RE: ctakes-web-rest changes

[Gandhi Rajan Natarajan]

Hi Tim,

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

Regards,
Gandhi

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

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

Please take a look at the following issue with the attached patch and let me 
know if there are any obvious problems.
https://issues.apache.org/jira/browse/CTAKES-529

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

Tim

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RE: Compiling Ctakes from Subversion

[Gandhi Rajan Natarajan]

Hi Peter,

I use Java 1.8.0_171. Checked out the source code from - 
https://svn.apache.org/repos/asf/ctakes/trunk

I don’t get any compilation issue in ctakes-temporal module running the command 
- " mvn clean install"

Regards,
Gandhi

-Original Message-
From: Peter Abramowitsch 
Sent: Sunday, November 11, 2018 4:50 PM
To: dev@ctakes.apache.org
Subject: Compiling Ctakes from Subversion

I cannot finds a configuration which permits a complete compile of the SVN
4.0.1 version of the code

Is anyone having this problem?

When compiling using JAVA 1.8.x  you get compile errors in ctakes-temporal 
There are various rather oblique assignments between Generic types, which 
produce errors of this sort.

[ERROR]
/Users/peterabramowitsch/projects/apache/ctakes/trunk2/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java:[899,45]
[unchecked] unchecked generic array creation for varargs parameter of type 
Collection[]
[ERROR]   where CAP#1 is a fresh type-variable:
CAP#1 extends TOP from capture of ? extends TOP

Then if you try to compile it using JAVA 1.9.x ctakes-temporal compiles but now 
you have a problem with ctakes-ytex which depends on some jaxb modules for the 
hibernate schema generation.
root cause:

Caused by: java.lang.ClassNotFoundException:
javax.activation.MimeTypeParseException
at
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:244)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:230)
... 48 more

These are no longer included by default with the JDK   Following help out
on the net, I added this dependencies to that projects's pom.


javax.activation
activation
1.1.1


But the problem did not go away.

*So my question is thia:   Has anybody been able to compile the current SVN
version from top to bottom, and if so, exactly what environment are you using 
to do it*
*Java Version?Mods to  POM files, Source Files etc.*

Peter
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RE: [Request for information] - how do I become a committer?

[Gandhi Rajan Natarajan]

Thanks for providing the access James.

@Rumpa, The broken link is corrected now.

Regards,
Gandhi

-Original Message-
From: James Masanz 
Sent: Friday, October 26, 2018 10:04 PM
To: dev@ctakes.apache.org
Subject: Re: [Request for information] - how do I become a committer?

Great to hear you are interested!  Welcome to the cTAKES community.

Thanks for pointing out the broken link. Here's the newer name for that
page:
https://ctakes.apache.org/pmc-faqs.html

If you send your apache confluence user ID, I can give you access to update the 
wiki pages for cTAKES.  You can get access to update the wiki before becoming a 
committer (of code).

-- James


On Thu, Oct 25, 2018 at 1:23 PM Rumpa Giri  wrote:

> Hello,
>
> I am just beginning my journey on cTakes.
>
> On the following link, trying to click the link on committer but it is
> a 404.
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES
>
> [image: image.png]
>
> The committer link points to this URL =
> http://ctakes.apache.org/ppmc-faqs.html but leads to a 404.
>
> I did acquire a username for apache confluence and would be happy to
> help fix the broken link if you can please share it with me.
>
> Looking forward to hearing back soon.
>
> Best Regards,
> Rumpa Giri
> (cTakes newbie 1 week old)
>
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RE: Question regarding Dictionary Creator GUI

[Gandhi Rajan Natarajan]

Hi Brihat,

I request you to check the dev mail archives. I have recently replied to a 
similar post.  The excerpt of the response is as follows:

I suggest you to have a look at this ctakes rest module - 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest

The custom dictionary XML needs to be placed in 
‘resources/org/apache/ctakes/dictionary/lookup/fast’ folder and ‘LookupXml’ 
attribute needs to be added in DictionarySubPipe.piper as follows:

add DefaultJCasTermAnnotator 
LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml

Regards,
Gandhi

-Original Message-
From: Brihat Sharma 
Sent: Friday, October 12, 2018 9:28 AM
To: dev@ctakes.apache.org
Subject: Re: Question regarding Dictionary Creator GUI

Hi Gandhi,

I was able to runDictionaryCreator via user interface and was able to build a 
dictionary. Now I am trying to point it following this link:
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary%2BCreator%2BGUI
In that link, it mentions that I have to set the fast dictionary parameter 
LookupXml to org/apache/ctakes/dictionary/lookup/fast/DictionaryName.xml. I 
wasn't able to figure out where I have to set the fast dictionary parameter 
exactly. Can you point me towards the right direction?

Thanks,
Brihat

On Wed, Oct 10, 2018 at 12:11 AM Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Brihat,
>
> Is your 'CTAKES_HOME' environment variable pointing to the right directory?
>
> Also I could see that you are trying to execute
> runDictionaryCreator.sh available under the checked out codebase from
> SVN. Did you build the complete cTAKES code before executing this?
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Brihat Sharma 
> Sent: Tuesday, October 9, 2018 10:32 PM
> To: dev@ctakes.apache.org
> Subject: Question regarding Dictionary Creator GUI
>
> Hi,
> I was trying to run custom dictionary creator GUI using the steps
> provided in the link below:
>
> https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+
> GUI
>
> I wasn't able to execute bin\runDictionaryCreator
>
> This is the error seen:
> ~/Brihat/cTakes/trunk/ctakes-distribution/src/main/bin$
> ./runDictionaryCreator.sh
> Error: Could not find or load main class
> org.apache.ctakes.gui.dictionary.DictionaryCreator
>
> Any help or suggestions to fix this issue?
>
>
> --
> Thank You,
> Brihat Sharma
> Email: brihat.sha...@gmail.com
> Cell: 817.773.9044
>
> *"Quality is much better than quantity. One home run is much better
> than two doubles."* - Steve Jobs This email and any files transmitted
> with it are confidential and intended solely for the use of the
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>


--
Thank You,
Brihat Sharma
Email: brihat.sha...@gmail.com
Cell: 817.773.9044

*"Quality is much better than quantity. One home run is much better than two 
doubles."* - Steve Jobs
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RE: Question regarding Dictionary Creator GUI

[Gandhi Rajan Natarajan]

Hi Brihat,

Is your 'CTAKES_HOME' environment variable pointing to the right directory?

Also I could see that you are trying to execute runDictionaryCreator.sh 
available under the checked out codebase from SVN. Did you build the complete 
cTAKES code before executing this?

Regards,
Gandhi

-Original Message-
From: Brihat Sharma 
Sent: Tuesday, October 9, 2018 10:32 PM
To: dev@ctakes.apache.org
Subject: Question regarding Dictionary Creator GUI

Hi,
I was trying to run custom dictionary creator GUI using the steps provided in 
the link below:

https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI

I wasn't able to execute bin\runDictionaryCreator

This is the error seen:
~/Brihat/cTakes/trunk/ctakes-distribution/src/main/bin$
./runDictionaryCreator.sh
Error: Could not find or load main class 
org.apache.ctakes.gui.dictionary.DictionaryCreator

Any help or suggestions to fix this issue?


--
Thank You,
Brihat Sharma
Email: brihat.sha...@gmail.com
Cell: 817.773.9044

*"Quality is much better than quantity. One home run is much better than two 
doubles."* - Steve Jobs
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RE: ctake web service [EXTERNAL]

[Gandhi Rajan Natarajan]

HI Sean,

We faced this issue while testing web service connecting to MySQL DB. So just 
wondering is there any time out setting option available in cTAKES 
implementation to retain connectivity?

-Original Message-
From: Finan, Sean 
Sent: Tuesday, August 21, 2018 7:33 PM
To: dev@ctakes.apache.org
Subject: RE: ctake web service [EXTERNAL]

Hi all,

Hsqldb is used as the (local) db server and the timeout most likely it is 
causing a timeout when read / write is inactive.  If anybody has the time it 
should be possible to manually disconnect after some ctakes inactivity and then 
manually connect when processing (re)starts.

I am really busy these days, and this is just an off-the-cuff idea, but if 
anybody out there can tackle this please let the devlist know about it.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Friday, August 17, 2018 9:43 AM
To: dev@ctakes.apache.org
Subject: RE: ctake web service [EXTERNAL]

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 
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
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RE: ctake web service

[Gandhi Rajan Natarajan]

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 
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
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RE: Family history identification in cTAKES

[Gandhi Rajan Natarajan]

Thanks James. Will have a check in this.

-Original Message-
From: James Masanz 
Sent: Friday, August 10, 2018 10:24 PM
To: dev@ctakes.apache.org
Subject: Re: Family history identification in cTAKES

Hi Gandhi,

The original annotator for discovering basic attributes of the original Named 
Entities used regular expressions to look for family history and was called NE 
Contexts when we were using XML descriptors for the annotators.
See the part about Status annotator on this wiki page:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+NE+Contexts


On Fri, Aug 10, 2018 at 8:21 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,
>
> Does cTAKES provides any annotators or any other mechanism to extract
> out family history information of a patient?
>
> For e.g, if the input is "Patient  has Cancer. His mother has arthritis".
> Is there a way to extract out arthritis as family disease history?
> 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,
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> information is strictly prohibited and against the law.
>
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Family history identification in cTAKES

[Gandhi Rajan Natarajan]

Hi All,

Does cTAKES provides any annotators or any other mechanism to extract out 
family history information of a patient?

For e.g, if the input is "Patient  has Cancer. His mother has arthritis". Is 
there a way to extract out arthritis as family disease history?
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RE: API to integrate programmatically

[Gandhi Rajan Natarajan]

Hi Ravi,

Please refer to the following github repository - 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest

This is a beta version of the cTAKES REST service implementation. Hope it helps.

-Original Message-
From: Ravindranath Oruganti 
Sent: Friday, July 27, 2018 3:13 PM
To: dev@ctakes.apache.org
Subject: API to integrate programmatically

Hi

Is there any API and sample tutorial on how to use cTAKES programmatically. We 
have big list of free text fields and the list keeps getting updated daily, so 
want to integrate in a service.

Regards
Ravi
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RE: UMLS credentials don't seem to let me run UMLS process XML files

[Gandhi Rajan Natarajan]

Hi Ken,

Similar issues are creeping up very frequently off late. Though I’m not sure 
what exactly is the issue here, in one of the recent mail chains Dmitriy has 
mentioned the following:

We had similar issues back in February (you can search the email archive). I 
was under impression
that this happened when multiple instances of cTAKES were run on the same 
machine under different
user names. A couple of times we were able to fix this problem by cleaning out 
a bunch of
files from /tmp (such as conn.xml), but that “fix” stopped working at some 
problem. We
weren’t able to determine the root cause of this problem...

Ultimately, we replaced CentOS with Ubuntu on that machine and the problem went 
away for good.


From: ken cottrell 
Sent: Tuesday, July 24, 2018 2:30 AM
To: dev@ctakes.apache.org
Subject: UMLS credentials don't seem to let me run UMLS process XML files

I've received my UMLS username and password and can login to UMLS site, but my 
credentials don't seem to be working properly on my local laptop cTAKES.

I can load this file ok - no errors:   - AggregatePlaintextProcessor.xml

But I get the attached errors on my command line, and popup window when I try 
to load either of these:

- AggregatePlaintextFastUMLSPRocessor.xml
- AggregatePlaintextUMLSPRocessor.xml

I assume this password is ok? I've tried both command line and entered into 
runctakesCVD.sh file (see attachments):

username = kencottrell
password = Cbug,2018

ERROR
--
23 Jul 2018 15:36:01  INFO UmlsUserApprover - Checking UMLS Account at 
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user kencottrell:

23 Jul 2018 15:36:02 ERROR UmlsUserApprover - java.lang.RuntimeException: 
Unexpected error: java.security.InvalidAlgorithmParameterException: the 
trustAnchors parameter must be non-empty

Ken Cottrell
(mobile)214-546-5100
(private email)cottrell@gmail.com
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RE: Run cTAKES continuously

[Gandhi Rajan Natarajan]

Hi Peter,

I do understand  that the module requires all ctakes dependency in place before 
building it. But the original plan was to commit this module into ctakes 
codebase so that it gets built along with other modules of ctakes and the war 
file will be ready for deployment.

In your case, the null content may be due to some XML parsing failure which was 
more specific to our requirement. Infact, if required you can send back the XML 
file returned from ctakes as is from REST service and do further processing 
based on your requirement. Unfortunately, we are not yet able to close this 
module completely to check-in the code to ctakes SVN as most of us are slammed 
with other works.


Regards,
Gandhi


-Original Message-
From: Peter Abramowitsch [mailto:pabramowit...@gmail.com]
Sent: Thursday, June 14, 2018 10:40 PM
To: dev@ctakes.apache.org
Subject: Re: Run cTAKES continuously

Hi Gandhi

I also had difficulty building it, and then finally when it built after I
tweaked some code in ctakes-temporal, it just returned null content.   I
figured it was in a state of flux.

But additionally as I discussed with Matthew Vita one of your colleagues, the 
project could be more useful if there were a way of building and developing 
with it also outside docker.  As currently packaged, it seems optimized for 
one-off fetch and build from straight to finish.  At the moment delegating all 
the heavy lifting to the shell script which docker-compose invokes means that 
for each trivial change, the system has to re-do a large amount of downloading 
and building.


On Thu, Jun 14, 2018 at 4:53 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Ted,
>
> Try building 'ctakes-web-rest' module in https://github.com/
> GoTeamEpsilon/ctakes-rest-service . Please let me know what's the
> issue you are facing.
>
> Please have a look at readme file once. You need to have all the
> ctakes dependency jars before building this module.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Ted Pikul [mailto:tedpik...@gmail.com]
> Sent: Thursday, June 14, 2018 8:12 PM
> To: dev@ctakes.apache.org
> Subject: Re: Run cTAKES continuously
>
> Thank you Peter and Gandhi.
>
> I’ve not been able to get the ctakes-rest-service to run successfully
> (using docker). I’m also not sure it supports UMLS credentials and it
> looks like the UMLS database is a local copy although I could be
> misunderstanding that. Due to the license confusion around running a
> local copy of UMLS database I’d rather just avoid that.
>
> I’ll try the implementation suggested by Peter.
>
> I also found that Tika has a cTAKES REST API, but unfortunately it
> loads the model on each request.
>
> On Wednesday, June 13, 2018, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com> wrote:
>
> > Hi Ted,
> >
> > The implementation suggested by Peter is already available in
> > https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/cta
> > ke
> > s-
> > web-rest
> >
> > Building this project will give you a WAR file which you need to
> > deploy in Tomcat.
> >
> > Regards,
> > Gandhi
> >
> > -Original Message-
> > From: Peter Abramowitsch [mailto:pabramowit...@gmail.com]
> > Sent: Wednesday, June 13, 2018 2:40 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: Run cTAKES continuously
> >
> > Sorry,  The mail sent before I was ready This is pseudocode
> >
> >// __aae is your analysis engine (there could be multiple)
> >while(more notes) {
> >  jcas.setDocumentText(note.getFree_text());
> >  _aae.process(jcas);
> >  // do something with the jcas contents here
> >  jcas.reset()
> >   }
> >
> > On Tue, Jun 12, 2018 at 11:06 PM, Peter Abramowitsch <
> > pabramowit...@gmail.com> wrote:
> >
> > > The best solution would be to put it in a server framework.  I was
> > > not able to get the EpsilonTeam server to work, but there's
> > > another tiny server version written in Scala which you can try.  I
> > > ended up doing one
> > using the
> > > Spark REST framework.   You can build a non server / non UI version
> which
> > > does run at the command line by coding it up (in Java) to create
> > > the pipeline or using a piper, then create a jCas which you
> > > use/reset/reuse
> > >
> > > The core of it would be a loop like this
> > >
> > > jcas.setDocumentText(note.getFree_text());
> > > _aae.process(jcas);
> > >
> > > On Tue, Jun 12, 2018 at 8:05 PM, Ted Pikul 
> wrote:
> > >
> > >> H

RE: Run cTAKES continuously

[Gandhi Rajan Natarajan]

Hi Ted,

Try building 'ctakes-web-rest' module in 
https://github.com/GoTeamEpsilon/ctakes-rest-service . Please let me know 
what's the issue you are facing.

