________
> > From: Jeffrey Miller <je...@gmail.com>
> > Sent: Friday, March 8, 2019 11:23 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Is there any known reason that you can't create a pipeline pool, but keep
> > everything in the same process? Is it safe to load multiple pipelines in
> > the same process as long as only one thread can access each one at a time
> > (we plan to use this in a Spark pipeline). One caveat I have noticed- it
> > seems like if I use the thread safe components to build a pipeline pool,
> > only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> > process. For example, I was trying to take advantage of the ability to
> > switch pipelines via a query parameter that is suggested at in the code
> for
> > the rest service. The two pipelines used different ontology dictionaries,
> > but it seemed like with the thread safe components it must have reduced
> > the DefaultJCasTermAnnotator to a singleton object in memory, because it
> > only used the first dictionary instantiated. Either way, given how Sean
> > described how the thread safe components worked above, you probably
> > wouldn't want to use them in a pipeline pool, assuming that the problems
> > with threading was limited to multiple threads access the same pipeline
> at
> > the same time, and not having multiple pipelines loaded into memory each
> > accessed by only a single thread.
> >
> > On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> > wrote:
> >
> > > I thought about creating a queue that acts as traffic cop.  Only the
> > > traffic cop calls the WS.  I also want to test multiple WS running on
> > > different port.  Traffic cop calls which every WS is available and keep
> > > track of WS statuses.  With all this processing going, it might kill
> the
> > > power for blocks.
> > >
> > > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> > > Sean.Finan@childrens.harvard.edu> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I guess that a quick test could be run with a multi-threaded
> pipeline.
> > > > Tim, for some reason I recall you checking in one with a dockerfile.
> > > Maybe
> > > > not, and it might not be the default in the service.  Anyway, you
> could
> > > set
> > > > the procs to something like 50 and throw 50 users at it.  It
> definitely
> > > > does not scale anything close to linearly.  ctakes aes aren't build
> for
> > > > thread-safety, so they are all wrapped with locks and there is a lot
> of
> > > > thread contention.  However, running such a test might indicate the
> > > source
> > > > of the problem.
> > > >
> > > > The other option is to create a queue that collects post calls and
> > doles
> > > > them out serially to a single pipeline.  User #50 would probably not
> > > > appreciate it though ...
> > > > ________________________________________
> > > > From: gandhi rajan <ga...@gmail.com>
> > > > Sent: Friday, March 8, 2019 10:02 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: ctake web service [EXTERNAL]
> > > >
> > > > Hi Kathy,
> > > >
> > > > I guess the initializations happens in post construct method. So if
> we
> > > > could synchronize that I feel we can get away from the problem.
> > > > Unfortunately I m not able to tet this as my setup is gone with my
> old
> > > job.
> > > > Try it out.
> > > >
> > > > Regards,
> > > > Gandhi.
> > > >
> > > > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com>
> > wrote:
> > > >
> > > > > Tim,
> > > > >
> > > > > Thanks for reply.  I'm continuing the research.  With all the
> layers
> > > that
> > > > > wrap around this, you would think we can handle this suggestion.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > > >
> > > > > > That's a good question that I've also heard from others, and
> > > > > unfortunately
> > > > > > I don't know the answer. My use cases are typically a single job
> > at a
> > > > > time
> > > > > > making sequential calls, so I wasn't stressing it with multiple
> > > > > > asynchronous calls. I would've thought that the Tomcat container
> > > would
> > > > > have
> > > > > > some ability to manage that though!
> > > > > > Tim
> > > > > >
> > > > > > ________________________________________
> > > > > > From: Kathy Ferro <he...@gmail.com>
> > > > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > > > To: dev@ctakes.apache.org
> > > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > > >
> > > > > > Tim,
> > > > > >
> > > > > > Does docker solution handle multiple instances?  I tested the
> Rest
> > > Web
> > > > > > Service with 2 requests at the same time, it errors out.  I
> removed
> > > the
> > > > > > part that write the result xml file to the disc; it still error
> > out.
> > > > > >
> > > > > > Best,
> > > > > > Kathy
> > > > > >
> > > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > > > 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 <ga...@gmail.com>
> > > > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > > > To: 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>
> > > > > 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> 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
> > > > > > > > > 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
> > > > > > > !!!"
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Regards,
> > > > Gandhi
> > > >
> > > > "The best way to find urself is to lose urself in the service of
> others
> > > > !!!"
> > > >
> > >
> >
>

Re: ctake web service [EXTERNAL]

[Jeffrey Miller <je...@gmail.com>]

Hi Sean,

I just wanted to follow up on this one more time with a few follow-up.

From Peter's description of how he is using a pool of pipelines:

>  I started from scratch to create a pipeline pool that sizes itself
according to the memory that’s available.  Each instance contains the
complete pipeline including the Term Annotator and a re-settable JCas
object.   I don’t use any of the thread constructs in piper files - to not
confuse the issue.  All of this is accessed via a web service with a multi
threaded dispatcher (SparkJava).

and our experience with doing something similar, it seems that this does
not lead to crashing, at least not with the components in the Default
Clinical Pipeline. We did have crashes when we tried to access the same
pipeline from two threads, but that was expected. I just wanted to verify
that you have seen problems with this specific setup- that is, a pool of
pipelines, where each one is only accessed in a single thread
simultaneously. It sounds like you have from your prior messages, but I am
just trying make sure I have not confused something.

We are not that concerned with the initial startup cost of loading the
piper file multiple times. I am hesitant to use use the wrapped thread-safe
components because we are concerned with compute time and I suspect that
much of the time in our pipeline is spent in the DefaultJCasTermAnnotator
and the threads would just have to wait in line.

With respect to you message:

>  Anyway, if I am running on a cluster (etc.) then it is a completely
different ballgame.  When I do that I don't bother with the TS pipeline.

When you are running on a cluster do you just use multiple processes, one
pipeline per process?

Lastly, do you know what the piper file "threads" command actually enforces
(
https://github.com/apache/ctakes/blob/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/TsDefaultFastPipeline.piper#L4
)?