Please have a look at readme file once. You need to have all the ctakes 
dependency jars before building this module.

Regards,
Gandhi


-Original Message-
From: Ted Pikul [mailto:tedpik...@gmail.com]
Sent: Thursday, June 14, 2018 8:12 PM
To: dev@ctakes.apache.org
Subject: Re: Run cTAKES continuously

Thank you Peter and Gandhi.

I’ve not been able to get the ctakes-rest-service to run successfully (using 
docker). I’m also not sure it supports UMLS credentials and it looks like the 
UMLS database is a local copy although I could be misunderstanding that. Due to 
the license confusion around running a local copy of UMLS database I’d rather 
just avoid that.

I’ll try the implementation suggested by Peter.

I also found that Tika has a cTAKES REST API, but unfortunately it loads the 
model on each request.

On Wednesday, June 13, 2018, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Ted,
>
> The implementation suggested by Peter is already available in
> https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctake
> s-
> web-rest
>
> Building this project will give you a WAR file which you need to
> deploy in Tomcat.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Peter Abramowitsch [mailto:pabramowit...@gmail.com]
> Sent: Wednesday, June 13, 2018 2:40 AM
> To: dev@ctakes.apache.org
> Subject: Re: Run cTAKES continuously
>
> Sorry,  The mail sent before I was ready This is pseudocode
>
>// __aae is your analysis engine (there could be multiple)
>while(more notes) {
>  jcas.setDocumentText(note.getFree_text());
>  _aae.process(jcas);
>  // do something with the jcas contents here
>  jcas.reset()
>   }
>
> On Tue, Jun 12, 2018 at 11:06 PM, Peter Abramowitsch <
> pabramowit...@gmail.com> wrote:
>
> > The best solution would be to put it in a server framework.  I was
> > not able to get the EpsilonTeam server to work, but there's another
> > tiny server version written in Scala which you can try.  I ended up
> > doing one
> using the
> > Spark REST framework.   You can build a non server / non UI version which
> > does run at the command line by coding it up (in Java) to create the
> > pipeline or using a piper, then create a jCas which you
> > use/reset/reuse
> >
> > The core of it would be a loop like this
> >
> > jcas.setDocumentText(note.getFree_text());
> > _aae.process(jcas);
> >
> > On Tue, Jun 12, 2018 at 8:05 PM, Ted Pikul  wrote:
> >
> >> Hi- I’ve been able to successfully run cTAKES from the command line
> >> as documented here:
> >> https://cwiki.apache.org/confluence/display/ctakes/default+
> >> clinical+pipeline
> >>
> >> This works great, but each time it runs it has to make the database
> >> connection using jdbc and load the model, which takes 15 seconds or so.
> >>
> >> Is there another script besides the runClinicalPipeline.sh that I
> >> can run to just keep this running and send new notes to it rather
> >> than getting the db connection and loading the model each time?
> >>
> >> I know there is the cTAKES rest server project:
> >> https://github.com/GoTeamEpsilon/ctakes-rest-service which I think
> >> might do what I’m looking to do.  but as it’s still in alpha stage,
> >> especially the docker piece of it, and I don’t really need a server
> >> I can just run from command line, I’m not sure this is the right
> >> solution for me.
> >>
> >> I tried looking at how the runctakesCVD.sh script works, as it does
> >> what I need but with the CVD UI, but I couldn’t quite figure it out
> >> from looking at the UIMA code.
> >>
> >> Any guidance here is greatly appreciated. Thank you
> >>
> >
> >
> 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,
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> information is strictly prohibited and against the law.
>
This email and any files transmitted with it are 

RE: Run cTAKES continuously

[Gandhi Rajan Natarajan]

Hi Ted,

The implementation suggested by Peter is already available in 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest

Building this project will give you a WAR file which you need to deploy in 
Tomcat.

Regards,
Gandhi

-Original Message-
From: Peter Abramowitsch [mailto:pabramowit...@gmail.com]
Sent: Wednesday, June 13, 2018 2:40 AM
To: dev@ctakes.apache.org
Subject: Re: Run cTAKES continuously

Sorry,  The mail sent before I was ready This is pseudocode

   // __aae is your analysis engine (there could be multiple)
   while(more notes) {
 jcas.setDocumentText(note.getFree_text());
 _aae.process(jcas);
 // do something with the jcas contents here
 jcas.reset()
  }

On Tue, Jun 12, 2018 at 11:06 PM, Peter Abramowitsch < pabramowit...@gmail.com> 
wrote:

> The best solution would be to put it in a server framework.  I was not
> able to get the EpsilonTeam server to work, but there's another tiny
> server version written in Scala which you can try.  I ended up doing one 
> using the
> Spark REST framework.   You can build a non server / non UI version which
> does run at the command line by coding it up (in Java) to create the
> pipeline or using a piper, then create a jCas which you
> use/reset/reuse
>
> The core of it would be a loop like this
>
> jcas.setDocumentText(note.getFree_text());
> _aae.process(jcas);
>
> On Tue, Jun 12, 2018 at 8:05 PM, Ted Pikul  wrote:
>
>> Hi- I’ve been able to successfully run cTAKES from the command line
>> as documented here:
>> https://cwiki.apache.org/confluence/display/ctakes/default+
>> clinical+pipeline
>>
>> This works great, but each time it runs it has to make the database
>> connection using jdbc and load the model, which takes 15 seconds or so.
>>
>> Is there another script besides the runClinicalPipeline.sh that I can
>> run to just keep this running and send new notes to it rather than
>> getting the db connection and loading the model each time?
>>
>> I know there is the cTAKES rest server project:
>> https://github.com/GoTeamEpsilon/ctakes-rest-service which I think
>> might do what I’m looking to do.  but as it’s still in alpha stage,
>> especially the docker piece of it, and I don’t really need a server I
>> can just run from command line, I’m not sure this is the right
>> solution for me.
>>
>> I tried looking at how the runctakesCVD.sh script works, as it does
>> what I need but with the CVD UI, but I couldn’t quite figure it out
>> from looking at the UIMA code.
>>
>> Any guidance here is greatly appreciated. Thank you
>>
>
>
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RE: Batching Queries in Ctakes Web Rest

[Gandhi Rajan Natarajan]

Even if you send it in batch, the processing will be sequential I guess. You 
may have to run multiple instances of REST service to process huge volume of 
records.

Regards,
Gandhi

-Original Message-
From: Zakir Saifi [mailto:zakir.sa...@raxa.com]
Sent: Monday, May 21, 2018 4:23 PM
To: dev@ctakes.apache.org
Subject: Batching Queries in Ctakes Web Rest

I am using ctakesRestService to process unstructured clinical text. I have a 
long list of records which I want to be structured. On average Ctakes service 
for me is taking 3.6 seconds to process a record. I want to *batch this 
process* in order to reduce time. Is there any way in which I can sent number 
of queries to the ctakes web rest service in batch and get the appropriate 
result from it. My Ctakes version is 4.0.1. I have also changed the default 
piper file and added other annotators for extracting more information like 
BackwardsTimeAnnotator, DocTimeRelAnnotator etc.
​
This email and any files transmitted with it are confidential and intended 
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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 
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information is strictly prohibited and against the law.

RE: Query on ctakes

[Gandhi Rajan Natarajan]

Hi,

As far as I know, there is no annotations available in cTAKES to extract person 
specific details as I checked with Sean earlier. May be he can elaborate more 
on this.

Regards,
Gandhi

-Original Message-
From: IBIL Global [mailto:ibilglob...@gmail.com]
Sent: Wednesday, May 09, 2018 10:50 AM
To: dev@ctakes.apache.org
Subject: Query on ctakes

Hi Sean,

We are currently working on ctakes. while checking the output from ctakes we 
are not able to get annotations for journal details,author details,reporter 
details and patient details.
Could you please let us know is there any annotations available for above 
details.

Thanks
ibil
This email and any files transmitted with it are confidential and intended 
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this e-mail. Please notify the sender or system manager by email immediately if 
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RE: issues with line endings

[Gandhi Rajan Natarajan]

Hi Tim,

Though I'm not an expert in git, I guess there is a setting to turn off this 
feature of auto correcting line endings in git-svn.

Just have a look at this link - 
https://dzone.com/articles/git-showing-file-modified-even and see if it helps.

Regards,
Gandhi


-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Saturday, May 05, 2018 2:25 AM
To: dev@ctakes.apache.org
Subject: issues with line endings

I'm trying to use git-svn to do ctakes development but it has this weird issue 
where it auto "fixes" line endings (mainly in -ytex*
modules) to be LF from CRLF. So it won't let me pull until I've checked in 
those changes. And because it's automatic I can't clean my local copy (if I try 
they just show up again, it's like trying to strangle a ghost). Anyways, should 
we just to a brute force commit of all files to LF endings?
Tim
This email and any files transmitted with it are confidential and intended 
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this e-mail. Please notify the sender or system manager by email immediately if 
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RE: Ctakes not running on docker

[Gandhi Rajan Natarajan]

Hi Zakir,

I could see that you are using customDictionary.xml as dictionary descriptor. 
Does that XML file contains valid jdbcUrl property?

Regards,
Gandhi


-Original Message-
From: Zakir Saifi [mailto:zakir.sa...@raxa.com]
Sent: Tuesday, May 01, 2018 11:32 AM
To: dev@ctakes.apache.org
Subject: Ctakes not running on docker

Hi, I am new to ctakes and I have a Project on ctakes 4.0 which is running fine 
on my local machine but when I am running its War on the Docker it is giving 
following Error.

30 Apr 2018 08:31:47  INFO AbstractJCasTermAnnotator - Exclusion tagset
loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP 
VBZ WDT WP WPS WRB
30 Apr 2018 08:31:47  INFO AbstractJCasTermAnnotator - Using minimum term text 
span: 3
30 Apr 2018 08:31:47  INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
30 Apr 2018 08:31:47  INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class 
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator"
failed.  (Descriptor: )
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(
UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(
UIMAFramework.java:354)
at org.apache.ctakes.rest.service.CtakesRestController.
init(CtakesRestController.java:76)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at 
sun.reflect.NativeMethodAccessorImpl.invoke(
NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(
DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.annotation.
InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(
InitDestroyAnnotationBeanPostProcessor.java:366)
at org.springframework.beans.factory.annotation.
InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(
InitDestroyAnnotationBeanPostProcessor.java:311)
at org.springframework.beans.factory.annotation.
InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(
InitDestroyAnnotationBeanPostProcessor.java:134)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFac
tory.applyBeanPostProcessorsBeforeInitialization(
AbstractAutowireCapableBeanFactory.java:409)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFac
tory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFac
tory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFac
tory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.
getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.
getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(
AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(
AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.
preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.
finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(
AbstractApplicationContext.java:543)
at 

RE: Question about piper system

[Gandhi Rajan Natarajan]

Hi Peter,

I hope this link - 
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files should help you 
out. Also as far as I know, I doubt JsonCasSerializer has been packaged for 
Piper.

Sean could elaborate more on this but I guess he is on vacation.

Regards,
Gandhi

-Original Message-
From: Peter Abramowitsch [mailto:pabramowit...@gmail.com]
Sent: Friday, April 27, 2018 10:58 AM
To: dev@ctakes.apache.org
Subject: Question about piper system

I've been using ctakes for several years, coding my own pipelines and 
configuring XML files manually, but decided to try using the piper system
for fun.   However, hasn't been that easy, and just trying from the
documentation with the Creator GUI, a lot of permutations don't seem to work - 
at least without knowing each component's idiosyncracies.  I was wondering if 
there was some unofficial documentation to supplement what is out there on your 
site.

(Unfortunately I have changed emails to change of work, so I don't have the 
archive of previous suggestions where this may have already been covered)

1.  Using the Piper CreaterGUI What does it mean when I include a component, 
for instance XMIWriter2 and on validation shows up in red even though it has no 
unfulfilled mandatory parameters?

2If I use one of the example piper files from the distribution, it
runs.  But I notice there they contain no output components.  But if I "add" 
any output XMI output method, it fails with an exception like
this:  *MESSAGE
LOCALIZATION FAILED: Can't find resource for bundle 
java.util.PropertyResourceBundle, key Not AnalysisComponent
org.apache.ctakes.core.cc.CasConsumer.* (many other components have
similar error messages when I add them)

Only one of the pretty print methods works with "add".

NB the writeXmis shortcut works.

3.  Has the JsonCasSerializer been packaged for the Piper?
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RE: Rest API

[Gandhi Rajan Natarajan]

Hi Abilash,

It is not yet available in CATKES codebase but the module is more or less 
complete. You can check out the beta version of it under 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest

We will check-in the same to CTAKES codebase after getting buy in from 
stakeholders like Sean, Tim, James and others once the cTAKES GUI for MySQL 
support is completed .

If you have any suggestions on this REST module, you can email me.

Regards,
Gandhi

-Original Message-
From: abilash.mat...@cognizant.com [mailto:abilash.mat...@cognizant.com]
Sent: Tuesday, April 10, 2018 10:54 AM
To: dev@ctakes.apache.org
Subject: Rest API

Hi,

I have a requirement to expose rest API to a different application. Is the 
CTAKES Rest API feature currently  available or still in progress?

Thanks,
Abilash Mathew


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RE: consequences of change to typesystem [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

Please find the response from Sean Finan for the similar question I asked him 
earlier:

"Ctakes doesn't really have a steadfast process for making upgrades.

You should create a jira item or use an existing one.  Any commits should have 
a comment/message starting with the jira item.  For instance "CTAKES-441: Add 
LabValueFinder".

You can use patch files, attaching them to a jira item and requesting that 
somebody test them before the changes are committed.  You may want to create 
the patch using your git version and then commit it to ctakes using svn.
https://www.devroom.io/2009/10/26/how-to-create-and-apply-a-patch-with-git/
https://www.devroom.io/2007/07/03/how-to-create-and-apply-a-patch-with-subversion/

If the change is significant then you could create an svn branch of ctakes and 
then commit your changes to that branch.  Ask for assistance testing the branch 
and then merge the branch into trunk."

Hope it makes sense.

Regards,
Gandhi

-Original Message-
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Tuesday, April 03, 2018 11:28 PM
To: 'Finan, Sean' ; dev@ctakes.apache.org
Subject: RE: consequences of change to typesystem [EXTERNAL]

I have made some minor changes to DocumentMapperServiceImpl.java to fix this. 
The bodyLocation attributes now get added via the anno_link table in the 
database. I created JIRA issue 503 [0] for this issue, per the cTAKES wiki.

Since this is my first time committing a change to the project I'm not sure how 
to go about it. Is there a tutorial on how to file a pull request I can 
reference?

[0] https://issues.apache.org/jira/browse/CTAKES-503

Thanks,
Sean

-Original Message-
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Wednesday, March 28, 2018 6:54 PM
To: 'Finan, Sean'; dev@ctakes.apache.org
Subject: RE: consequences of change to typesystem [EXTERNAL]

Sean,

Glad I asked. I will try either what you suggested or the similar approach of 
adding some code to handle the bare-annotation-as-feature case similarly to how 
annotations inside FSArrays are handled.