Thanks again for your help.
Jeff


On Sat, Mar 9, 2019 at 10:24 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Jeff,
>
> >  I assumed the TS wrappers were so you could avoid creating multiple
> pipelines and just run one instance of the pipeline with a separate JCAS
> per thread.
>
> -- Your assumption was correct.  The idea is to have only a single copy of
> any resource in memory : Dictionary, ML models (which can get big), graphs,
> etc.  The other advantage is a single initialization.  It may not seem like
> a big deal, but I have inits that take > 2 minutes, and parallel inits
> don't work too well wrt disk thrashing.  So, if I'm just running a 5 minute
> test, I'd rather run 3 threads with a single init.  And on my laptop 3
> instances of a memory hog is not really an option.  Yes, thread copies, but
> it is still more friendly.   Anyway, if I am running on a cluster (etc.)
> then it is a completely different ballgame.  When I do that I don't bother
> with the TS pipeline.
>
>
> > Do you know if this is a problem for any of the annotators in the
> default clinical pipeline
>
> -- Oh yeah.  That is why I made the TS wrappers.   A good number of the
> default AEs are not thread safe.  And really, it only takes 1 to ruin your
> day.  Resources, static variables and collections, i/o ...  And really,
> some things are not ctakes per se, but 3rd party libraries that are used by
> several -standard- AEs.
>
>
> > I'd like to really understand thread-safe with respect to core cTAKES
> components
>
> -- I don't know if anybody has done a formal writeup or anything of the
> sort.  I set out to do a deep dive into the code and refactor for TS, but
> quickly changed my mind.  See mention of 3rd parties above, though that
> certainly wasn't everything.  It was easier to write the wrappers.  Plus, I
> could rubber stamp and quickly wrap any ae that I came across for testing
> or use to be ts.
>
>
> Cheers for the curiosity,
>
> Sean
>
>
>
>
> ________________________________________
> From: Jeffrey Miller <je...@gmail.com>
> Sent: Saturday, March 9, 2019 12:20 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctake web service [EXTERNAL]
>
> Thanks for your response Sean- we are still working on this (and have some
> things to look into given your last response), but I will share details
> when we have it working. We are still deciding on whether to use Spark or
> Apache Beam.
>
> Just to clarify my previous confusion, I assumed the TS wrappers were so
> you could avoid creating multiple pipelines and just run one instance of
> the pipeline with a separate JCAS per thread. I thought the main motivation
> behind that would be to avoid loading >1 dictionaries into memory, for
> example. But it sounds like I was mistaken. With respect to sharing
> resources, are static variables the main concern? Do you know if this is a
> problem for any of the annotators in the default clinical pipeline (the
> regular components, not the thread safe ones)? From Peter's response (I am
> not sure if that split off into another forum thread because the subject
> changed), it sounds like it may not be a problem? I'd like to really
> understand thread-safe with respect to core cTAKES components (with the
> caveat that community-created annotators could be implemented in any number
> of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy
> to contribute documentation back to the wiki once I feel I have a solid
> grasp on it.
>
> Peter- have you made your pipeline pool code available anywhere?
>
> On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi all,
> >
> > >Is there any known reason that you can't create a pipeline pool, but
> keep
> > everything in the same process?
> > -- No, but ...
> > > Is it safe to load multiple pipelines in
> > the same process as long as only one thread can access each one at a time
> > (we plan to use this in a Spark pipeline).
> > -- If you are talking about oob ctakes being the process, only a single
> > pipeline will run on multiple threads.  The threads will share resources,
> > static variables, etc. and the  pipeline will give you terrible results
> and
> > very quickly crash.  That is why I wrote the thread-safe wrappers.
> > -- That being said, supposedly you can configure spark to handle this by
> > keeping everything contained in a unique copy per thread.  Sort of like
> > ThreadLocal (I think), but more effective on a full-pipeline level.
> >
> > > it must have reduced the DefaultJCasTermAnnotator to a singleton object
> > in memory.
> > -- Yes.  The thread-safe pipeline is not meant to have siblings in the
> > same process - the wrappers can only do so much.  That being said, I am
> > pretty sure that the Default... is thread-safe so it doesn't actually
> need
> > the wrapper.  Regardless, the rest of the pipeline would crash.
> >
> > Jeff, can you share information about your efforts on spark?  If we could
> > get that working and in standard ctakes it would be fantastic.
> >
> > I hope that this information is useful.
> >
> > Sean
> >
> >
> >
> > ________________________________________
> > From: Jeffrey Miller <je...@gmail.com>
> > Sent: Friday, March 8, 2019 11:23 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Is there any known reason that you can't create a pipeline pool, but keep
> > everything in the same process? Is it safe to load multiple pipelines in
> > the same process as long as only one thread can access each one at a time
> > (we plan to use this in a Spark pipeline). One caveat I have noticed- it
> > seems like if I use the thread safe components to build a pipeline pool,
> > only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> > process. For example, I was trying to take advantage of the ability to
> > switch pipelines via a query parameter that is suggested at in the code
> for
> > the rest service. The two pipelines used different ontology dictionaries,
> > but it seemed like with the thread safe components it must have reduced
> > the DefaultJCasTermAnnotator to a singleton object in memory, because it
> > only used the first dictionary instantiated. Either way, given how Sean
> > described how the thread safe components worked above, you probably
> > wouldn't want to use them in a pipeline pool, assuming that the problems
> > with threading was limited to multiple threads access the same pipeline
> at
> > the same time, and not having multiple pipelines loaded into memory each
> > accessed by only a single thread.
> >
> > On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> > wrote:
> >
> > > I thought about creating a queue that acts as traffic cop.  Only the
> > > traffic cop calls the WS.  I also want to test multiple WS running on
> > > different port.  Traffic cop calls which every WS is available and keep
> > > track of WS statuses.  With all this processing going, it might kill
> the
> > > power for blocks.
> > >
> > > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> > > Sean.Finan@childrens.harvard.edu> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I guess that a quick test could be run with a multi-threaded
> pipeline.
> > > > Tim, for some reason I recall you checking in one with a dockerfile.
> > > Maybe
> > > > not, and it might not be the default in the service.  Anyway, you
> could
> > > set
> > > > the procs to something like 50 and throw 50 users at it.  It
> definitely
> > > > does not scale anything close to linearly.  ctakes aes aren't build
> for
> > > > thread-safety, so they are all wrapped with locks and there is a lot
> of
> > > > thread contention.  However, running such a test might indicate the
> > > source
> > > > of the problem.
> > > >
> > > > The other option is to create a queue that collects post calls and
> > doles
> > > > them out serially to a single pipeline.  User #50 would probably not
> > > > appreciate it though ...
> > > > ________________________________________
> > > > From: gandhi rajan <ga...@gmail.com>
> > > > Sent: Friday, March 8, 2019 10:02 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: ctake web service [EXTERNAL]
> > > >
> > > > Hi Kathy,
> > > >
> > > > I guess the initializations happens in post construct method. So if
> we
> > > > could synchronize that I feel we can get away from the problem.
> > > > Unfortunately I m not able to tet this as my setup is gone with my
> old
> > > job.
> > > > Try it out.
> > > >
> > > > Regards,
> > > > Gandhi.
> > > >
> > > > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com>
> > wrote:
> > > >
> > > > > Tim,
> > > > >
> > > > > Thanks for reply.  I'm continuing the research.  With all the
> layers
> > > that
> > > > > wrap around this, you would think we can handle this suggestion.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > > >
> > > > > > That's a good question that I've also heard from others, and
> > > > > unfortunately
> > > > > > I don't know the answer. My use cases are typically a single job
> > at a
> > > > > time
> > > > > > making sequential calls, so I wasn't stressing it with multiple
> > > > > > asynchronous calls. I would've thought that the Tomcat container
> > > would
> > > > > have
> > > > > > some ability to manage that though!
> > > > > > Tim
> > > > > >
> > > > > > ________________________________________
> > > > > > From: Kathy Ferro <he...@gmail.com>
> > > > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > > > To: dev@ctakes.apache.org
> > > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > > >
> > > > > > Tim,
> > > > > >
> > > > > > Does docker solution handle multiple instances?  I tested the
> Rest
> > > Web
> > > > > > Service with 2 requests at the same time, it errors out.  I
> removed
> > > the
> > > > > > part that write the result xml file to the disc; it still error
> > out.
> > > > > >
> > > > > > Best,
> > > > > > Kathy
> > > > > >
> > > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > > > 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 <ga...@gmail.com>
> > > > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > > > To: 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>
> > > > > 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> 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
> > > > > > > > > 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
> > > > > > > !!!"
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Regards,
> > > > Gandhi
> > > >
> > > > "The best way to find urself is to lose urself in the service of
> others
> > > > !!!"
> > > >
> > >
> >
>