Thanks,
Sean

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 8:40 AM
To: dev@ctakes.apache.org
Subject: Re: consequences of change to typesystem [EXTERNAL]

Hi Sean,

In case nobody else has replied,
Yes, this would definitely break a whole lot of things.  I am not saying that 
it is a bad idea, just that the current BinaryTextRelation interface is used 
as-is in probably a thousand places, and while some refactoring might be 
trivial I wouldn't bet that it all would be as easy as one would like.

I haven't looked at the ytex DBConsumer, but could it possibly be easier to add 
some code there that would check BinaryTextRelations and create a new FSArray 
for each?  Stick those arrays in the cas immediately before and db write() and 
you should be able to do what you want without impacting the rest of ctakes.

Sean

From: Mullane, Sean *HS 
Sent: Tuesday, March 27, 2018 6:05 PM
To: dev@ctakes.apache.org
Subject: consequences of change to typesystem [EXTERNAL]

I am trying out a change to the typesystem (explained below). If it works as I 
hope, I would want to contribute this back to the trunk. Before I invest too 
much time into this, can anyone tell me if this is likely to break things for 
other users? I am thinking of this causing problems reading existing annotated 
corpora, like SHARP.

Problem I'm trying to fix:
The DBConsumer database writer from YTEX seems to ignore 
BinaryTextRelation types (e.g. LocationOfTextRelation, used for the 
bodyLocation feature on annotations like DiseaseDisorderMention). This is 
because they are not added to the default AnnotationIndex index and are not 
contained in FSArrays or FSLists inside other annotation types, like the 
UmlsConcept annotations inside the ontologyConceptArr feature are.

It seems that if I were to change the bodyLocation feature to be a FSArray of 
annotations instead of a bare annotation, the DBConsumer should write it to the 
output table and add an entry in the anno_link table.

Would changing the type of the bodyLocation feature in certain 
IdentifiedAnnotations break things for others?

Thanks,
Sean




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RE: How to change and build project source code?

[Gandhi Rajan Natarajan]

>> ​$ ​
>> cp ctakes-gui/target/ctakes-gui-4.0.1-SNAPSHOT.jar
>> ../apache-ctakes-4.0.1-SNAPSHOT/lib/
>>
>
> ​(note that the apache-ctakes-4.0.1-SNAPSHOT folder was extracted to
> the same directory level as trunk from trunk/ctakes-distribution/
> target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz from an earlier
> successful build following the dev install guide (skipping the
> tests))​, then doing
>
>
>> ➜
>> ​trunk​
>> $ cd ../apache-ctakes-4.0.1-SNAPSHOT
>>
> ​
>> ​​
>> ➜  apache-ctakes-4.0.1-SNAPSHOT
>> ​ $​
>> ls -lhR lib | grep ctakes-gui
>> ​ ​
>>
>
>  -rw-r--r-- 1 reedv reedv 272K  
>> ctakes-gui-4.0.1-SNAPSHOT.jar​
>>
>
> ​ ​
>
> ➜  apache-ctakes-4.0.1-SNAPSHOT
>> ​ $​
>> ./bin/runPiperCreator.sh
>> 
>> log4j: Setting property [conversionPattern] to [%d{dd MMM 
>> HH:mm:ss} %5p %c{1} - %m%n].
>> log4j: Adding appender named [consoleAppender] to category [root].
>> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>> at javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.
>> getTableCellRendererComponent(SynthTableHeaderUI.java:234)
>> at org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2.
>> java:94)
>> at org.apache.ctakes.gui.pipeline.MainPanel2.createMainPanel(MainPanel2.
>> java:139)
>> at
>> org.apache.ctakes.gui.pipeline.MainPanel2.(MainPanel2.java:76)
>> at org.apache.ctakes.gui.pipeline.PiperCreator.
>> createMainPanel(PiperCreator.java:40)
>> at org.apache.ctakes.gui.pipeline.PiperCreator.lambda$
>> main$0(PiperCreator.java:53)
>> 
>
>
> I see that *the error line number is unchanged and the error is the
> same as in the original file*, which produced the similar error shown below:
>
> ➜  apache-ctakes-4.0.0 bin/runPiperCreator.sh
>> 
>> log4j: Adding appender named [consoleAppender] to category [root].
>> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>> at javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.
>> getTableCellRendererComponent(SynthTableHeaderUI.java:234)
>> at org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2.
>> java:94)
>> at org.apache.ctakes.gui.pipeline.MainPanel2.createMainPanel(MainPanel2.
>> java:139)
>> at
>> org.apache.ctakes.gui.pipeline.MainPanel2.(MainPanel2.java:76)
>> at org.apache.ctakes.gui.pipeline.PiperCreator.
>> createMainPanel(PiperCreator.java:40)
>> at org.apache.ctakes.gui.pipeline.PiperCreator.lambda$
>> main$0(PiperCreator.java:53)
>> 
>
>
> which was supposedly fixed in 4.0.1 (https://issues.apache.org/
> jira/browse/CTAKES-442), the error that I was initially trying to
> investigate (copying the 4.0.1 gui jar to this 4.0.0 binary download
> /lib dir. under the original 4.0.0 name still generates this error).
>
> Could you let me know what I'm doing wrong here?
> Would be interested in working with the code if I could just figure
> out how to actually use and test changes.
> Thank you.
>
>
>
>
>
> On Tue, Mar 27, 2018 at 5:29 AM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com> wrote:
>
>> Hi Reed,
>>
>> If you make any changes in ctakes-gui module, you can build the
>> ctakes-gui module using the following command:
>>
>> mvn clean install -Dmaven.test.skip=true
>>
>> Then you can pick up the updated ctakes-gui jar file from
>> 'ctakes-gui\target' folder and replace the same in your project from
>> where you are running cTAKES.
>>
>> Regards,
>> Gandhi
>>
>>
>> -Original Message-
>> From: Reed Villanueva [mailto:villanuevar...@gmail.com]
>> Sent: Tuesday, March 27, 2018 12:20 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: How to change and build project source code?
>>
>> I see. I was looking in the "ctakes-distribution/target" because that
>> seemed to be where the binary files where (which I assumed were the
>> final product of the build, having initially experienced ctakes as a
>> "user" and never worked on a maven project before). Would you be
>> willing to please explain a bit more about how to run the project
>> after building it (non-IDE-based install) for someone with less maven
>> and java experience (which I think may be my main confusion)?
>>
>> On Mon, Mar 26, 2018 at 2:49 AM, Gandhi Rajan Natarajan <
>> gandhi.natara...@arisglobal.com> wrote:
>>
>> > Hi Reed,
>> >
>> > 

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Sean,

This is phenomenal commitment.  I appreciate your dedication and passion. You 
are such an inspiration to the open source contributors.

Thanks for taking time out amidst busy schedule and having a look at this. Will 
check this change and keep you posted.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 9:12 PM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Guilt is such a powerful motivator ...

The problem is that ctakes traditionally identifies a bunch of those terms as 
Medications, not Labs.  So, I added a parameter named "useDrugs" to the 
LabValueFinder.  If you set that to "true" then the Lab/Medication values come 
through shining.

I also added some (commented out) code to the LabValueFinderTester to use the 
default dictionary instead of the test dictionary.  By default the test 
dictionary is used and all counts match.  If you use the default dictionary you 
can expect the test to fail because it finds 23 labs instead of 24 - but Kean's 
test code kindly prints the labs and values found so you can look at the test 
results.

The code just went into trunk.

Enjoy,
Sean

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 9:03 AM
To: dev@ctakes.apache.org
Subject: Re: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

Hi Gandhi,

I know that I just sent an email to the devlist, but that seemed like an item 
that had wide-impact.  Because of some critical work (job that pays the bills) 
I am still "dark" as far as ctakes goes - no free nights and only partial 
weekends.  My apologies.  I know that there are a lot of issues building up, 
and I will try to try to address them asap; I don't know when I'll have the 
time and energy to get back to the devlist.

Feeling a bit guilty,
Sean
________
From: Gandhi Rajan Natarajan <gandhi.natara...@arisglobal.com>
Sent: Wednesday, March 28, 2018 8:56 AM
To: dev@ctakes.apache.org
Subject: RE: Query on LabValueFinder [EXTERNAL]

Hi Sean,



Can you throw some light on this?



Regards,

Gandhi





-Original Message-

From: Kean Kaufmann [mailto:k...@recordsone.com]

Sent: Monday, March 19, 2018 8:35 PM

To: dev@ctakes.apache.org

Subject: Re: Query on LabValueFinder



Gandhi, at first blush, I can't replicate your result using the code I 
submitted...

but my code and config differ from trunk, so Sean is probably the best person 
to ask.

I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.

Sean, any insight?





On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:



> Hi All,

>

> I'm using LabValueFinder annotator in my piper file and when I analyze

> the following text:

>

>

> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -

> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844

> (*) 42 -

> 121 IU/L" as mentioned in

> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JMvtiTFymmqWfE6zZ1z5oPfqlSFrG0nZKJ0bhEBltrc=2EcJhW06YyWZpdLla-yruHEw4Il9CyHMLBrKoHaDVlc=

>

>

>

> The resulted XML generated using XmiCasSerializer contains only one

> LabMention as mentioned below:

>

>

>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"

> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"

> conditional="false" generic="false" historyOf="0" labValue="3907" />

>

> 

>

> 

>

>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"

> arg1="3917" arg2="3922" />

>

>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"

> uncertainty="0" conditional="false" generic="false" historyOf="0" />

>

>

> But as per the comments in the issue, it is supposed to identify 3 lab

> mentions. Any thoughts on this on how to achieve it ?

>

> Regards,

> Gandhi

>

> This email and any files transmitted with it are confidential and

> intended solely for the use of the individual or entity to whom they are 
> addressed.

> If you are not the named addressee you should not disseminate,

> distribute or copy this e-mail. Please notify the sender or system

> manager by email immediately if you have received this e-mail by

&

RE: Query on LabValueFinder

[Gandhi Rajan Natarajan]

Hi Sean,

Can you throw some light on this?

Regards,
Gandhi


-Original Message-
From: Kean Kaufmann [mailto:k...@recordsone.com]
Sent: Monday, March 19, 2018 8:35 PM
To: dev@ctakes.apache.org
Subject: Re: Query on LabValueFinder

Gandhi, at first blush, I can't replicate your result using the code I 
submitted...
but my code and config differ from trunk, so Sean is probably the best person 
to ask.
I included unit tests with a mini-dictionary for ProcedureMentions, but they 
probably didn't play nicely with the rest of the framework.
Sean, any insight?


On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,
>
> I'm using LabValueFinder annotator in my piper file and when I analyze
> the following text:
>
>
> "HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 -
> 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844
> (*) 42 -
> 121 IU/L" as mentioned in
> https://issues.apache.org/jira/browse/CTAKES-441
>
>
>
> The resulted XML generated using XmiCasSerializer contains only one
> LabMention as mentioned below:
>
>
>  ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0"
> discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0"
> conditional="false" generic="false" historyOf="0" labValue="3907" />
>
> 
>
> 
>
>  confidence="0.0" polarity="0" uncertainty="0" conditional="false"
> arg1="3917" arg2="3922" />
>
>  id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0"
> uncertainty="0" conditional="false" generic="false" historyOf="0" />
>
>
> But as per the comments in the issue, it is supposed to identify 3 lab
> mentions. Any thoughts on this on how to achieve it ?
>
> Regards,
> Gandhi
>
> This email and any files transmitted with it are confidential and
> intended solely for the use of the individual or entity to whom they are 
> addressed.
> If you are not the named addressee you should not disseminate,
> distribute or copy this e-mail. Please notify the sender or system
> manager by email immediately if you have received this e-mail by
> mistake and delete this e-mail from your system. If you are not the
> intended recipient you are notified that disclosing, copying,
> distributing or taking any action in reliance on the contents of this
> information is strictly prohibited and against the law.
>
This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
you have received this e-mail by mistake and delete this e-mail from your 
system. If you are not the intended recipient you are notified that disclosing, 
copying, distributing or taking any action in reliance on the contents of this 
information is strictly prohibited and against the law.

RE: How to change and build project source code?

[Gandhi Rajan Natarajan]

Hi Reed,

If you make any changes in ctakes-gui module, you can build the ctakes-gui 
module using the following command:

mvn clean install -Dmaven.test.skip=true

Then you can pick up the updated ctakes-gui jar file from 'ctakes-gui\target' 
folder and replace the same in your project from where you are running cTAKES.

Regards,
Gandhi


-Original Message-
From: Reed Villanueva [mailto:villanuevar...@gmail.com]
Sent: Tuesday, March 27, 2018 12:20 AM
To: dev@ctakes.apache.org
Subject: Re: How to change and build project source code?

I see. I was looking in the "ctakes-distribution/target" because that seemed to 
be where the binary files where (which I assumed were the final product of the 
build, having initially experienced ctakes as a "user" and never worked on a 
maven project before). Would you be willing to please explain a bit more about 
how to run the project after building it (non-IDE-based install) for someone 
with less maven and java experience (which I think may be my main confusion)?

On Mon, Mar 26, 2018 at 2:49 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Reed,
>
> I'm not sure whether I got your question right. But if you make any
> changes in ctakes-gui module, the updated jar files will be available
> under ' ctakes-gui\target' folder.
>
> Not sure what you are looking for under 'ctakes-distribution/target'
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Reed Villanueva [mailto:villanuevar...@gmail.com]
> Sent: Monday, March 26, 2018 3:02 AM
> To: dev@ctakes.apache.org
> Subject: How to change and build project source code?
>
> New user. Tried editing
> ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.jav
> a to look into potential bug that was supposedly resolved in
> https://issues.apache.org/jira/browse/CTAKES-442 but appears to still
> be causing error...
>
>
> > log4j: Adding appender named [consoleAppender] to category [root].
> >
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>
> at
> > javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.getTableCel
> > lR
> > endererComponent(SynthTableHeaderUI.java:234)
>
> at
> > org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2
> > .j
> > ava:94)
>
> ​
> >
> >
> in version 4.0.1. Yet when changing the code snippet to...
>
>
> > ​
> >
>private JComponent createWestPanel() {
>
>   final JTable fakeTable = new JTable();
>
>   LOGGER.info( "** DEBUG: fakeTable: " + fakeTable );
>
>   LOGGER.info( "** DEBUG: fakeTable: " + fakeTable );
>
>   final JTableHeader fakeHeader = fakeTable.getTableHeader();
>
>   LOGGER.info( "** DEBUG: fakeHeader: " + fakeHeader );
>
>   final Component header = fakeHeader.getDefaultRenderer()
>
> .getTableCellRendererComponent(
> fakeTable,
> > ​ ​
> > "Available Pipe Bits", false, false, -1, -1 );
>
> ​
> >
>
>
> trying to build with...
>
> ​
> >
> mvn --fail-at-end --errors --update-snapshots clean install
> sonar:sonar
> > -DskipTests=true -Dsonar.scm.provider=svn -Dsonar.host.url=
> > https://builds.apache.org/analysis
>
> ​
> >
>
>
> and extracting the binaries via...
>
> ​➜  trunk cp
> > ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz
> > ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz.m
> > d5
> > ../​
> >
> >
> (by the way, I explicitly show the steps I took only because I have
> never worked on a maven project before so giving a chance for someone
> to point out if I'm doing something wrong here), yet still seeing
> error
>
> log4j: Adding appender named [consoleAppender] to category [root].
> >
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
>
> at
> > javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.getTableCel
> > lR
> > endererComponent(SynthTableHeaderUI.java:234)
>
> at
> > org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2
> > .j
> > ava:94)
>
> ​
> >
>
> Notice it states the error is on line 94 as if the change that I
> implemented is not actually affecting the code that is being used (yet
> running
>
> ​
> >
> ➜  trunk find . -name 'MainPanel2.java'
> >
>
> ./ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.j
> ava
>
> ​
> >
> >
> in the trunk directory shows that this is the only place that that
> file exists).
>
> Am I missing somethin

RE: How to change and build project source code?