Re: ctake web service [EXTERNAL]

["Finan, Sean" <Se...@childrens.harvard.edu>]

Hi Jeff,

>  I assumed the TS wrappers were so you could avoid creating multiple pipelines and just run one instance of the pipeline with a separate JCAS per thread. 

-- Your assumption was correct.  The idea is to have only a single copy of any resource in memory : Dictionary, ML models (which can get big), graphs, etc.  The other advantage is a single initialization.  It may not seem like a big deal, but I have inits that take > 2 minutes, and parallel inits don't work too well wrt disk thrashing.  So, if I'm just running a 5 minute test, I'd rather run 3 threads with a single init.  And on my laptop 3 instances of a memory hog is not really an option.  Yes, thread copies, but it is still more friendly.   Anyway, if I am running on a cluster (etc.) then it is a completely different ballgame.  When I do that I don't bother with the TS pipeline.


> Do you know if this is a problem for any of the annotators in the default clinical pipeline 

-- Oh yeah.  That is why I made the TS wrappers.   A good number of the default AEs are not thread safe.  And really, it only takes 1 to ruin your day.  Resources, static variables and collections, i/o ...  And really, some things are not ctakes per se, but 3rd party libraries that are used by several -standard- AEs.


> I'd like to really understand thread-safe with respect to core cTAKES components 

-- I don't know if anybody has done a formal writeup or anything of the sort.  I set out to do a deep dive into the code and refactor for TS, but quickly changed my mind.  See mention of 3rd parties above, though that certainly wasn't everything.  It was easier to write the wrappers.  Plus, I could rubber stamp and quickly wrap any ae that I came across for testing or use to be ts.


Cheers for the curiosity,

Sean




________________________________________
From: Jeffrey Miller <je...@gmail.com>
Sent: Saturday, March 9, 2019 12:20 PM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]

Thanks for your response Sean- we are still working on this (and have some
things to look into given your last response), but I will share details
when we have it working. We are still deciding on whether to use Spark or
Apache Beam.

Just to clarify my previous confusion, I assumed the TS wrappers were so
you could avoid creating multiple pipelines and just run one instance of
the pipeline with a separate JCAS per thread. I thought the main motivation
behind that would be to avoid loading >1 dictionaries into memory, for
example. But it sounds like I was mistaken. With respect to sharing
resources, are static variables the main concern? Do you know if this is a
problem for any of the annotators in the default clinical pipeline (the
regular components, not the thread safe ones)? From Peter's response (I am
not sure if that split off into another forum thread because the subject
changed), it sounds like it may not be a problem? I'd like to really
understand thread-safe with respect to core cTAKES components (with the
caveat that community-created annotators could be implemented in any number
of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy
to contribute documentation back to the wiki once I feel I have a solid
grasp on it.

Peter- have you made your pipeline pool code available anywhere?

On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi all,
>
> >Is there any known reason that you can't create a pipeline pool, but keep
> everything in the same process?
> -- No, but ...
> > Is it safe to load multiple pipelines in
> the same process as long as only one thread can access each one at a time
> (we plan to use this in a Spark pipeline).
> -- If you are talking about oob ctakes being the process, only a single
> pipeline will run on multiple threads.  The threads will share resources,
> static variables, etc. and the  pipeline will give you terrible results and
> very quickly crash.  That is why I wrote the thread-safe wrappers.
> -- That being said, supposedly you can configure spark to handle this by
> keeping everything contained in a unique copy per thread.  Sort of like
> ThreadLocal (I think), but more effective on a full-pipeline level.
>
> > it must have reduced the DefaultJCasTermAnnotator to a singleton object
> in memory.
> -- Yes.  The thread-safe pipeline is not meant to have siblings in the
> same process - the wrappers can only do so much.  That being said, I am
> pretty sure that the Default... is thread-safe so it doesn't actually need
> the wrapper.  Regardless, the rest of the pipeline would crash.
>
> Jeff, can you share information about your efforts on spark?  If we could
> get that working and in standard ctakes it would be fantastic.
>
> I hope that this information is useful.
>
> Sean
>
>
>
> ________________________________________
> From: Jeffrey Miller <je...@gmail.com>
> Sent: Friday, March 8, 2019 11:23 AM
> To: dev@ctakes.apache.org
> Subject: Re: ctake web service [EXTERNAL]
>
> Is there any known reason that you can't create a pipeline pool, but keep
> everything in the same process? Is it safe to load multiple pipelines in
> the same process as long as only one thread can access each one at a time
> (we plan to use this in a Spark pipeline). One caveat I have noticed- it
> seems like if I use the thread safe components to build a pipeline pool,
> only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> process. For example, I was trying to take advantage of the ability to
> switch pipelines via a query parameter that is suggested at in the code for
> the rest service. The two pipelines used different ontology dictionaries,
> but it seemed like with the thread safe components it must have reduced
> the DefaultJCasTermAnnotator to a singleton object in memory, because it
> only used the first dictionary instantiated. Either way, given how Sean
> described how the thread safe components worked above, you probably
> wouldn't want to use them in a pipeline pool, assuming that the problems
> with threading was limited to multiple threads access the same pipeline at
> the same time, and not having multiple pipelines loaded into memory each
> accessed by only a single thread.
>
> On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> wrote:
>
> > I thought about creating a queue that acts as traffic cop.  Only the
> > traffic cop calls the WS.  I also want to test multiple WS running on
> > different port.  Traffic cop calls which every WS is available and keep
> > track of WS statuses.  With all this processing going, it might kill the
> > power for blocks.
> >
> > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > Hi all,
> > >
> > > I guess that a quick test could be run with a multi-threaded pipeline.
> > > Tim, for some reason I recall you checking in one with a dockerfile.
> > Maybe
> > > not, and it might not be the default in the service.  Anyway, you could
> > set
> > > the procs to something like 50 and throw 50 users at it.  It definitely
> > > does not scale anything close to linearly.  ctakes aes aren't build for
> > > thread-safety, so they are all wrapped with locks and there is a lot of
> > > thread contention.  However, running such a test might indicate the
> > source
> > > of the problem.
> > >
> > > The other option is to create a queue that collects post calls and
> doles
> > > them out serially to a single pipeline.  User #50 would probably not
> > > appreciate it though ...
> > > ________________________________________
> > > From: gandhi rajan <ga...@gmail.com>
> > > Sent: Friday, March 8, 2019 10:02 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: ctake web service [EXTERNAL]
> > >
> > > Hi Kathy,
> > >
> > > I guess the initializations happens in post construct method. So if we
> > > could synchronize that I feel we can get away from the problem.
> > > Unfortunately I m not able to tet this as my setup is gone with my old
> > job.
> > > Try it out.
> > >
> > > Regards,
> > > Gandhi.
> > >
> > > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com>
> wrote:
> > >
> > > > Tim,
> > > >
> > > > Thanks for reply.  I'm continuing the research.  With all the layers
> > that
> > > > wrap around this, you would think we can handle this suggestion.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > >
> > > > > That's a good question that I've also heard from others, and
> > > > unfortunately
> > > > > I don't know the answer. My use cases are typically a single job
> at a
> > > > time
> > > > > making sequential calls, so I wasn't stressing it with multiple
> > > > > asynchronous calls. I would've thought that the Tomcat container
> > would
> > > > have
> > > > > some ability to manage that though!
> > > > > Tim
> > > > >
> > > > > ________________________________________
> > > > > From: Kathy Ferro <he...@gmail.com>
> > > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > >
> > > > > Tim,
> > > > >
> > > > > Does docker solution handle multiple instances?  I tested the Rest
> > Web
> > > > > Service with 2 requests at the same time, it errors out.  I removed
> > the
> > > > > part that write the result xml file to the disc; it still error
> out.
> > > > >
> > > > > Best,
> > > > > Kathy
> > > > >
> > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > > 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 <ga...@gmail.com>
> > > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > > To: 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 <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> 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
> > > > > > > > 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
> > > > > > !!!"
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Regards,
> > > Gandhi
> > >
> > > "The best way to find urself is to lose urself in the service of others
> > > !!!"
> > >
> >
>

Re: ctake web service [EXTERNAL]

[Jeffrey Miller <je...@gmail.com>]

Thanks for your response Sean- we are still working on this (and have some
things to look into given your last response), but I will share details
when we have it working. We are still deciding on whether to use Spark or
Apache Beam.

Just to clarify my previous confusion, I assumed the TS wrappers were so
you could avoid creating multiple pipelines and just run one instance of
the pipeline with a separate JCAS per thread. I thought the main motivation
behind that would be to avoid loading >1 dictionaries into memory, for
example. But it sounds like I was mistaken. With respect to sharing
resources, are static variables the main concern? Do you know if this is a
problem for any of the annotators in the default clinical pipeline (the
regular components, not the thread safe ones)? From Peter's response (I am
not sure if that split off into another forum thread because the subject
changed), it sounds like it may not be a problem? I'd like to really
understand thread-safe with respect to core cTAKES components (with the
caveat that community-created annotators could be implemented in any number
of ways, making it hard to declare cTAKES is "thread-safe"). I'd be happy
to contribute documentation back to the wiki once I feel I have a solid
grasp on it.

Peter- have you made your pipeline pool code available anywhere?