[Gandhi Rajan Natarajan]

Hi Reed,

I'm not sure whether I got your question right. But if you make any changes in 
ctakes-gui module, the updated jar files will be available under ' 
ctakes-gui\target' folder.

Not sure what you are looking for under 'ctakes-distribution/target'

Regards,
Gandhi

-Original Message-
From: Reed Villanueva [mailto:villanuevar...@gmail.com]
Sent: Monday, March 26, 2018 3:02 AM
To: dev@ctakes.apache.org
Subject: How to change and build project source code?

New user. Tried editing
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java
to look into potential bug that was supposedly resolved in
https://issues.apache.org/jira/browse/CTAKES-442 but appears to still be 
causing error...


> log4j: Adding appender named [consoleAppender] to category [root].
>
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException

at
> javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.getTableCellR
> endererComponent(SynthTableHeaderUI.java:234)

at
> org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2.j
> ava:94)

​
>
>
in version 4.0.1. Yet when changing the code snippet to...


> ​
>
   private JComponent createWestPanel() {

  final JTable fakeTable = new JTable();

  LOGGER.info( "** DEBUG: fakeTable: " + fakeTable );

  LOGGER.info( "** DEBUG: fakeTable: " + fakeTable );

  final JTableHeader fakeHeader = fakeTable.getTableHeader();

  LOGGER.info( "** DEBUG: fakeHeader: " + fakeHeader );

  final Component header = fakeHeader.getDefaultRenderer()

.getTableCellRendererComponent( fakeTable,
> ​ ​
> "Available Pipe Bits", false, false, -1, -1 );

​
>


trying to build with...

​
>
mvn --fail-at-end --errors --update-snapshots clean install sonar:sonar
> -DskipTests=true -Dsonar.scm.provider=svn -Dsonar.host.url=
> https://builds.apache.org/analysis

​
>


and extracting the binaries via...

​➜  trunk cp
> ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz
> ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz.md5
> ../​
>
>
(by the way, I explicitly show the steps I took only because I have never 
worked on a maven project before so giving a chance for someone to point out if 
I'm doing something wrong here), yet still seeing error

log4j: Adding appender named [consoleAppender] to category [root].
>
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException

at
> javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.getTableCellR
> endererComponent(SynthTableHeaderUI.java:234)

at
> org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2.j
> ava:94)

​
>

Notice it states the error is on line 94 as if the change that I implemented is 
not actually affecting the code that is being used (yet running

​
>
➜  trunk find . -name 'MainPanel2.java'
>

./ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java

​
>
>
in the trunk directory shows that this is the only place that that file exists).

Am I missing something here (never worked on a maven project before, so I'm 
thinking that I may not be changing the right file here)? How can I change the 
code so that it actually gets used in the compiled binaries? Thanks
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.

Query on LabValueFinder

[Gandhi Rajan Natarajan]

Hi All,

I'm using LabValueFinder annotator in my piper file and when I analyze the 
following text:


"HEPATIC FUNCTION PANEL  Result Value Ref Range  Albumin 2.2 (*) 3.7 - 5.1 g/dL 
Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844 (*) 42 - 121 
IU/L" as mentioned in https://issues.apache.org/jira/browse/CTAKES-441



The resulted XML generated using XmiCasSerializer contains only one LabMention 
as mentioned below:













But as per the comments in the issue, it is supposed to identify 3 lab 
mentions. Any thoughts on this on how to achieve it ?

Regards,
Gandhi

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

RE: Regarding Duration of a given symptom

[Gandhi Rajan Natarajan]

Hi Anurag,

I believe you have to use TemporalSubPipe.piper to get duration related 
information.

Regards,
Gandhi


-Original Message-
From: Anurag Shukla [mailto:anurag.shu...@raxa.com]
Sent: Monday, March 19, 2018 5:01 PM
To: dev@ctakes.apache.org
Subject: Regarding Duration of a given symptom

Hi ,

I have just started on ctakes . I want to know How can I get duration of a 
given sympyom.

Eg. " Patient has fever since 3 days and is having headache"

On analyzing I get ,

"SignSymptomMention": [
"FEVER",
"HEADACHE"
],

How can retrieve the information that duration of fever has been 3 days ?

Regards

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

RE: Build failure in Ctakes developer installation

[Gandhi Rajan Natarajan]

Try disabling test cases and building it.  Try using the following command:

"mvn install -Dmaven.test.skip=true"

Regards,
Gandhi


-Original Message-
From: ama...@acolade.co.in [mailto:ama...@acolade.co.in]
Sent: Friday, March 16, 2018 12:04 PM
To: dev@ctakes.apache.org
Subject: Build failure in Ctakes developer installation

 [INFO] Scanning for projects...
[INFO] 
[INFO] Reactor Build Order:
[INFO]
[INFO] Apache cTAKES
[INFO] ctakes-gui-res
[INFO] Apache cTAKES Resources coreference
[INFO] Apache cTAKES Resources temporal
[INFO] Apache cTAKES Resources relation-extractor
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res
[INFO] Apache cTAKES Resources core
[INFO] Apache cTAKES common type system
[INFO] Apache cTAKES utils
[INFO] Apache cTAKES core
[INFO] Apache cTAKES dictionary lookup fast
[INFO] Apache cTAKES document preprocessor
[INFO] Apache cTAKES Resources lvg
[INFO] Apache cTAKES LVG lexical tools
[INFO] Apache cTAKES Resources ne-contexts
[INFO] Apache cTAKES named entity contexts
[INFO] Apache cTAKES Resources assertion
[INFO] Apache cTAKES Resources constituency-parser
[INFO] Apache cTAKES Constituency Parser
[INFO] Apache cTAKES Resources dependency-parser
[INFO] Apache cTAKES Resources pos-tagger
[INFO] Apache cTAKES part-of-speech tagger
[INFO] Apache cTAKES Dependency Parser
[INFO] Apache cTAKES context dependent tokenizer
[INFO] Apache cTAKES Resources ctakes-chunker-res
[INFO] Apache cTAKES chunker
[INFO] Apache cTAKES Assertion
[INFO] ctakes-clinical-pipeline-res
[INFO] Apache cTAKES ctakes-clinical-pipeline
[INFO] Apache cTAKES Relation Extractor
[INFO] Apache cTAKES Temporal Information Extraction
[INFO] Apache cTAKES CoReference Resolver
[INFO] ctakes-gui
[INFO] Apache cTAKES Resources dictionary-lookup
[INFO] Apache cTAKES dictionary lookup
[INFO] Apache cTAKES Resources drug-ner
[INFO] Apache cTAKES Drug NER
[INFO] Apache cTAKES Resources side-effect
[INFO] Apache cTAKES Side Effects
[INFO] Apache cTAKES Resources smoking-status
[INFO] Apache cTAKES Smoking Status
[INFO] Apache cTAKES Resources assertion-zoner
[INFO] Apache cTAKES Assertion's zoner
[INFO] ctakes-examples-res
[INFO] ctakes-examples
[INFO] Apache cTAKES Resources ctakes-ytex-res
[INFO] Apache cTAKES YTEX
[INFO] Apache cTAKES YTEX UIMA
[INFO] Apache cTAKES YTEX Web
[INFO] Apache cTAKES Distribution
[INFO] Apache cTAKES Regression-test
[INFO] Apache cTAKES template filler
[INFO]
[INFO] 
[INFO] Building Apache cTAKES 4.0.1-SNAPSHOT
[INFO] 
[INFO]
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes ---
[INFO]
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes 
---
[INFO]
[INFO] 
[INFO] Building ctakes-gui-res 4.0.1-SNAPSHOT
[INFO] 
[INFO]
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-gui-res 
---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ 
ctakes-gui-res ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 85 resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-gui-res 
---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ 
ctakes-gui-res ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory 
C:\Users\AMAL\eclipse-workspace\ctakes\ctakes-gui-res\src\test\resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ 
ctakes-gui-res ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @ ctakes-gui-res ---
[INFO] Surefire report directory: 
C:\Users\AMAL\eclipse-workspace\ctakes\ctakes-gui-res\target\surefire-reports
 ---
 T E S T S
---
 Results :
 Tests run: 0, Failures: 0, Errors: 0, Skipped: 0
 [INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-gui-res ---
[INFO] Building jar: 
C:\Users\AMAL\eclipse-workspace\ctakes\ctakes-gui-res\target\ctakes-gui-res-4.0.1-SNAPSHOT.jar
[INFO]
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ 
ctakes-gui-res ---
[INFO]
[INFO] 
[INFO] Building Apache cTAKES Resources coreference 4.0.1-SNAPSHOT
[INFO] 
[INFO]
[INFO] --- 

RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Thanks a lot for the response Chen. Appreciate your time.

Regards,
Gandhi


-Original Message-
From: Lin, Chen [mailto:chen@childrens.harvard.edu]
Sent: Wednesday, March 14, 2018 9:20 PM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Thank you for testing the temporal model in detail. As I can recall, the 
changes made between the two versions include added features and tuned 
parameters. We do see significant improvement in our test corpus so that we 
switch to the new model. The improvement is gauged statistically, not for every 
single instance. I am sure there would be some instances that the demo version 
cannot pick up but our new model can.

For your listed case, it's an event-event temporal relation. Event-event 
relations generally have a lower annotation quality (lower Inter Annotator 
Agreement). Through development we do observe the annotation quality decreases 
as the distance increases. We did try enforcing to reason event-event arguments 
that are within a certain distance like six-word.
But for your case, it's still considered as a good distance. So I would say 
it's a system error, assuming you can identify both events("HBA1c" and
"good") correctly using the current system.

Best,
Chen

On 3/14/18, 11:20 AM, "Gandhi Rajan Natarajan"
<gandhi.natara...@arisglobal.com> wrote:

>Hi Chen/Sean,
>
>As per our earlier discussion, I was under the impression that tlinks
>will not be able to pick only the long distance relationship in the
>latest version of cTAKES. But even when I try smaller text like the one
>below, the tlinks is not getting picked up:
>
>"HBA1c is normal which is good"
>
>But when I try out the same text in demo URL -
>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080
>_in
>dex.jsp=DwIFAw=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=PZ241C
>wYZ
>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=SEMrHyMpFRLj8NCb6iYM5ST92ybV8iqKkY
>2b2 iu7brc=iC5PBgT3lI7HbZ0xGDGBRF_ADnEnyWlgTTGOHbTCjMo= , I get the
>following tlink:
>
>" HBA1c CONTAINS good"
>
>Any change in the latest version impacted this functionality or is it
>the expected behavior? Could you please provide some more info on this?
>
>Regards,
>Gandhi
>
>-Original Message-
>From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
>Sent: Monday, February 12, 2018 11:00 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Thanks Sean and Chen for your response.  I really appreciate your time.
>
>Regards,
>Gandhi
>
>
>-Original Message-
>From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 9:18 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Hi Chen,
>
>No worries!  I often throw out answers before checking code myself.  We
>are all busy with other items.  Besides, If I recall (without checking
>code), it is because of an improvement in the Event annotator code that
>the Copy*** was no longer needed ... and you wrote that improvement!
>hurrah!
>
>I thank you for taking the time to answer questions on temporal
>matters, as well as being one of the developers involved working on the module!
>
>Cheers,
>Sean
>
>-Original Message-
>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:43 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Thanks to Sean. My bad, I should check the code first before any answer
>attempt.
>
>Best,
>Chen
>
>On 2/12/18, 10:40 AM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
>wrote:
>
>>It should have nothing to do with the tlink extraction.  It copied
>>properties from events to eventmentions and was in the pipeline after
>>the tlink annotation, not before.
>>
>>-Original Message-
>>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 10:33 AM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>>
>>Mmm. Frankly, I don't know the rational behind commenting out
>>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>>in that piper file. The TLINK model does take some of the event
>>properties (polarity, uncertainty, contextual modality, semantic
>>types,
>>etc.) for classification features. Without those features the
>>classifier may lose its grip. Have you tried commenting back the lin

RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Chen/Sean,

As per our earlier discussion, I was under the impression that tlinks will not 
be able to pick only the long distance relationship in the latest version of 
cTAKES. But even when I try smaller text like the one below, the tlinks is not 
getting picked up:

"HBA1c is normal which is good"

But when I try out the same text in demo URL - 
http://54.68.117.30:8080/index.jsp , I get the following tlink:

" HBA1c CONTAINS good"

Any change in the latest version impacted this functionality or is it the 
expected behavior? Could you please provide some more info on this?

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Monday, February 12, 2018 11:00 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Thanks Sean and Chen for your response.  I really appreciate your time.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, February 12, 2018 9:18 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Hi Chen,

No worries!  I often throw out answers before checking code myself.  We are all 
busy with other items.  Besides, If I recall (without checking code), it is 
because of an improvement in the Event annotator code that the Copy*** was no 
longer needed ... and you wrote that improvement!  hurrah!

I thank you for taking the time to answer questions on temporal matters, as 
well as being one of the developers involved working on the module!

Cheers,
Sean

-Original Message-
From: Lin, Chen [mailto:chen@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Thanks to Sean. My bad, I should check the code first before any answer attempt.

Best,
Chen

On 2/12/18, 10:40 AM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:

>It should have nothing to do with the tlink extraction.  It copied
>properties from events to eventmentions and was in the pipeline after
>the tlink annotation, not before.
>
>-Original Message-
>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><gandhi.natara...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-Original Message-
>>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick
>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation
>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>pick up some longer-distance relationship as well, but obliviously it
>>fails for your case for long distance relations. We are currently
>>researching a LSTM-based model, which can take more consideration of
>>sentence structure and long-distance relationship. Will update more
>>details in the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><gandhi.natara...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>&

RE: Query on ctakes [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Amal,

If I am right, the grouping of related information together is not yet 
available in cTAKES out of the box.

Also to generate output in a structured format, you can make use of HTMLWriter. 
For more detailed info on this, you can check out Sean’s response for “Output 
formats - CPE - cTAKES - Persist in 
database”
 thread under  
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201803.mbox/browser

Regards,
Gandhi

From: ama...@acolade.co.in [mailto:ama...@acolade.co.in]
Sent: Monday, March 12, 2018 4:09 PM
To: dev@ctakes.apache.org
Subject: RE: Query on ctakes [EXTERNAL]

Hi Sean,

Please find the attachment of input and output text of ctakes.

From the ctakes output we can't identify which one is drug, disease, labtest 
etc.
(for example : tocilizumab is a drug, but the output text may not specify what 
is it?)

Also, is there a way where we can group related information together? (e.g:- 
For each drug, identify the dosage/ root of administration/dosage strength/ 
Dosage Frequency etc?)

How can we generate above expected output in a structured format? (HTML/JSON 
etc)

Thanks & Regards
 AMAL M
9633746869



- Original Message -
Subject: Re: Query on ctakes [EXTERNAL]
From: "Finan, Sean" 
>
Date: 3/9/18 7:46 pm
To: "dev@ctakes.apache.org" 
>

Hi Amal,

Could you please provide a full example sentence with expected vs. produced 
output? ctakes isn't perfect but something like "fever" should be tagged.