On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi all,
>
> >Is there any known reason that you can't create a pipeline pool, but keep
> everything in the same process?
> -- No, but ...
> > Is it safe to load multiple pipelines in
> the same process as long as only one thread can access each one at a time
> (we plan to use this in a Spark pipeline).
> -- If you are talking about oob ctakes being the process, only a single
> pipeline will run on multiple threads.  The threads will share resources,
> static variables, etc. and the  pipeline will give you terrible results and
> very quickly crash.  That is why I wrote the thread-safe wrappers.
> -- That being said, supposedly you can configure spark to handle this by
> keeping everything contained in a unique copy per thread.  Sort of like
> ThreadLocal (I think), but more effective on a full-pipeline level.
>
> > it must have reduced the DefaultJCasTermAnnotator to a singleton object
> in memory.
> -- Yes.  The thread-safe pipeline is not meant to have siblings in the
> same process - the wrappers can only do so much.  That being said, I am
> pretty sure that the Default... is thread-safe so it doesn't actually need
> the wrapper.  Regardless, the rest of the pipeline would crash.
>
> Jeff, can you share information about your efforts on spark?  If we could
> get that working and in standard ctakes it would be fantastic.
>
> I hope that this information is useful.
>
> Sean
>
>
>
> ________________________________________
> From: Jeffrey Miller <je...@gmail.com>
> Sent: Friday, March 8, 2019 11:23 AM
> To: dev@ctakes.apache.org
> Subject: Re: ctake web service [EXTERNAL]
>
> Is there any known reason that you can't create a pipeline pool, but keep
> everything in the same process? Is it safe to load multiple pipelines in
> the same process as long as only one thread can access each one at a time
> (we plan to use this in a Spark pipeline). One caveat I have noticed- it
> seems like if I use the thread safe components to build a pipeline pool,
> only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> process. For example, I was trying to take advantage of the ability to
> switch pipelines via a query parameter that is suggested at in the code for
> the rest service. The two pipelines used different ontology dictionaries,
> but it seemed like with the thread safe components it must have reduced
> the DefaultJCasTermAnnotator to a singleton object in memory, because it
> only used the first dictionary instantiated. Either way, given how Sean
> described how the thread safe components worked above, you probably
> wouldn't want to use them in a pipeline pool, assuming that the problems
> with threading was limited to multiple threads access the same pipeline at
> the same time, and not having multiple pipelines loaded into memory each
> accessed by only a single thread.
>
> On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> wrote:
>
> > I thought about creating a queue that acts as traffic cop.  Only the
> > traffic cop calls the WS.  I also want to test multiple WS running on
> > different port.  Traffic cop calls which every WS is available and keep
> > track of WS statuses.  With all this processing going, it might kill the
> > power for blocks.
> >
> > On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> > > Hi all,
> > >
> > > I guess that a quick test could be run with a multi-threaded pipeline.
> > > Tim, for some reason I recall you checking in one with a dockerfile.
> > Maybe
> > > not, and it might not be the default in the service.  Anyway, you could
> > set
> > > the procs to something like 50 and throw 50 users at it.  It definitely
> > > does not scale anything close to linearly.  ctakes aes aren't build for
> > > thread-safety, so they are all wrapped with locks and there is a lot of
> > > thread contention.  However, running such a test might indicate the
> > source
> > > of the problem.
> > >
> > > The other option is to create a queue that collects post calls and
> doles
> > > them out serially to a single pipeline.  User #50 would probably not
> > > appreciate it though ...
> > > ________________________________________
> > > From: gandhi rajan <ga...@gmail.com>
> > > Sent: Friday, March 8, 2019 10:02 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: ctake web service [EXTERNAL]
> > >
> > > Hi Kathy,
> > >
> > > I guess the initializations happens in post construct method. So if we
> > > could synchronize that I feel we can get away from the problem.
> > > Unfortunately I m not able to tet this as my setup is gone with my old
> > job.
> > > Try it out.
> > >
> > > Regards,
> > > Gandhi.
> > >
> > > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com>
> wrote:
> > >
> > > > Tim,
> > > >
> > > > Thanks for reply.  I'm continuing the research.  With all the layers
> > that
> > > > wrap around this, you would think we can handle this suggestion.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > > Timothy.Miller@childrens.harvard.edu> wrote:
> > > >
> > > > > That's a good question that I've also heard from others, and
> > > > unfortunately
> > > > > I don't know the answer. My use cases are typically a single job
> at a
> > > > time
> > > > > making sequential calls, so I wasn't stressing it with multiple
> > > > > asynchronous calls. I would've thought that the Tomcat container
> > would
> > > > have
> > > > > some ability to manage that though!
> > > > > Tim
> > > > >
> > > > > ________________________________________
> > > > > From: Kathy Ferro <he...@gmail.com>
> > > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: Re: ctake web service [EXTERNAL]
> > > > >
> > > > > Tim,
> > > > >
> > > > > Does docker solution handle multiple instances?  I tested the Rest
> > Web
> > > > > Service with 2 requests at the same time, it errors out.  I removed
> > the
> > > > > part that write the result xml file to the disc; it still error
> out.
> > > > >
> > > > > Best,
> > > > > Kathy
> > > > >
> > > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > > 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 <ga...@gmail.com>
> > > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > > To: 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 <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> 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
> > > > > > > > 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
> > > > > > !!!"
> > > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Regards,
> > > Gandhi
> > >
> > > "The best way to find urself is to lose urself in the service of others
> > > !!!"
> > >
> >
>

Re: ctake web service [EXTERNAL]

["Finan, Sean" <Se...@childrens.harvard.edu>]

Hi all,

>Is there any known reason that you can't create a pipeline pool, but keep
everything in the same process?
-- No, but ...
> Is it safe to load multiple pipelines in
the same process as long as only one thread can access each one at a time
(we plan to use this in a Spark pipeline).
-- If you are talking about oob ctakes being the process, only a single pipeline will run on multiple threads.  The threads will share resources, static variables, etc. and the  pipeline will give you terrible results and very quickly crash.  That is why I wrote the thread-safe wrappers.
-- That being said, supposedly you can configure spark to handle this by keeping everything contained in a unique copy per thread.  Sort of like ThreadLocal (I think), but more effective on a full-pipeline level.

> it must have reduced the DefaultJCasTermAnnotator to a singleton object in memory.
-- Yes.  The thread-safe pipeline is not meant to have siblings in the same process - the wrappers can only do so much.  That being said, I am pretty sure that the Default... is thread-safe so it doesn't actually need the wrapper.  Regardless, the rest of the pipeline would crash.

Jeff, can you share information about your efforts on spark?  If we could get that working and in standard ctakes it would be fantastic.

I hope that this information is useful.

Sean



________________________________________
From: Jeffrey Miller <je...@gmail.com>
Sent: Friday, March 8, 2019 11:23 AM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]

Is there any known reason that you can't create a pipeline pool, but keep
everything in the same process? Is it safe to load multiple pipelines in
the same process as long as only one thread can access each one at a time
(we plan to use this in a Spark pipeline). One caveat I have noticed- it
seems like if I use the thread safe components to build a pipeline pool,
only one dictionary for the DefaultJCasTermAnnotator can be loaded per
process. For example, I was trying to take advantage of the ability to
switch pipelines via a query parameter that is suggested at in the code for
the rest service. The two pipelines used different ontology dictionaries,
but it seemed like with the thread safe components it must have reduced
the DefaultJCasTermAnnotator to a singleton object in memory, because it
only used the first dictionary instantiated. Either way, given how Sean
described how the thread safe components worked above, you probably
wouldn't want to use them in a pipeline pool, assuming that the problems
with threading was limited to multiple threads access the same pipeline at
the same time, and not having multiple pipelines loaded into memory each
accessed by only a single thread.

On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
wrote:

> I thought about creating a queue that acts as traffic cop.  Only the
> traffic cop calls the WS.  I also want to test multiple WS running on
> different port.  Traffic cop calls which every WS is available and keep
> track of WS statuses.  With all this processing going, it might kill the
> power for blocks.
>
> On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi all,
> >
> > I guess that a quick test could be run with a multi-threaded pipeline.
> > Tim, for some reason I recall you checking in one with a dockerfile.
> Maybe
> > not, and it might not be the default in the service.  Anyway, you could
> set
> > the procs to something like 50 and throw 50 users at it.  It definitely
> > does not scale anything close to linearly.  ctakes aes aren't build for
> > thread-safety, so they are all wrapped with locks and there is a lot of
> > thread contention.  However, running such a test might indicate the
> source
> > of the problem.
> >
> > The other option is to create a queue that collects post calls and doles
> > them out serially to a single pipeline.  User #50 would probably not
> > appreciate it though ...
> > ________________________________________
> > From: gandhi rajan <ga...@gmail.com>
> > Sent: Friday, March 8, 2019 10:02 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Hi Kathy,
> >
> > I guess the initializations happens in post construct method. So if we
> > could synchronize that I feel we can get away from the problem.
> > Unfortunately I m not able to tet this as my setup is gone with my old
> job.
> > Try it out.
> >
> > Regards,
> > Gandhi.
> >
> > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:
> >
> > > Tim,
> > >
> > > Thanks for reply.  I'm continuing the research.  With all the layers
> that
> > > wrap around this, you would think we can handle this suggestion.
> > >
> > >
> > >
> > >
> > >
> > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > Timothy.Miller@childrens.harvard.edu> wrote:
> > >
> > > > That's a good question that I've also heard from others, and
> > > unfortunately
> > > > I don't know the answer. My use cases are typically a single job at a
> > > time
> > > > making sequential calls, so I wasn't stressing it with multiple
> > > > asynchronous calls. I would've thought that the Tomcat container
> would
> > > have
> > > > some ability to manage that though!
> > > > Tim
> > > >
> > > > ________________________________________
> > > > From: Kathy Ferro <he...@gmail.com>
> > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: ctake web service [EXTERNAL]
> > > >
> > > > Tim,
> > > >
> > > > Does docker solution handle multiple instances?  I tested the Rest
> Web
> > > > Service with 2 requests at the same time, it errors out.  I removed
> the
> > > > part that write the result xml file to the disc; it still error out.
> > > >
> > > > Best,
> > > > Kathy
> > > >
> > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > 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 <ga...@gmail.com>
> > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > To: 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 <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> 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
> > > > > > > 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
> > > > > !!!"
> > > > >
> > > >
> > >
> >
> >
> > --
> > Regards,
> > Gandhi
> >
> > "The best way to find urself is to lose urself in the service of others
> > !!!"
> >
>

Re: ctake web service and multi-threading

[Peter Abramowitsch <pa...@gmail.com>]

After seeing some of the thread contention issues last year, I started from scratch to create a pipeline pool that sizes itself according to the memory that’s available.  Each instance contains the complete pipeline including the Term Annotator and a re-settable JCas object.   I don’t use any of the thread constructs in piper files - to not confuse the issue.  All of this is accessed via a web service with a multi threaded dispatcher (SparkJava).  This implementation does allow each of the pool members to initialize its pipeline serially though.  It only starts handling requests when all members are ready.

It seems to be completely stable - running for hours with as many clients as the memory can handle.   Looking at performance stats, one can see that, single threaded, there are latencies introduced by dictionary lookups, and these ‘holes’ are filled when multi threading, allowing a much greater ability to saturate the cpu.  After a certain point, of course, when all cores are saturated, the performance curve flattens out. But there are no exceptions.   

Introducing a wait  in the pool’s getMember() allows the system to deal effectively with overloading - ie, what to do when all members are busy: there are more requests than the pool-size will handle.  

I don’t think there would be a problem to have pool members with differently configured pipelines, but I never tried that.  And I suppose it could be that one of the annotators in the community might not work if it had any statics.  But I’m guessing that they would primarily be configuration items set in the annotator’s initialization phase.   

Long story short - with a bit of extra packaging, you can get it to work without tampering with the core code.

Peter
Sent from my iPad

> On Mar 8, 2019, at 08:23, Jeffrey Miller <je...@gmail.com> wrote:
> 
> Is there any known reason that you can't create a pipeline pool, but keep
> everything in the same process? Is it safe to load multiple pipelines in
> the same process as long as only one thread can access each one at a time
> (we plan to use this in a Spark pipeline). One caveat I have noticed- it
> seems like if I use the thread safe components to build a pipeline pool,
> only one dictionary for the DefaultJCasTermAnnotator can be loaded per
> process. For example, I was trying to take advantage of the ability to
> switch pipelines via a query parameter that is suggested at in the code for
> the rest service. The two pipelines used different ontology dictionaries,
> but it seemed like with the thread safe components it must have reduced
> the DefaultJCasTermAnnotator to a singleton object in memory, because it
> only used the first dictionary instantiated. Either way, given how Sean
> described how the thread safe components worked above, you probably
> wouldn't want to use them in a pipeline pool, assuming that the problems
> with threading was limited to multiple threads access the same pipeline at
> the same time, and not having multiple pipelines loaded into memory each
> accessed by only a single thread.
> 
> On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
> wrote:
> 
>> I thought about creating a queue that acts as traffic cop.  Only the
>> traffic cop calls the WS.  I also want to test multiple WS running on
>> different port.  Traffic cop calls which every WS is available and keep
>> track of WS statuses.  With all this processing going, it might kill the
>> power for blocks.
>> 
>> On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
>> Sean.Finan@childrens.harvard.edu> wrote:
>> 
>>> Hi all,
>>> 
>>> I guess that a quick test could be run with a multi-threaded pipeline.
>>> Tim, for some reason I recall you checking in one with a dockerfile.
>> Maybe
>>> not, and it might not be the default in the service.  Anyway, you could
>> set
>>> the procs to something like 50 and throw 50 users at it.  It definitely
>>> does not scale anything close to linearly.  ctakes aes aren't build for
>>> thread-safety, so they are all wrapped with locks and there is a lot of
>>> thread contention.  However, running such a test might indicate the
>> source
>>> of the problem.
>>> 
>>> The other option is to create a queue that collects post calls and doles
>>> them out serially to a single pipeline.  User #50 would probably not
>>> appreciate it though ...
>>> ________________________________________
>>> From: gandhi rajan <ga...@gmail.com>
>>> Sent: Friday, March 8, 2019 10:02 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: ctake web service [EXTERNAL]
>>> 
>>> Hi Kathy,
>>> 
>>> I guess the initializations happens in post construct method. So if we
>>> could synchronize that I feel we can get away from the problem.
>>> Unfortunately I m not able to tet this as my setup is gone with my old
>> job.
>>> Try it out.
>>> 
>>> Regards,
>>> Gandhi.
>>> 
>>>> On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:
>>>> 
>>>> Tim,
>>>> 
>>>> Thanks for reply.  I'm continuing the research.  With all the layers
>> that
>>>> wrap around this, you would think we can handle this suggestion.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
>>>> Timothy.Miller@childrens.harvard.edu> wrote:
>>>> 
>>>>> That's a good question that I've also heard from others, and
>>>> unfortunately
>>>>> I don't know the answer. My use cases are typically a single job at a
>>>> time
>>>>> making sequential calls, so I wasn't stressing it with multiple
>>>>> asynchronous calls. I would've thought that the Tomcat container
>> would
>>>> have
>>>>> some ability to manage that though!
>>>>> Tim
>>>>> 
>>>>> ________________________________________
>>>>> From: Kathy Ferro <he...@gmail.com>
>>>>> Sent: Thursday, March 7, 2019 6:10 PM
>>>>> To: dev@ctakes.apache.org
>>>>> Subject: Re: ctake web service [EXTERNAL]
>>>>> 
>>>>> Tim,
>>>>> 
>>>>> Does docker solution handle multiple instances?  I tested the Rest
>> Web
>>>>> Service with 2 requests at the same time, it errors out.  I removed
>> the
>>>>> part that write the result xml file to the disc; it still error out.
>>>>> 
>>>>> Best,
>>>>> Kathy
>>>>> 
>>>>> On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
>>>>> 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 <ga...@gmail.com>
>>>>>> Sent: Monday, March 4, 2019 10:43 AM
>>>>>> To: 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 <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> 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
>>>>>>>> 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
>>>>>> !!!"
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> Regards,
>>> Gandhi
>>> 
>>> "The best way to find urself is to lose urself in the service of others
>>> !!!"
>>> 
>> 