Thanks,
Sean

From: ama...@acolade.co.in 
>
Sent: Friday, March 9, 2018 12:59 AM
To: dev@ctakes.apache.org
Subject: Query on ctakes [EXTERNAL]

Hello, Am a newbie to cTakes.
So far I am able to complete user installation and able to generate the 
processed output.
I am finding the extracted data NOT getting tagged with relevant 
concepts(contexts) like Drugs, Disease. Lab results etc...which is a real 
concern.
Would appreciate if somebody could help me to achieve tagging of the extracted 
data.
(e:g:- Fever to be tagged as Problem/Disease and abdominopelvic CT as Test(lab 
test))


Thanks & Regards
AMAL M
9633746869
This email and any files transmitted with it are confidential and intended 
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you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
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RE: Output formats - CPE - cTAKES - Persist in database

[Gandhi Rajan Natarajan]

Hi Manuel,

As far as I know cTAKES supports Pretty print and HTML format too. For more 
info on this, you may have to look at the cTAKES demo webapp code under 
https://github.com/healthnlp/examples/blob/master/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/DemoServlet.java

Also if you are looking for help on parsing XML output, have a look at the beta 
version of cTAKES REST service XML parsing code under 
https://github.com/GoTeamEpsilon/ctakes-rest-service/blob/master/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/XMLParser.java

Regards,
Gandhi


-Original Message-
From: Manuel Lamy [mailto:mmvp...@gmail.com]
Sent: Monday, March 05, 2018 8:59 AM
To: dev@ctakes.apache.org
Subject: Output formats - CPE - cTAKES - Persist in database

Hello everyone,

I'm using cTAKES clinical pipeline in order to process a lot of documents in a 
row.

I'm using this command in the command line:  runClinicalPipeline.bat  -i input 
--xmiOut output  --user username  --pass password

This works, adapted to my credentials and my paths of course. My problem is 
that I can only output in XMI format.

My questions are the following:

-Is it possible to output a different kind of format than XMI? If yes, what 
should I change in this command and what are the available formats?

-It is of my interest to persist the structured clinical information extracted 
by cTAKES directly in a database. Is there a format that is more suitable to 
that task? At the moment, I can only output in XMI format. I built a parser in 
Perl with a lot of regex in order to process all the information in the XMI 
file and persist in a database. However, the XMI file has a complex structure 
and the script, despite of working well, is taking more time than it should to 
run and persist.

If someone could give me some advice about what my possibilities are, I would 
be appreciated.

Best regards,

Manuel
This email and any files transmitted with it are confidential and intended 
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you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
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information is strictly prohibited and against the law.

RE: UmlsUserApprover Error [EXTERNAL]

[Gandhi Rajan Natarajan]

I guess you are running the build with test cases as I see the below messages 
in my case only while running build with test cases:

>> log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is  [INFO].
> > log4j: ProgressAppender level set to INFO


Could you try building ' ctakes-temporal' module by skipping test case using 
the command  - " mvn clean install -Dmaven.test.skip=true" ?

Regards,
Gandhi

-Original Message-
From: Andrew Phillips [mailto:aphilli...@luc.edu]
Sent: Tuesday, February 27, 2018 7:08 AM
To: dev@ctakes.apache.org
Subject: Re: UmlsUserApprover Error [EXTERNAL]

Thanks for the ideas.

There hasn't been any such changes, and network connectivity shouldn't be an 
issue. I ran my script earlier, which automatically runs the same pipeline on 
several different folders, and only the first run was successful. The others 
failed with the same error. My latest attempt is to remove the .m2 directory 
and recompile and reinstall, and it is currently processing the first 
directory, so I don't know if it will fail on the next as yet.

My primary interface is over SSH to a remote server, and this is the script:
UmlsLP () { mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
-Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java 
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
-Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished 
UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}

Thank you.


*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech

On 26 February 2018 at 13:00, Miller, Timothy < 
timothy.mil...@childrens.harvard.edu> wrote:

> Is it possible there is some network issue preventing connectivity?
> New institutional firewall maybe?
>
> Otherwise, it looks like somehow your credentials are not getting into
> the right place. Possible a configuration file had them before and
> it's been changed out from under you?
>
> One thing you can try, if you are using an IDE, you can directly put
> your credentials into the VM options for your run configuration with:
> -Dctakes.umlsuser= -Dctakes.umlspw
>
> and see if you still get the issue.
>
> Tim
>
>
> On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> > Hello,
> >
> > I am getting an error after recompiling a script in my pipeline. My
> > setup was working fine the last time I did a compile several months
> > ago, and I have logged into my UMLS account to ensure it isn't an
> > issue with my credentials, as well as done a complete reinstall from
> > the GitHub repo and checked out the 4.0.0 release. The minor change
> > I made in the script was just uncommenting something that I've used
> > before, so I know there are no errors in it. Any insights as to what
> > the issue may be? I've included the complete output below. Thank
> > you.
> >
> >
> > [INFO] Scanning for projects...
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available [WARNING] Failed to
> > retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apac
> > h
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&
> > r
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository, resolution will not
> > be reattempted until the update interval of central has elapsed or
> > updates are forced [INFO] [INFO]
> > ---
> > -
> > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> > SNAPSHOT [INFO]
> > ---
> > -
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available [WARNING] Failed to
> > retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apac
> > h
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&
> > r
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > 

RE: Fast UMLS dictionary lookup description

[Gandhi Rajan Natarajan]

Hi Masoud,

In this link - 
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Fast+Dictionary+Lookup,
 I could see an information stating " A paper on rare word indexing is 
currently in progress."

May be Sean or Tim will be able to provide info on this I feel.

Regards,
Gandhi

-Original Message-
From: Masoud Rouhizadeh [mailto:m...@jhu.edu]
Sent: Thursday, February 22, 2018 9:57 PM
To: dev@ctakes.apache.org
Subject: Fast UMLS dictionary lookup description

Hello, cTAKES developing team,

We are using and comparing various NLP tools (including cTAKES) for processing 
over 5 million clinical notes within Johns Hopkins Medical Institutes. As a 
part of our comparisons, we are exploring the architecture of the NER and 
(UMLS) concept linking components of the tools.

I was able to find the description on the cTAKES default/original dictionary 
look up in the Savova et. al. 2010 paper but I was not able to find a paper or 
tech report describing the fast UMLS dictionary lookup (Fast UMLS Processor) 
yet.

Any description of the fast dictionary lookup algorithm is highly appreciated.

Thank you,
Masoud Rouhizadeh


Masoud Rouhizadeh, PhD

NLP Specialist / Software Engineer
Institute for Clinical and Translational Research Center for Clinical Data 
Analysis School of Medicine, Johns Hopkins University
http://pages.jh.edu/~mrouhiz1

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 
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RE: using umls dictionary lookup offline [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean, Thanks for the additional info.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, February 14, 2018 9:42 PM
To: dev@ctakes.apache.org
Subject: RE: using umls dictionary lookup offline [EXTERNAL]

Hi Gandhi, all,

JdbcDictionary and JdbcConceptFactory are probably the way to go.  Just to add, 
you don't need to load the dictionary into another database (mysql) to use 
Jdbc* classes.  They will work out-of-box with the default dictionary.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, February 14, 2018 11:08 AM
To: dev@ctakes.apache.org
Subject: RE: using umls dictionary lookup offline [EXTERNAL]

Hi Razu,

You can load the UMLS data in database like MySQL and use JdbcConceptFactory 
instead of UmlsJdbcConceptFactory.

Regards,
Gandhi


-Original Message-
From: Razu Sharif [mailto:razu.cse10.r...@gmail.com]
Sent: Wednesday, February 14, 2018 2:53 PM
To: dev@ctakes.apache.org
Subject: using umls dictionary lookup offline

Dear,

Every time I run cTakes it calls out internet to check our credentials.
Whats required to make it work without internet or credential check.

Thanks
Razu Sharif
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RE: using umls dictionary lookup offline

[Gandhi Rajan Natarajan]

Hi Razu,

You can load the UMLS data in database like MySQL and use JdbcConceptFactory 
instead of UmlsJdbcConceptFactory.

Regards,
Gandhi


-Original Message-
From: Razu Sharif [mailto:razu.cse10.r...@gmail.com]
Sent: Wednesday, February 14, 2018 2:53 PM
To: dev@ctakes.apache.org
Subject: using umls dictionary lookup offline

Dear,

Every time I run cTakes it calls out internet to check our credentials.
Whats required to make it work without internet or credential check.

Thanks
Razu Sharif
This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
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RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Thanks Sean and Chen for your response.  I really appreciate your time.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, February 12, 2018 9:18 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Hi Chen,

No worries!  I often throw out answers before checking code myself.  We are all 
busy with other items.  Besides, If I recall (without checking code), it is 
because of an improvement in the Event annotator code that the Copy*** was no 
longer needed ... and you wrote that improvement!  hurrah!

I thank you for taking the time to answer questions on temporal matters, as 
well as being one of the developers involved working on the module!

Cheers,
Sean

-Original Message-
From: Lin, Chen [mailto:chen@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] 
[SUSPICIOUS]

Thanks to Sean. My bad, I should check the code first before any answer attempt.

Best,
Chen

On 2/12/18, 10:40 AM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:

>It should have nothing to do with the tlink extraction.  It copied
>properties from events to eventmentions and was in the pipeline after
>the tlink annotation, not before.
>
>-Original Message-
>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><gandhi.natara...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-Original Message-
>>From: Lin, Chen [mailto:chen@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick
>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation
>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>pick up some longer-distance relationship as well, but obliviously it
>>fails for your case for long distance relations. We are currently
>>researching a LSTM-based model, which can take more consideration of
>>sentence structure and long-distance relationship. Will update more
>>details in the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><gandhi.natara...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>>>
>>>Also if I run the following text - "I had fever due to smoking so
>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A80
>>>8
>>>0
>>>_in
>>>dex.jsp=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=PZ24
>>>1
>>>C
>>>wYZ
>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKT
>>>G q IrJ RkC7Yk=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M= , I
>>>get the following TLinks:
>>>
>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>CONTAINS paracetomol"
>>>
>>>But if I run the same text in the latest cTAKES using
>>>TemporalSubPipe.piper, I get onl

Regarding cTAKES Tlinks

[Gandhi Rajan Natarajan]

Hi,

I have a question related to cTAKES Tlinks.

Is there any particular reason why 
FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator is 
commented in TemporalSubPipe.piper?

Also if I run the following text - "I had fever due to smoking so took 
paracetomol on 12th June 2018" in temporal demo link - 
http://54.68.117.30:8080/index.jsp , I get the following TLinks:

"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018 CONTAINS 
paracetomol"

But if I run the same text in the latest cTAKES using TemporalSubPipe.piper, I 
get only "12th June 2018 CONTAINS paracetomol" as Tlinks.

Is it due to any recent changes in cTAKES?

Please advise.


Regards,
Gandhi

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RE: Issue Regarding cTakes Installation

[Gandhi Rajan Natarajan]

Hi Neha,

I tried doing the same by checking out latest cTAKES code from SVN and build 
using 'mvn clean install -Dmaven.test.skip=true'

The build was successful. Please find the console message as follows:

[INFO] ctakes-examples  SUCCESS [  1.622 s]
[INFO] Apache cTAKES Resources ctakes-ytex-res  SUCCESS [  1.937 s]
[INFO] Apache cTAKES YTEX . SUCCESS [02:31 min]
[INFO] Apache cTAKES YTEX UIMA  SUCCESS [01:02 min]
[INFO] Apache cTAKES YTEX Web . SUCCESS [01:28 min]
[INFO] Apache cTAKES Distribution . SUCCESS [04:21 min]
[INFO] Apache cTAKES Regression-test .. SUCCESS [  7.022 s]
[INFO] Apache cTAKES template filler .. SUCCESS [  1.591 s]
[INFO] 
[INFO] BUILD SUCCESS
[INFO] 
[INFO] Total time: 15:02 min
[INFO] Finished at: 2018-01-31T10:58:03+05:30
[INFO] Final Memory: 126M/786M
[INFO] 


Could you please send the complete trace of build failure to figure out what 
exactly is the issue?

Regards,
Gandhi

From: Goel, Neha [mailto:ng...@luc.edu]
Sent: Wednesday, January 31, 2018 3:17 AM
To: dev@ctakes.apache.org
Subject: Issue Regarding cTakes Installation




I did the following steps for installing cTakes but having error in Installing 
cTakes YTEX due to which build is failing.



  1.  I Created the cTakes directory, Cloned the git repo.
  2.  Did mvn clean compile
  3.  Did mvn install -Dmaven.test.skip=true


But after 3rd step I am not able to successfully complete the Build.



Please find Below and attached the output:



[INFO] ctakes-examples  SUCCESS [  1.374 s]

[INFO] Apache cTAKES Resources ctakes-ytex-res  SUCCESS [  0.143 s]

[INFO] Apache cTAKES YTEX . FAILURE [  1.352 s]

[INFO] Apache cTAKES YTEX UIMA  SKIPPED

[INFO] Apache cTAKES YTEX Web . SKIPPED

[INFO] Apache cTAKES Distribution . SKIPPED

[INFO] Apache cTAKES Regression-test .. SKIPPED

[INFO] Apache cTAKES template filler .. SKIPPED

[INFO] 

[INFO] BUILD FAILURE

[INFO] 

[INFO] Total time: 01:21 min

[INFO] Finished at: 2018-01-30T15:30:28-06:00

[INFO] Final Memory: 50M/167M

[INFO] 



Thanks & Regards

Neha Goel

MS Computer Science | CTSDH Graduate Fellow

President & Club Facilitator Girls Who Code

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RE: Can we build CollectionReader from database [EXTERNAL]

[Gandhi Rajan Natarajan]

I guess that should be the database resource name.

You can have a look at the following file - 
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?view=markup
 where you could see db resource name like ' DbConnection', ' 
OrangeBookIndexReader' etc.

Regards,
Gandhi


-Original Message-
From: kishore [mailto:kasaraneni.kish...@gmail.com]
Sent: Monday, January 22, 2018 4:55 PM
To: dev@ctakes.apache.org
Subject: Re: Can we build CollectionReader from database [EXTERNAL]

Hi Tim,

I tried as you suggested. but I couldn't understand the variable 
PARAM_DB_CONN_RESRC.
Do we need to pass "driver_url;connection_string;user;password".

Thanks,
Kishore.

On Fri, Jan 12, 2018 at 4:59 PM, Miller, Timothy < 
timothy.mil...@childrens.harvard.edu> wrote:

> Hi Kishore,
> Take a look in this directory for many different collection reader options:
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/
> main/java/org/apache/ctakes/core/cr/
>
> JcdbCollectionReader may work for you.
>
> here are the parameters with comments:
>
> 59  /**
> 60   * SQL statement to retrieve the document.
> 61   */
> 62  public static final String PARAM_SQL = "SqlStatement";
> 63
> 64  /**
> 65   * Name of column from resultset that contains the document
> text. Supported
> 66   * column types are CHAR, VARCHAR, and CLOB.
> 67   */
> 68  public static final String PARAM_DOCTEXT_COL =
> "DocTextColName";
> 69
> 70  /**
> 71   * Name of external resource for database connection.
> 72   */
> 73  public static final String PARAM_DB_CONN_RESRC =
> "DbConnResrcName";
> 74
> 75  /**
> 76   * Optional parameter. Specifies column names that will be
> used to form a
> 77   * document ID.
> 78   */
> 79  public static final String PARAM_DOCID_COLS = "DocIdColNames";
> 80
> 81  /**
> 82   * Optional parameter. Specifies delimiter used when document
> ID is built.
> 83   */
> 84  public static final String PARAM_DOCID_DELIMITER =
> "DocIdDelimiter";
> 85
>
>
> Tim
>
> 
> From: kishore 
> Sent: Friday, January 12, 2018 6:26 AM
> To: dev@ctakes.apache.org
> Subject: Can we build CollectionReader from database [EXTERNAL]
>
> Hi,
> I got to know we can build CollectionReader using FileCollectionReader.
> Do we have option to build CollectionReader from database? Can you
> suggest me how to do that?
>
> Thanks,
> Kishore.
>
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RE: Unable to understand the importance of attributes in IdentifiedAnnotations

[Gandhi Rajan Natarajan]

Try out this link - 
"https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Assertion;

Regards,
Gandhi


-Original Message-
From: Kumari,Puja [mailto:puja.kuma...@cerner.com]
Sent: Thursday, January 04, 2018 3:11 PM
To: dev@ctakes.apache.org
Subject: Re: Unable to understand the importance of attributes in 
IdentifiedAnnotations

Hi,

Thanks for your reply Krishnareddy but the link given says “page not found”. 
Any other suggestions/links that you can share would be appreciable.