Re: ctake web service [EXTERNAL]

[Jeffrey Miller <je...@gmail.com>]

Is there any known reason that you can't create a pipeline pool, but keep
everything in the same process? Is it safe to load multiple pipelines in
the same process as long as only one thread can access each one at a time
(we plan to use this in a Spark pipeline). One caveat I have noticed- it
seems like if I use the thread safe components to build a pipeline pool,
only one dictionary for the DefaultJCasTermAnnotator can be loaded per
process. For example, I was trying to take advantage of the ability to
switch pipelines via a query parameter that is suggested at in the code for
the rest service. The two pipelines used different ontology dictionaries,
but it seemed like with the thread safe components it must have reduced
the DefaultJCasTermAnnotator to a singleton object in memory, because it
only used the first dictionary instantiated. Either way, given how Sean
described how the thread safe components worked above, you probably
wouldn't want to use them in a pipeline pool, assuming that the problems
with threading was limited to multiple threads access the same pipeline at
the same time, and not having multiple pipelines loaded into memory each
accessed by only a single thread.

On Fri, Mar 8, 2019 at 11:06 AM Kathy Ferro <he...@gmail.com>
wrote:

> I thought about creating a queue that acts as traffic cop.  Only the
> traffic cop calls the WS.  I also want to test multiple WS running on
> different port.  Traffic cop calls which every WS is available and keep
> track of WS statuses.  With all this processing going, it might kill the
> power for blocks.
>
> On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi all,
> >
> > I guess that a quick test could be run with a multi-threaded pipeline.
> > Tim, for some reason I recall you checking in one with a dockerfile.
> Maybe
> > not, and it might not be the default in the service.  Anyway, you could
> set
> > the procs to something like 50 and throw 50 users at it.  It definitely
> > does not scale anything close to linearly.  ctakes aes aren't build for
> > thread-safety, so they are all wrapped with locks and there is a lot of
> > thread contention.  However, running such a test might indicate the
> source
> > of the problem.
> >
> > The other option is to create a queue that collects post calls and doles
> > them out serially to a single pipeline.  User #50 would probably not
> > appreciate it though ...
> > ________________________________________
> > From: gandhi rajan <ga...@gmail.com>
> > Sent: Friday, March 8, 2019 10:02 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Hi Kathy,
> >
> > I guess the initializations happens in post construct method. So if we
> > could synchronize that I feel we can get away from the problem.
> > Unfortunately I m not able to tet this as my setup is gone with my old
> job.
> > Try it out.
> >
> > Regards,
> > Gandhi.
> >
> > On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:
> >
> > > Tim,
> > >
> > > Thanks for reply.  I'm continuing the research.  With all the layers
> that
> > > wrap around this, you would think we can handle this suggestion.
> > >
> > >
> > >
> > >
> > >
> > > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > > Timothy.Miller@childrens.harvard.edu> wrote:
> > >
> > > > That's a good question that I've also heard from others, and
> > > unfortunately
> > > > I don't know the answer. My use cases are typically a single job at a
> > > time
> > > > making sequential calls, so I wasn't stressing it with multiple
> > > > asynchronous calls. I would've thought that the Tomcat container
> would
> > > have
> > > > some ability to manage that though!
> > > > Tim
> > > >
> > > > ________________________________________
> > > > From: Kathy Ferro <he...@gmail.com>
> > > > Sent: Thursday, March 7, 2019 6:10 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: ctake web service [EXTERNAL]
> > > >
> > > > Tim,
> > > >
> > > > Does docker solution handle multiple instances?  I tested the Rest
> Web
> > > > Service with 2 requests at the same time, it errors out.  I removed
> the
> > > > part that write the result xml file to the disc; it still error out.
> > > >
> > > > Best,
> > > > Kathy
> > > >
> > > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > > 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 <ga...@gmail.com>
> > > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > > To: 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 <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> 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
> > > > > > > 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
> > > > > !!!"
> > > > >
> > > >
> > >
> >
> >
> > --
> > Regards,
> > Gandhi
> >
> > "The best way to find urself is to lose urself in the service of others
> > !!!"
> >
>

Re: ctake web service [EXTERNAL]

[Kathy Ferro <he...@gmail.com>]

I thought about creating a queue that acts as traffic cop.  Only the
traffic cop calls the WS.  I also want to test multiple WS running on
different port.  Traffic cop calls which every WS is available and keep
track of WS statuses.  With all this processing going, it might kill the
power for blocks.

On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi all,
>
> I guess that a quick test could be run with a multi-threaded pipeline.
> Tim, for some reason I recall you checking in one with a dockerfile.  Maybe
> not, and it might not be the default in the service.  Anyway, you could set
> the procs to something like 50 and throw 50 users at it.  It definitely
> does not scale anything close to linearly.  ctakes aes aren't build for
> thread-safety, so they are all wrapped with locks and there is a lot of
> thread contention.  However, running such a test might indicate the source
> of the problem.
>
> The other option is to create a queue that collects post calls and doles
> them out serially to a single pipeline.  User #50 would probably not
> appreciate it though ...
> ________________________________________
> From: gandhi rajan <ga...@gmail.com>
> Sent: Friday, March 8, 2019 10:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: ctake web service [EXTERNAL]
>
> Hi Kathy,
>
> I guess the initializations happens in post construct method. So if we
> could synchronize that I feel we can get away from the problem.
> Unfortunately I m not able to tet this as my setup is gone with my old job.
> Try it out.
>
> Regards,
> Gandhi.
>
> On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:
>
> > Tim,
> >
> > Thanks for reply.  I'm continuing the research.  With all the layers that
> > wrap around this, you would think we can handle this suggestion.
> >
> >
> >
> >
> >
> > On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> > Timothy.Miller@childrens.harvard.edu> wrote:
> >
> > > That's a good question that I've also heard from others, and
> > unfortunately
> > > I don't know the answer. My use cases are typically a single job at a
> > time
> > > making sequential calls, so I wasn't stressing it with multiple
> > > asynchronous calls. I would've thought that the Tomcat container would
> > have
> > > some ability to manage that though!
> > > Tim
> > >
> > > ________________________________________
> > > From: Kathy Ferro <he...@gmail.com>
> > > Sent: Thursday, March 7, 2019 6:10 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: ctake web service [EXTERNAL]
> > >
> > > Tim,
> > >
> > > Does docker solution handle multiple instances?  I tested the Rest Web
> > > Service with 2 requests at the same time, it errors out.  I removed the
> > > part that write the result xml file to the disc; it still error out.
> > >
> > > Best,
> > > Kathy
> > >
> > > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > > 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 <ga...@gmail.com>
> > > > Sent: Monday, March 4, 2019 10:43 AM
> > > > To: 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 <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> 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
> > > > > > 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
> > > > !!!"
> > > >
> > >
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>