Thanks
Puja Kumari

On 1/4/18, 2:51 PM, "Krishnareddy"  wrote:

Hi,

  You can find related information about these attributes in following link


_*https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcwiki.apache.org%2Fconfluence%2Fdisplay%2FCTAKES%2FcTAKES%2B4.0%2B-%2BAssertion*_=02%7C01%7CPuja.Kumari3%40cerner.com%7C738752ad0ee24b8bae6208d553547f25%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C636506544740520408=TjBeskHtrWn8ycT16NaoDopB8bTX0SJTNfWMOG8%2B5fo%3D=0


Thank You

Krishna Reddy


On Thursday 04 January 2018 12:31 PM, Kumari,Puja wrote:
> Hi,
> I am working on IdentifiedAnnotations in apache cTAKES and I am not able 
to  interpret the meaning of the following attributes under 
IdentifiedAnnotations:
> 1.Uncertainty
> 2.History
> 3.Confidence
> 4.Discovery Techniques
>
> What is the importance of these attributes?
> How can we make use of these to make our work efficient?
> Any suggestion / link to understand more would be helpful.
>
>
> Thanks.
> Puja Kumari
> puja.kuma...@cerner.com
>
>
>
>
>
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RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]

[Gandhi Rajan Natarajan]

Great Work Matthew. This will be very handy for cTAKEs MySQL integration. 
Cheers.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Sunday, December 31, 2017 12:47 PM
To: dev@ctakes.apache.org
Cc: Sandeep Byatha Gururaja rao ; Shane Chesnutt 

Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 
1 Concern [EXTERNAL]

Just wanted to note that I've made a good bit of progress on the GUI dictionary 
piece. I'll post some screenshots when it is further along, but I am definitely 
seeing the tables in my MySQL database (tested with CPT and ICD10).

I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is to 
point cTAKES (within the context of the rest service) at MySQL :).

Thanks,

Matthew Vita
www.matthewvita.com

On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> Hi Matthew,
>
> I've heard of CouchDB but know nothing about it.  At a glance it looks
> like it is pretty versatile.
>
> Sean
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Monday, December 18, 2017 3:52 PM
> To: dev@ctakes.apache.org
> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
> Progress + 1 Concern [EXTERNAL]
>
> Okay, thanks for that Sean.
>
> I have a CRAZY idea... how about I try it with CouchDB instead? It's
> a) by Apache b) can be ran in Docker c) Has a JDBC connector on Github
> and d) Is
> 1 of the 2 databases used in OpenEMR so our cTAKES module users
> wouldn't get too confused.
>
> Again, that last item is nice to have, don't read into it too much :).
>
> Thoughts?
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Fantastic!
> >
> > I am glad that you found the issue - that wouldn't have been a
> > straightforward causal to track down.
> >
> > Unfortunately we cannot package and ship any binaries that aren't
> > fully Apache license compliant etc.  However, we can do two
> > different
> things:
> > - We can still grab mysql from maven central for developers to use
> > in a developer environment, just like we do with the default umls
> dictionary.
> > - We can provide an easy means for fetching the library
> > post-installation.  A Dockerfile for ctakes, a downloader that
> > launches when mysql is selected, or a good old fashioned
> > installation
> script.
> > Luckily the mysql library is easily available and we wouldn't need
> > to put together a runtime package like APR.
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.co
> > m_
> > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26=DwIFaQ=qS4goWBT7poplM
> > 69
> > zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d
> > 4g
> > Tao=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc=-fxY4QiBU8SayGVE
> > zX
> > 8LVPEPzmgsYP6ANRsuTUkHkrY=
> > lpg=PA14=apache+license+mysql=bl=uOpifTcI2E=-qlWP2
> > - pXtEkwPM8BsKd73GvX9g=en=X=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A
> > GM4ChDoAQhMMAY#v=onepage=apache%20license%20mysql=false
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_
> > do
> > wnload.cgi=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> > fs
> > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=n53T6SD3EzUyJps9w7LjgVaY
> > GA
> > 5GQjR3h-9GBGppwBc=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g=
> >
> > I think that we could make a class that searches for mysql in the
> > environment if the mysql option is selected.   ctakes-gui has a
> dependency
> > that makes this easy.  Then a little downloader that throws a driver
> > into the lib/ directory.  If needed we could create a factory that
> > returns a wrapper for the required mysql driver classes, and the
> > factory could contain a class loader that guarantees the jar is
> > discovered post-installation.  That way a restart of the gui
> > wouldn't be
> necessary ...
> > though that may not be a big deal.
> >
> > I am just throwing out some ideas.  There is probably a very nice
> > solution that I haven't considered.
> >
> > Sean
> >
> >
> >
> > -Original Message-
> > From: Matthew Vita [mailto:matthewvit...@gmail.com]
> > Sent: Monday, December 18, 2017 1:23 AM
> > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane
> > Chesnutt
> > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
> > Progress +
> > 1 Concern [EXTERNAL]
> >
> > Hi Gandhi, Sean, Tim, Alex, James,
> >
> > Good news, I was able to get MySQL running in the `ctakes-gui`
> > (recall that I am building in a toggle so that folks can create
> > dictionaries using MySQL rather than HSQLDB script files).
> >
> > I found out the source of the issue with bringing in the MySQL
> dependency.
> > This one definitely took me a while and was super subtle! If you
> > visit 

RE: Custom Dictionary connected to mysql

[Gandhi Rajan Natarajan]

I feel Sean and Tim will be the right persons to answer this.

Regards,
Gandhi

-Original Message-
From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Thursday, December 21, 2017 7:32 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql

Hi Gandhi, Thank you for your help. It's working now. In the 
customDictionary.xml, I changed 
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary to 
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
and org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory to 
org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory. For single 
word term, this worked without any change, but for a multi-word term, this was 
returning empty results. When I debugged, I found that the issue was coming at 
code below in DefaultJCasTermAnnotator class line 103- if ( hitTokens[ hit 
].equals(allTokens.get( i ).getText() ) || hitTokens[ hit ].equals( 
allTokens.get( i ).getVariant() ) ); This was happening due to the difference 
in string case. The input string is converted to lowercase, but the string from 
MySQL database is not converted. Right now I have to put all terms in my 
database in lower case to make it work. Do you know any configuration so that I 
don't have to deal with the case issue without changing 
DefaultJCasTermAnnotator file? When using BSV file, I am getting lower case 
sting for both input and term.



Regards
Chahal Arora
Software Engineer
Raxa

On Tue, Dec 19, 2017 at 11:23 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Chahal,
>
> Looking at the error trace:
> ‘javax.servlet.ServletException,java.io.IOException
> 19 Dec 2017 17:56:01  INFO RequestMappingHandlerAdapter - Looking for
> @ControllerAdvice: WebApplicationContext for namespace
> 'ctakes-rest-service-servlet'’
>
> It looks like you are trying to mix match codes from both
> ctakes-rest-service and ctakes-web-rest module I guess.
> Ctakes-rest-service module is obsolete now and request you to consider
> only ctakes-web-rest module  in
> https://github.com/GoTeamEpsilon/ctakes-rest-
> service/tree/master/ctakes-web-rest
>
> Regards,
> Gandhi
>
> From: Chahal Arora [mailto:chahal.ar...@raxa.com]
> Sent: Tuesday, December 19, 2017 8:20 PM
> To: dev@ctakes.apache.org
> Subject: Re: Custom Dictionary connected to mysql
>
> Hi Gandhi,
>
> With updated customDictionary.xml all errors were gone.
>
> I am not sure about the schema of the tables used. I have taken
> reference from JdbcRareWordDictionary.java -
> https://github.com/apache/
> ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/
> main/java/org/apache/ctakes/dictionary/lookup2/dictionary/
> JdbcRareWordDictionary.java  and JdbcConceptFactory.java -
> https://github.com/apache/ctakes/blob/trunk/ctakes-
> dictionary-lookup-fast/src/main/java/org/apache/ctakes/
> dictionary/lookup2/concept/JdbcConceptFactory.java
>
> I am using the ctakes-rest-web server and getting all the annotation
> array as empty in the result json.
>
> Attached tomcat logs again.
>
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>
> On Tue, Dec 19, 2017 at 6:44 PM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com<mailto:gandhi.natara...@arisglobal.com
> >>
> wrote:
> Not able to see any tomcat logs attached.
>
> Do you see any errors in tomcat console?
>
> Regards,
> Gandhi
>
> From: Chahal Arora [mailto:chahal.ar...@raxa.com chahal.ar...@raxa.com>]
> Sent: Tuesday, December 19, 2017 6:09 PM
> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> Subject: Re: Custom Dictionary connected to mysql
>
> Hi,
>
> I have updated the customDictionary.xml and all the erros have gone
> but still not getting any result. I am attaching the latest
> customDictionary.xml and tomcat logs file.
>
>
>
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>
> On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora <chahal.ar...@raxa.com
> <mailto:chahal.ar...@raxa.com><mailto:chahal.ar...@raxa.com hahal.ar...@raxa.com>>> wrote:
> Hi All,
>
> I was working on moving the terms from custom dictionary BSV file to
> MySQL database in LabValueFinder. I am able to connect to the database
> but not sure about the database schema.
>
> Is there an example available where the custom dictionary is connected
> to mysql database instead of a bsv file or hsql database?
>
> Attached is the customDictionary.xml file that I am using.
>
>
> Regards
> Chahal Arora
> Software Engineer
> Raxa
>
> 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 
> ad

RE: Custom Dictionary connected to mysql

[Gandhi Rajan Natarajan]

Hi Chahal,

Looking at the error trace:
‘javax.servlet.ServletException,java.io.IOException
19 Dec 2017 17:56:01  INFO RequestMappingHandlerAdapter - Looking for 
@ControllerAdvice: WebApplicationContext for namespace 
'ctakes-rest-service-servlet'’

It looks like you are trying to mix match codes from both ctakes-rest-service 
and ctakes-web-rest module I guess. Ctakes-rest-service module is obsolete now 
and request you to consider only ctakes-web-rest module  in 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest

Regards,
Gandhi

From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Tuesday, December 19, 2017 8:20 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql

Hi Gandhi,

With updated customDictionary.xml all errors were gone.

I am not sure about the schema of the tables used. I have taken reference from 
JdbcRareWordDictionary.java - 
https://github.com/apache/ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
  and JdbcConceptFactory.java -  
https://github.com/apache/ctakes/blob/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java

I am using the ctakes-rest-web server and getting all the annotation array as 
empty in the result json.

Attached tomcat logs again.

Regards
Chahal Arora
Software Engineer
Raxa

On Tue, Dec 19, 2017 at 6:44 PM, Gandhi Rajan Natarajan 
<gandhi.natara...@arisglobal.com<mailto:gandhi.natara...@arisglobal.com>> wrote:
Not able to see any tomcat logs attached.

Do you see any errors in tomcat console?

Regards,
Gandhi

From: Chahal Arora [mailto:chahal.ar...@raxa.com<mailto:chahal.ar...@raxa.com>]
Sent: Tuesday, December 19, 2017 6:09 PM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: Re: Custom Dictionary connected to mysql

Hi,

I have updated the customDictionary.xml and all the erros have gone but still 
not getting any result. I am attaching the latest customDictionary.xml and 
tomcat logs file.



Regards
Chahal Arora
Software Engineer
Raxa

On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora 
<chahal.ar...@raxa.com<mailto:chahal.ar...@raxa.com><mailto:chahal.ar...@raxa.com<mailto:chahal.ar...@raxa.com>>>
 wrote:
Hi All,

I was working on moving the terms from custom dictionary BSV file to MySQL 
database in LabValueFinder. I am able to connect to the database but not sure 
about the database schema.

Is there an example available where the custom dictionary is connected to mysql 
database instead of a bsv file or hsql database?

Attached is the customDictionary.xml file that I am using.


Regards
Chahal Arora
Software Engineer
Raxa

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

RE: Custom Dictionary connected to mysql

[Gandhi Rajan Natarajan]

Not able to see any tomcat logs attached.

Do you see any errors in tomcat console?

Regards,
Gandhi

From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Tuesday, December 19, 2017 6:09 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql

Hi,

I have updated the customDictionary.xml and all the erros have gone but still 
not getting any result. I am attaching the latest customDictionary.xml and 
tomcat logs file.



Regards
Chahal Arora
Software Engineer
Raxa

On Tue, Dec 19, 2017 at 5:45 PM, Chahal Arora 
> wrote:
Hi All,

I was working on moving the terms from custom dictionary BSV file to MySQL 
database in LabValueFinder. I am able to connect to the database but not sure 
about the database schema.

Is there an example available where the custom dictionary is connected to mysql 
database instead of a bsv file or hsql database?

Attached is the customDictionary.xml file that I am using.


Regards
Chahal Arora
Software Engineer
Raxa

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

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Jeff,

We have now upgraded from Spring 3x to Spring 4.3.12 now.

Since cTAKES was using Spring 3x version only for very few modules in it and 
not Spring's extensive functionality, we decided to upgrade to the latest 
version of the Spring rather than Spring Boot.

But as  you mentioned, cTAKES REST module will generate one WAR file that can 
be deployed to any application server.

In fact, plans are already on to dockerize the complete deployment so that 
everything can be handled by single click.

Regards,
Gandhi


-Original Message-
From: Jeff Headley [mailto:jeffun...@gmail.com]
Sent: Monday, December 18, 2017 12:13 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

My use of ctakes is for a part-time side job and I haven’t been able to read 
every email in here. Apologies in advance if this idea has come up before.

Spring Boot. It appears that ctakes is already using spring. Older version I 
think. If ctakes was to use a newer spring and use spring boot, I think people 
would like the possibilities. You could build a fat jar that could be easily 
executed with an embedded server to provide these rest endpoints. Built in 
metrics and all the stuff spring boot brings with it. It could still be 
deployed as a war to a server and should be easy to deploy in the cloud as 
well. We use spring boot at my full-time job in an AWS environment and we are 
quite happy with Spring Boot for our rest services.

Sent from my iPhone

> On Dec 17, 2017, at 11:33 AM, Finan, Sean <sean.fi...@childrens.harvard.edu> 
> wrote:
>
> Cheers all!
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Saturday, December 16, 2017 1:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [SUSPICIOUS]
>
> I should note that my main work item at the moment is getting the
> Dictionary GUI tool to write straight to MySQL to make this (and other
> solutions) more streamlined. I have read over the code and understand it 
> pretty well. Just fighting to load in the MySQL driver despite what I thought 
> was the right approach ( 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_ctakes-2Drest-2Dservice_issues_2-23issuecomment-2D351921458=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=SNOWoRw_Hkp1F9ybCI6H8JeisqZQQKapVBXOXwKpy98=fAORUifZYDKtiRuE_7TcoYAcw29S-Q6k6uNcyjhfQFI=).
> Going to spend some time on it over the weekend :).
>
> I'm very grateful for Gandhi and you all.
>
> cTAKES + REST = many possibilities as we enter into the new year!
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Fri, Dec 15, 2017 at 9:56 PM, Matthew Vita
> <matthewvit...@gmail.com>
> wrote:
>
>>> could be wrapped in a docker container that would be really
>>> powerful,
>>
>> ​I am on it!​
>>
>>
>> Thanks,
>>
>> Matthew Vita
>> www.matthewvita.com
>>
>> On Fri, Dec 15, 2017 at 6:46 AM, Miller, Timothy <
>> timothy.mil...@childrens.harvard.edu> wrote:
>>
>>> Great, that's very helpful.
>>>
>>> I'll be happy to help with extracting the information needed from
>>> the CAS the easy way. Sean, am I remembering right that there was an
>>> API started for that somewhere? Or maybe that was part of DeepPhe?
>>>
>>> Tim
>>>
>>>
>>>> On Fri, 2017-12-15 at 03:52 +, Gandhi Rajan Natarajan wrote:
>>>> Hi Tim,
>>>>
>>>> Thanks for taking time out and having a look at this. As you
>>>> mentioned, the dictionary descriptor file contains details specific
>>>> to my setup which needs to be changes to 127.0.0.1 by default. Will
>>>> make the change accordingly.
>>>>
>>>> The only reason we went ahead with the approach of parsing XML to
>>>> JSON is due to our lack of in-depth knowledge in cTAKES
>>>> implementations. If I could get some guidance on how to get the
>>>> required JSON details directly from type systems, will be happy to
>>>> implement the same as it will be a huge performance gain.
>>>>
>>>> Also as you said we have two directories names ctakes-web-rest and
>>>> ctakes-rest-service. Ctakes-rest-service directory is no longer
>>>> active and its obsolete. We are just maintaining it for some
>>>> reference for the time being. We will knock it off soon.
>>>>
>>>> Thanks again for the detailed feedback.
>>>>
>>>> Regards,
>>>> Gandhi
>>>>
>>>>
>>&

RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern

[Gandhi Rajan Natarajan]

Hi Matthew,

It's indeed a great news. Glad you cracked it. Cheers.

Regards,
Gandhi

-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Monday, December 18, 2017 11:53 AM
To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao 
; Shane Chesnutt 
Subject: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 
Concern

Hi Gandhi, Sean, Tim, Alex, James,

Good news, I was able to get MySQL running in the `ctakes-gui` (recall that I 
am building in a toggle so that folks can create dictionaries using MySQL 
rather than HSQLDB script files).

I found out the source of the issue with bringing in the MySQL dependency.
This one definitely took me a while and was super subtle! If you visit 
/ctakes/ctakes-distribution/src/main/assembly/bin.xml,
mysql:*is present because it's a n  non-asf compliant 
dependency used by ytex.

Removing the exclude and addingin
mysql:mysql-connector-java gets the correct result:

/ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib
matthew
​​
% ls -lash | grep mysql
  3912 -rw-r--r--   1 matthew  staff   1.9M Dec 14 20:23
mysql-connector-java-6.0.6.jar

Just for completeness, this is the exact POM entry:

  
 mysql
 mysql-connector-java
 6.0.6
 


Is there anyway we can use MySQL in cTAKES in a way that is compliant with ASF? 
I wonder if MariaDB or Postgresql would be better because they work with JDBC 
and are free/open source. Of course, I am biased towards MySQL/MariaDB because 
the (near) future users of cTAKES Rest Service in the OpenEMR space are going 
to want MySQL/MariaDB users :). Not a huge deal though.

Thanks,

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

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Tim,

Thanks for taking time out and having a look at this. As you mentioned, the 
dictionary descriptor file contains details specific to my setup which needs to 
be changes to 127.0.0.1 by default. Will make the change accordingly.

The only reason we went ahead with the approach of parsing XML to JSON is due 
to our lack of in-depth knowledge in cTAKES implementations. If I could get 
some guidance on how to get the required JSON details directly from type 
systems, will be happy to implement the same as it will be a huge performance 
gain.

Also as you said we have two directories names ctakes-web-rest and 
ctakes-rest-service. Ctakes-rest-service directory is no longer active and its 
obsolete. We are just maintaining it for some reference for the time being. We 
will knock it off soon.

Thanks again for the detailed feedback.

Regards,
Gandhi


-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Friday, December 15, 2017 1:25 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

I looked at this today. Looks like a great start!

I was able to get as far as deploying to tomcat, seeing the web form, and 
submitting, but didn't get correct feedback because I don't have a mysql 
dictionary set up, which the default descriptor points at. I didn't see any 
instructions for building that and didn't have time to figure that out.

I think I mentioned in a different thread that if this whole thing could be 
wrapped in a docker container that would be really powerful, but if not, there 
are a few things that are obvious to you as developers but would make it easier 
for novices (like me) to deploy.

* download tomcat bin and start with bin/startup.sh (check at
localhost:8080)
* run mvn install on my ctakes installation to populate jar files in the .m2 
directory that were missing
* run mvn package inside the ctakes-web-rest subdirectory
* copy the .war file into the webapps directory in my tomcat installation.
* While I couldn't get the dictionary to work pointing to mysql, I noticed that 
the dictionary descriptor file has a hardcoded IP address when maybe it should 
be 127.0.0.1?

One other thing I noticed in the code is that in sending back JSON it looks 
like you're turning the JCas into xml and then parsing it yourself. It should 
be easier just to access typesystem objects directly. Sean may have some API 
code laying around to simplify that as well.

To iterate over signs/symptoms, for example, you would do:

for(SignSymptomMention ss : JCasUtil.select(jcas, SignSymptomMention.class)){
  int begin = ss.getBegin(); // begin offset
  int end = ss.getEnd(): // end offset ...
}

Using the typesystem directly may help you to speed up that code or make it 
easier to read. But maybe there is a reason to write it to xml that I'm not 
aware of.

Finally, I see there are two sub-directories with similar names, 
ctakes-rest-service and ctakes-web-rest. If they are duplicates can you delete 
the old one?

I'll keep poking around, but hopefully this is helpful feedback for you guys. 
Thanks again for getting this off the ground!

Tim




On Thu, 2017-12-07 at 14:16 +, Miller, Timothy wrote:
> I am really interested in this too, just waiting until I have a few
> free hours to look around. Don't want you to think it's not of
> interest.
> Tim
>
>
> On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote:
> >
> > Hi all,
> >
> > I am trying to clear a backlog at work.  I will most likely not be
> > able to do anything with ctakes for another week.  Hopefully some
> > rest expert out there can prove their worth by testing ...
> >
> > Sean
> >
> > -Original Message-
> > From: Matthew Vita [mailto:matthewvit...@gmail.com]
> > Sent: Tuesday, December 05, 2017 1:58 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: cTAKES as REST service [EXTERNAL]
> >
> >
> > Hi Gandhi, Sean, Tim, Alex, James,
> >
> > I'm still getting back into the swing of things after my trip (I'm
> > on business traveling at the moment, here in the states). I will be
> > jumping right back into cTAKES REST development next week personally
> > and with a new team mate from the open source team.
> >
> > I'm so sorry for my silence/lack of updates!!! Very excited to see
> > what Gandhi's updates are looking like and enriching the JSON
> > response payload.
> >
> > Thanks,
> >
> > Matthew Vita
> > www.matthewvita.com
> >
> > On Tue, Dec 5, 2017 at 10:24 AM, Gandhi Rajan Natarajan <
> > Gandhi.Nata ra...@arisglobal.com> wrote:
> >
> > >
> > >
> > > Could someone help me out on the resources cleanup atleast if not
> > > review?
> > >
> > > Regards,
> > >

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

am really interested in this too, just waiting until I have a few
> > free hours to look around. Don't want you to think it's not of
> > interest.
> > Tim
> >
> >
> > On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote:
> > >
> > >
> > > Hi all,
> > >
> > > I am trying to clear a backlog at work.  I will most likely not be
> > > able to do anything with ctakes for another week.  Hopefully some
> > > rest expert out there can prove their worth by testing ...
> > >
> > > Sean
> > >
> > > -Original Message-
> > > From: Matthew Vita [mailto:matthewvit...@gmail.com]
> > > Sent: Tuesday, December 05, 2017 1:58 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: cTAKES as REST service [EXTERNAL]
> > >
> > >
> > > Hi Gandhi, Sean, Tim, Alex, James,
> > >
> > > I'm still getting back into the swing of things after my trip (I'm
> > > on business traveling at the moment, here in the states). I will
> > > be jumping right back into cTAKES REST development next week
> > > personally and with a new team mate from the open source team.
> > >
> > > I'm so sorry for my silence/lack of updates!!! Very excited to see
> > > what Gandhi's updates are looking like and enriching the JSON
> > > response payload.
> > >
> > > Thanks,
> > >
> > > Matthew Vita
> > > www.matthewvita.com
> > >
> > > On Tue, Dec 5, 2017 at 10:24 AM, Gandhi Rajan Natarajan <
> > > Gandhi.Nata ra...@arisglobal.com> wrote:
> > >
> > > >
> > > >
> > > >
> > > > Could someone help me out on the resources cleanup atleast if
> > > > not review?
> > > >
> > > > Regards,
> > > > Gandhi
> > > >
> > > >
> > > > -Original Message-
> > > > From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisgloba
> > > > l.
> > > > co
> > > > m]
> > > > Sent: Monday, December 04, 2017 10:05 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: RE: cTAKES as REST service [EXTERNAL]
> > > >
> > > > Hi Sean, Tim, Alex, Matthew, James and All,
> > > >
> > > > I have placed the first cut version of cTAKES REST module in the
> > > > following path -
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com
> > > > _G
> > > > oT
> > > > eam
> > > > Epsilon_ctakes-2Drest-
> > > > 2Dservice_tree_=DwIFaQ=qS4goWBT7poplM69zy_3x
> > > > hKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d
> > > > 4g
> > > > Ta
> > > > o
> > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y=KZ65xiQopzQNQarV
> > > > c3
> > > > BP
> > > > MxK
> > > > izpqJwoUJtjIJZC8C6iA=
> > > > master/ctakes-web-rest/
> > > >
> > > > Things pending in the module:
> > > > 1) Index Page to test the rest module using AJAX call
> > > > 2) Revamping the final output XML
> > > >
> > > > Request you all to have a look at this module and provide your
> > > > feedback. I would also require expert advice to clean up the
> > > > resources folder -
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com
> > > > _G
> > > > oT
> > > > eam
> > > > Epsilon_ctakes-2Drest-
> > > > 2Dservice_tree_=DwIFaQ=qS4goWBT7poplM69zy_3x
> > > > hKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d
> > > > 4g
> > > > Ta
> > > > o
> > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y=KZ65xiQopzQNQarV
> > > > c3
> > > > BP
> > > > MxK
> > > > izpqJwoUJtjIJZC8C6iA= master/ctakes-web-
> > > > rest/src/main/resources/org
> > > >
> > > > This module can be deployed as a web-app in Tomcat using the
> > > > generated WAR file . It can be tested using any REST client
> > > > (like Chrome's Postman app) by accessing the following URL -
> > > > http://:/ctakes-web-rest/service/analyze
> > > > and providing the analysis text as request body.
> > > >
> > > > Sample input : "Patient has cancer and nausea. Earlier he has
> > > > been deducted for red eye."
> > > > Sample output:

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Could someone help me out on the resources cleanup atleast if not review?

Regards,
Gandhi


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Monday, December 04, 2017 10:05 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi Sean, Tim, Alex, Matthew, James and All,

I have placed the first cut version of cTAKES REST module in the following path 
- 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest/

Things pending in the module:
1) Index Page to test the rest module using AJAX call
2) Revamping the final output XML

Request you all to have a look at this module and provide your feedback. I 
would also require expert advice to clean up the resources folder - 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest/src/main/resources/org

This module can be deployed as a web-app in Tomcat using the generated WAR file 
. It can be tested using any REST client (like Chrome's Postman app) by 
accessing the following URL - 
http://:/ctakes-web-rest/service/analyze and providing the 
analysis text as request body.

Sample input : "Patient has cancer and nausea. Earlier he has been deducted for 
red eye."
Sample output:
 {
"DrugChangeStatusAnnotation": [],
"StrengthAnnotation": [],
"FractionStrengthAnnotation": [],
"FrequencyUnitAnnotation": [],
"CompanyAnnotation": [],
"DiseaseDisorderMention": [
"CANCER"
],
"SignSymptomMention": [
"RED EYE",
"NAUSEA"
],
"RouteAnnotation": [],
"DateAnnotation": [],
"MeasurementAnnotation": [],
    "ProcedureMention": [],
"TimeMention": [],
"StrengthUnitAnnotation": []
}

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 1:45 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi All,

Have completed cTAKES Spring upgrade changes and checked in the same to SVN. 
Please revert in case of any issues.

@Alex, Thanks a lot for taking time out and providing your review comments on 
Spring upgrade. Really appreciate it.

Now it will ease our effort in creating ctakes rest module.

Regards,
Gandhi


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 4:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi,

I have attached the patch file for cTAKES Spring upgrade in 
https://issues.apache.org/jira/browse/CTAKES-472  Unfortunately I'm not able to 
assign this issue to me as I don’t have access. Could someone help me out with 
the access?

For time being I have commented out the DataAnnotatorTest failure in the patch.

Could someone test the patch and let us know so that I can commit the changes 
in SVN?

This change will lay the foundation for REST module implementation in cTAKES.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Wednesday, November 01, 2017 8:24 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Alex,

Gandhi covered everything we are working on. Please do mail me if you'd like to 
join in and I can give you some open tasks.

Thanks,

Matthew Vita
www.matthewvita.com

On Mon, Oct 30, 2017 at 8:46 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Alex and Sean,
>
> Thanks for the acknowledgement.
>
> As mentioned earlier in the thread, I have sent the github link -
> https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes
> - SVN-src  that contains changes to be made to upgrade cTAKES to
> Spring4x.
> I have done it on my local sandbox and it works. But as I mentioned
> earlier, I was not able to test ytex module changes as I'm not aware
> of those modules. Matthew is already testing the spring upgrade
> changes and hopefully we will able be close it. If you could test the
> ytex modules, it will be of great help I guess.
>
> Regarding docker works on cTAKES, hats off to Matthew. We can assist
> him if he needs any help out there.
>
> Regarding REST API, we are planning to use Spring REST service as
> introducing Jersey container may be an overhead I feel. Also regarding
> your idea on new module, I too agree with you. But in the new module,
> we can improvise Chei Pen's work in this link -
> https://github.com/healthnlp/
> examples/tree/master/ctakes-temporal-demo and name it as 'ctakes-web'
> or 'ctakes-web-rest' so that the module can be used to build cTAKES as
> both traditional web app as well as expose it as an REST service. It's just a 
> thought f

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean, Tim, Alex, Matthew, James and All,

I have placed the first cut version of cTAKES REST module in the following path 
- 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest/

Things pending in the module:
1) Index Page to test the rest module using AJAX call
2) Revamping the final output XML

Request you all to have a look at this module and provide your feedback. I 
would also require expert advice to clean up the resources folder - 
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest/src/main/resources/org

This module can be deployed as a web-app in Tomcat using the generated WAR file 
. It can be tested using any REST client (like Chrome's Postman app) by 
accessing the following URL - 
http://:/ctakes-web-rest/service/analyze and providing the 
analysis text as request body.

Sample input : "Patient has cancer and nausea. Earlier he has been deducted for 
red eye."
Sample output:
 {
"DrugChangeStatusAnnotation": [],
"StrengthAnnotation": [],
"FractionStrengthAnnotation": [],
"FrequencyUnitAnnotation": [],
"CompanyAnnotation": [],
"DiseaseDisorderMention": [
"CANCER"
],
"SignSymptomMention": [
"RED EYE",
"NAUSEA"
],
"RouteAnnotation": [],
"DateAnnotation": [],
"MeasurementAnnotation": [],
    "ProcedureMention": [],
"TimeMention": [],
"StrengthUnitAnnotation": []
}

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 1:45 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi All,

Have completed cTAKES Spring upgrade changes and checked in the same to SVN. 
Please revert in case of any issues.

@Alex, Thanks a lot for taking time out and providing your review comments on 
Spring upgrade. Really appreciate it.

Now it will ease our effort in creating ctakes rest module.

Regards,
Gandhi


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 4:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]

Hi,

I have attached the patch file for cTAKES Spring upgrade in 
https://issues.apache.org/jira/browse/CTAKES-472  Unfortunately I'm not able to 
assign this issue to me as I don’t have access. Could someone help me out with 
the access?