Re: ctake web service [EXTERNAL]

["Finan, Sean" <Se...@childrens.harvard.edu>]

Hi all,

I guess that a quick test could be run with a multi-threaded pipeline.  Tim, for some reason I recall you checking in one with a dockerfile.  Maybe not, and it might not be the default in the service.  Anyway, you could set the procs to something like 50 and throw 50 users at it.  It definitely does not scale anything close to linearly.  ctakes aes aren't build for thread-safety, so they are all wrapped with locks and there is a lot of thread contention.  However, running such a test might indicate the source of the problem.

The other option is to create a queue that collects post calls and doles them out serially to a single pipeline.  User #50 would probably not appreciate it though ...
________________________________________
From: gandhi rajan <ga...@gmail.com>
Sent: Friday, March 8, 2019 10:02 AM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]

Hi Kathy,

I guess the initializations happens in post construct method. So if we
could synchronize that I feel we can get away from the problem.
Unfortunately I m not able to tet this as my setup is gone with my old job.
Try it out.

Regards,
Gandhi.

On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:

> Tim,
>
> Thanks for reply.  I'm continuing the research.  With all the layers that
> wrap around this, you would think we can handle this suggestion.
>
>
>
>
>
> On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> > That's a good question that I've also heard from others, and
> unfortunately
> > I don't know the answer. My use cases are typically a single job at a
> time
> > making sequential calls, so I wasn't stressing it with multiple
> > asynchronous calls. I would've thought that the Tomcat container would
> have
> > some ability to manage that though!
> > Tim
> >
> > ________________________________________
> > From: Kathy Ferro <he...@gmail.com>
> > Sent: Thursday, March 7, 2019 6:10 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Tim,
> >
> > Does docker solution handle multiple instances?  I tested the Rest Web
> > Service with 2 requests at the same time, it errors out.  I removed the
> > part that write the result xml file to the disc; it still error out.
> >
> > Best,
> > Kathy
> >
> > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > 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 <ga...@gmail.com>
> > > Sent: Monday, March 4, 2019 10:43 AM
> > > To: 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 <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> 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
> > > > > 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
> > > !!!"
> > >
> >
>


--
Regards,
Gandhi

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

Re: ctake web service [EXTERNAL]

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

Hi Kathy,

I guess the initializations happens in post construct method. So if we
could synchronize that I feel we can get away from the problem.
Unfortunately I m not able to tet this as my setup is gone with my old job.
Try it out.

Regards,
Gandhi.

On Friday, March 8, 2019, Kathy Ferro <he...@gmail.com> wrote:

> Tim,
>
> Thanks for reply.  I'm continuing the research.  With all the layers that
> wrap around this, you would think we can handle this suggestion.
>
>
>
>
>
> On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> > That's a good question that I've also heard from others, and
> unfortunately
> > I don't know the answer. My use cases are typically a single job at a
> time
> > making sequential calls, so I wasn't stressing it with multiple
> > asynchronous calls. I would've thought that the Tomcat container would
> have
> > some ability to manage that though!
> > Tim
> >
> > ________________________________________
> > From: Kathy Ferro <he...@gmail.com>
> > Sent: Thursday, March 7, 2019 6:10 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctake web service [EXTERNAL]
> >
> > Tim,
> >
> > Does docker solution handle multiple instances?  I tested the Rest Web
> > Service with 2 requests at the same time, it errors out.  I removed the
> > part that write the result xml file to the disc; it still error out.
> >
> > Best,
> > Kathy
> >
> > On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> > 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 <ga...@gmail.com>
> > > Sent: Monday, March 4, 2019 10:43 AM
> > > To: 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 <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> 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
> > > > > 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
> > > !!!"
> > >
> >
>


-- 
Regards,
Gandhi

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

Re: ctake web service [EXTERNAL]

[Kathy Ferro <he...@gmail.com>]

Tim,

Thanks for reply.  I'm continuing the research.  With all the layers that
wrap around this, you would think we can handle this suggestion.





On Thu, Mar 7, 2019 at 8:01 PM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> That's a good question that I've also heard from others, and unfortunately
> I don't know the answer. My use cases are typically a single job at a time
> making sequential calls, so I wasn't stressing it with multiple
> asynchronous calls. I would've thought that the Tomcat container would have
> some ability to manage that though!
> Tim
>
> ________________________________________
> From: Kathy Ferro <he...@gmail.com>
> Sent: Thursday, March 7, 2019 6:10 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctake web service [EXTERNAL]
>
> Tim,
>
> Does docker solution handle multiple instances?  I tested the Rest Web
> Service with 2 requests at the same time, it errors out.  I removed the
> part that write the result xml file to the disc; it still error out.
>
> Best,
> Kathy
>
> On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
> 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 <ga...@gmail.com>
> > Sent: Monday, March 4, 2019 10:43 AM
> > To: 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 <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> 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
> > > > 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
> > !!!"
> >
>

Re: ctake web service [EXTERNAL]

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

That's a good question that I've also heard from others, and unfortunately I don't know the answer. My use cases are typically a single job at a time making sequential calls, so I wasn't stressing it with multiple asynchronous calls. I would've thought that the Tomcat container would have some ability to manage that though!
Tim

________________________________________
From: Kathy Ferro <he...@gmail.com>
Sent: Thursday, March 7, 2019 6:10 PM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]

Tim,

Does docker solution handle multiple instances?  I tested the Rest Web
Service with 2 requests at the same time, it errors out.  I removed the
part that write the result xml file to the disc; it still error out.

Best,
Kathy

On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
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 <ga...@gmail.com>
> Sent: Monday, March 4, 2019 10:43 AM
> To: 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 <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> 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
> > > 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
> !!!"
>

Re: ctake web service [EXTERNAL]

[Kathy Ferro <he...@gmail.com>]

Tim,

Does docker solution handle multiple instances?  I tested the Rest Web
Service with 2 requests at the same time, it errors out.  I removed the
part that write the result xml file to the disc; it still error out.

Best,
Kathy

On Mon, Mar 4, 2019 at 10:52 AM Miller, Timothy <
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 <ga...@gmail.com>
> Sent: Monday, March 4, 2019 10:43 AM
> To: 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 <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> 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
> > > 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
> !!!"
>