For time being I have commented out the DataAnnotatorTest failure in the patch.

Could someone test the patch and let us know so that I can commit the changes 
in SVN?

This change will lay the foundation for REST module implementation in cTAKES.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Wednesday, November 01, 2017 8:24 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Alex,

Gandhi covered everything we are working on. Please do mail me if you'd like to 
join in and I can give you some open tasks.

Thanks,

Matthew Vita
www.matthewvita.com

On Mon, Oct 30, 2017 at 8:46 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Alex and Sean,
>
> Thanks for the acknowledgement.
>
> As mentioned earlier in the thread, I have sent the github link -
> https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes
> - SVN-src  that contains changes to be made to upgrade cTAKES to
> Spring4x.
> I have done it on my local sandbox and it works. But as I mentioned
> earlier, I was not able to test ytex module changes as I'm not aware
> of those modules. Matthew is already testing the spring upgrade
> changes and hopefully we will able be close it. If you could test the
> ytex modules, it will be of great help I guess.
>
> Regarding docker works on cTAKES, hats off to Matthew. We can assist
> him if he needs any help out there.
>
> Regarding REST API, we are planning to use Spring REST service as
> introducing Jersey container may be an overhead I feel. Also regarding
> your idea on new module, I too agree with you. But in the new module,
> we can improvise Chei Pen's work in this link -
> https://github.com/healthnlp/
> examples/tree/master/ctakes-temporal-demo and name it as 'ctakes-web'
> or 'ctakes-web-rest' so that the module can be used to build cTAKES as
> both traditional web app as well as expose it as an REST service. It's just a 
> thought from my side which we can discuss upon.
>
> Once the web-rest module is ready, I feel it will take cTAKES to a
> whole new level as you can even plug it with mobile applications that
> can send the clinical text for analysis and get JSON response that can
> be rendered on mobile app UI.
>
> Sugg

RE: Regarding cTakes version upadtion [EXTERNAL]

[Gandhi Rajan Natarajan]

tator.java:129)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> initialize(PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
> AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
> CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(
> AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> initialize(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(
> AnalysisEngineFactory.java:711)
> at
> org.apache.uima.fit.factory.AggregateBuilder.createAggregate(
> AggregateBuilder.java:207)
> at com.app.webservlet.cTakesWebClass.init(cTakesWebClass.java:36)
> at
> org.eclipse.jetty.servlet.ServletHolder.initServlet(
> ServletHolder.java:532)
> at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> org.eclipse.jetty.servlet.ServletHandler.initialize(
> ServletHandler.java:791)
> at
> org.eclipse.jetty.servlet.ServletContextHandler.startContext(
> ServletContextHandler.java:265)
> at
> org.eclipse.jetty.webapp.WebAppContext.startContext(
> WebAppContext.java:1242)
> at
> org.eclipse.jetty.server.handler.ContextHandler.
> doStart(ContextHandler.java:717)
> at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> org.eclipse.jetty.server.handler.HandlerWrapper.
> doStart(HandlerWrapper.java:95)
> at org.eclipse.jetty.server.Server.doStart(Server.java:282)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedAdapter.start(
> JettyEmbeddedAdapter.java:67)
> at
> net.sourceforge.eclipsejetty.starter.common.AbstractJettyLauncherMain.
> launch(AbstractJettyLauncherMain.java:84)
> at
> net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedLauncherMain.
> main(JettyEmbeddedLauncherMain.java:42)
> 2017-11-30 14:07:18.877:WARN:oejs.Holder:
> java.lang.ClassNotFoundException:
> com.sun.jersey.spi.container.servlet.ServletContainer
> at java.net.URLClassLoader.findClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at
> org.eclipse.jetty.webapp.WebAppClassLoader.loadClass(
> WebAppClassLoader.java:430)
> at
> org.eclipse.jetty.webapp.WebAppClassLoader.loadClass(
> WebAppClassLoader.java:383)
> at org.eclipse.jetty.util.Loader.loadClass(Loader.java:100)
> at org.eclipse.jetty.util.Loader.loadClass(Loader.java:79)
> at org.eclipse.jetty.servlet.Holder.doStart(Holder.java:107)
> at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:298)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> org.eclipse.jetty.servlet.ServletHandler.initialize(
> ServletHandler.java:791)
> at
> org.eclipse.jetty.servlet.ServletContextHandler.startContext(
> ServletContextHandler.java:265)
> at
> org.eclipse.jetty.webapp.WebAppContext.startContext(
> WebAppContext.java:1242)
> at
> org.eclipse.jetty.server.handler.ContextHandler.
> doStart(ContextHandler.java:717)
> at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> org.eclipse.jetty.server.handler.HandlerWrapper.
> doStart(HandlerWrapper.java:95)
> at org.eclipse.jetty.server.Server.doStart(Server.java:282)
> at
> org.eclipse.jetty.util.component.AbstractLifeCycle.
> start(AbstractLifeCycle.java:64)
> at
> net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedAdapter.start(
> JettyEmbeddedAdapter.java:67)
> at
&g

RE: Regarding cTakes version upadtion

[Gandhi Rajan Natarajan]

Hey Sunder,

Do you have the required files in your webapp resources folder?

The below error shows the required files are missing:

Caused by:
java.io.FileNotFoundException:
\org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar (The system cannot 
find the path specified) at java.io.FileInputStream.open0(Native Method) at 
java.io.FileInputStream.open(Unknown Source) at 
java.io.FileInputStream.(Unknown Source) at 
java.io.FileInputStream.(Unknown Source)

Check out this link - 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo/src/main/resources

Regards,
Gandhi


-Original Message-
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent: Thursday, November 30, 2017 12:38 PM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTakes version upadtion

Thank you James,

just i am using Maven dependencies  and i created one pipline class in that one 
AggregateBuilder for fastlookup,

next i created one servlet for accessing AggregateBuilder.

i did every thing .. But i am getting this Exception..

//

log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM  HH:mm:ss} %5p 
%c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
30 Nov 2017 12:27:02  INFO LvgAnnotator - URL for lvg.properties 
=file:/C:/Users/NI3102/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
2017-11-30 12:27:11.055:WARN:/:unavailable
org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class "org.apache.ctakes.temporal.ae.EventEventRelationAnnotator"
failed.  (Descriptor: )
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
at
org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
at com.app.webservlet.cTakesWebClass.init(cTakesWebClass.java:36)
at
org.eclipse.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:532)
at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64)
at
org.eclipse.jetty.servlet.ServletHandler.initialize(ServletHandler.java:791)
at
org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:265)
at
org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1242)
at
org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:717)
at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64)
at
org.eclipse.jetty.server.handler.HandlerWrapper.doStart(HandlerWrapper.java:95)
at org.eclipse.jetty.server.Server.doStart(Server.java:282)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:64)
at
net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedAdapter.start(JettyEmbeddedAdapter.java:67)
at
net.sourceforge.eclipsejetty.starter.common.AbstractJettyLauncherMain.launch(AbstractJettyLauncherMain.java:84)
at
net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedLauncherMain.main(JettyEmbeddedLauncherMain.java:42)
Caused by:
org.apache.uima.resource.ResourceInitializationException
at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:137)
at
org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.initialize(TemporalRelationExtractorAnnotator.java:164)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
at

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

Now it works like a charm. Thanks again for your assistance.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, November 30, 2017 2:28 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

Try this:

AnalysisEngine engine = UIMAFramework.produceAnalysisEngine( pipeline );

Then for each post
JCas jcas = JCasFactory.createJCas();
jcas.setDocumentText(analysisText);
engine.process( jcas );


I think that should improve things.  I would also consider using a JCasPool.

JCasPool pool = new JCasPool( 100, engine );

For each post
JCas jcas = pool.getJCas( -1 );
jcas.setDocumentText(analysisText);
engine.process( jcas );
pool.releaseJCas( jcas );

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, November 29, 2017 3:27 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean,

I was able to make the custom dictionary XML work with "LookupXml" parameter.

But I face another issue  in the rest implementation in this new approach using 
PiperFileReader.  If I use the following lines of code, for each post request  
it makes a db connection once again and loads the annotator.

JCas jcas = JCasFactory.createJCas();
   jcas.setDocumentText(analysisText);
   SimplePipeline.runPipeline(jcas, pipeline);

This slows down the complete analysis and chokes the server. Is there an 
approach to load the annotators only once like in earlier approach so that it 
improves the performance?

Regards,
Gandhi


-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, November 22, 2017 1:35 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Thanks for the detailed explanation Sean. We will have a look at the 
PiperFileReader and try to implement the rest module in similar lines.

Will keep you posted. Thanks again.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to add that code.  There is already a parameter named 
"LookupXml" that can be used.

That being said, I just took a look at the code in github.  To be honest, I 
would not use the DemoServlet class.  It uses a hardcoded pipeline, complete 
with parameter values.  Instead I would write a new one that utilizes the 
PiperFileReader in core.  If you do that then you can start up a demo with any 
pipeline you want - there is no need to create new code for each different type 
of pipeline - e.g. default clinical vs. temporal.  You can set any custom 
parameter values in the piper file.

This is the gist:

 // Add a simple pre-defined existing pipeline from a file or resource
 PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );

// Get a description of the pipeline created from the file
PipelineBuilder builder = reader.getBuilder(); 
AnalysisEngineDescription pipeline = builder. getAnalysisEngineDesc();

// For each post, create a jcas object.  Consider using a caspool instead.
   JCas jcas = JCasFactory.createJCas();

   // Set the posted text and run the pipeline
 jcas.setDocumentText( TEXT );
 SimplePipeline.runPipeline( jcas, pipeline );

There may be a better way to run than with the SimplePipeline, but the above 
should suffice.

It would be cool if there was an option for response from the HtmlTextWriter, 
but I don't know how quick and easy that would be to implement.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 1:36 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean and Sirisha,

Thanks a lot for the response.

I tried building and deploying the war from the following repo - 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4=kiJMuwmqMs4szLaIFtTi_lAJVc2h5KK5VYAkmN6wJmU=

On server start, it looks for sno_rx_16ab.xml. Not sure what configuration 
exactly you are asking for.

Also as you said we are looking to set the parameter LookupXml dynamically  in 
AbstractJCasTermAnnotator.java file's initialize method as follows:

String _customDescriptorFilePath = System.getenv("CUSTOM_DESC_FILE_PATH");
  if(_customDescriptorFilePath != null) { LOGGER.info( "Using custom 
descriptor file path: " + _customDescriptorFilePath ); _descrip

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

I was able to make the custom dictionary XML work with "LookupXml" parameter.

But I face another issue  in the rest implementation in this new approach using 
PiperFileReader.  If I use the following lines of code, for each post request  
it makes a db connection once again and loads the annotator.

JCas jcas = JCasFactory.createJCas();
   jcas.setDocumentText(analysisText);
   SimplePipeline.runPipeline(jcas, pipeline);

This slows down the complete analysis and chokes the server. Is there an 
approach to load the annotators only once like in earlier approach so that it 
improves the performance?

Regards,
Gandhi


-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, November 22, 2017 1:35 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Thanks for the detailed explanation Sean. We will have a look at the 
PiperFileReader and try to implement the rest module in similar lines.

Will keep you posted. Thanks again.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to add that code.  There is already a parameter named 
"LookupXml" that can be used.

That being said, I just took a look at the code in github.  To be honest, I 
would not use the DemoServlet class.  It uses a hardcoded pipeline, complete 
with parameter values.  Instead I would write a new one that utilizes the 
PiperFileReader in core.  If you do that then you can start up a demo with any 
pipeline you want - there is no need to create new code for each different type 
of pipeline - e.g. default clinical vs. temporal.  You can set any custom 
parameter values in the piper file.

This is the gist:

 // Add a simple pre-defined existing pipeline from a file or resource
 PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );

// Get a description of the pipeline created from the file
PipelineBuilder builder = reader.getBuilder(); 
AnalysisEngineDescription pipeline = builder. getAnalysisEngineDesc();

// For each post, create a jcas object.  Consider using a caspool instead.
   JCas jcas = JCasFactory.createJCas();

   // Set the posted text and run the pipeline
 jcas.setDocumentText( TEXT );
 SimplePipeline.runPipeline( jcas, pipeline );

There may be a better way to run than with the SimplePipeline, but the above 
should suffice.

It would be cool if there was an option for response from the HtmlTextWriter, 
but I don't know how quick and easy that would be to implement.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 1:36 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean and Sirisha,

Thanks a lot for the response.

I tried building and deploying the war from the following repo - 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4=kiJMuwmqMs4szLaIFtTi_lAJVc2h5KK5VYAkmN6wJmU=

On server start, it looks for sno_rx_16ab.xml. Not sure what configuration 
exactly you are asking for.

Also as you said we are looking to set the parameter LookupXml dynamically  in 
AbstractJCasTermAnnotator.java file's initialize method as follows:

String _customDescriptorFilePath = System.getenv("CUSTOM_DESC_FILE_PATH");
  if(_customDescriptorFilePath != null) { LOGGER.info( "Using custom 
descriptor file path: " + _customDescriptorFilePath ); _descriptorFilePath = 
_customDescriptorFilePath; }

Is this approach fine?

Regards,
Gandhi



-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 9:32 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to have sno_rx_16ab* .  I don't know exactly how you are 
configured, but if you have another dictionary that you want to use instead of 
the default sno_rx then you just need to create it and then point the custom 
config .xml.  This can be done a couple of ways, but basically set the 
parameter LookupXml to point to your custom xml path.  This needs to be done at 
startup.  Once ctakes is running (i.e. as a service) you cannot change the 
dictionary.

This is briefly explained at the bottom of the wiki page:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs6

RE: ResourceInitializationException in DefaultJCasTermAnnotator

[Gandhi Rajan Natarajan]

Glad that you got it working. Cheers.

Regards,
Gandhi


-Original Message-
From: Ritwik Jain [mailto:ritwik.j...@raxa.com]
Sent: Wednesday, November 29, 2017 5:03 PM
To: dev@ctakes.apache.org
Subject: Re: ResourceInitializationException in DefaultJCasTermAnnotator

Hi Gandhi,

Thankyou for looking up into the issue and giving me your valuable solution to 
it. I will also try the method which you suggested. Even i was able to run the 
example project using tomcat. Two files were missing in WEB-INF folder when i 
have deployed the project. One was the cTakesHsql file and another one was the 
sno_rx_16ab file due to which this particular error was coming. Now I am able 
to fetch the result using tomcat. Once again thankyou for the solution.

Regards
Ritwik

On Wed, Nov 29, 2017 at 4:56 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Ritwik,
>
> If you run the demo app in Jetty server using 'mvn jetty:run' command
> as mentioned in this link - http://healthnlp.github.io/examples/ ,it
> should work fine.
>
> In Tomcat deployment, the HSQL in-memory DB implementation is the issue.
> You may have to use MySQL DB to make it work in Tomcat.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Ritwik Jain [mailto:ritwik.j...@raxa.com]
> Sent: Wednesday, November 29, 2017 2:15 PM
> To: dev@ctakes.apache.org
> Subject: ResourceInitializationException in DefaultJCasTermAnnotator
>
> Hi All,
>
> I have cloned the CTake-Temporal_demo from github repo. After that I
> run the query mvn clean install which allowed me to have a .war file.
> I have deployed the war file in my tomcat server but after putting the
> Text like
> :- "Potassium 40" and hitting the submit button, I am getting the
> error -
> "*org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> (Descriptor: )*"
>
> I have even installed the resources again and replace it with the
> resources that have been there earlier but it is of no use. I have
> even clones the trunk repo of Ctake and installed the maven
> dependencies but this method also goes in vain. Can anyone please help
> in it. I am really badly stuck in this point.
>
> Regards
> Ritwik
> --
> Ritwik Jain
> 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.
>



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

RE: Having trouble creating the first annotator.

[Gandhi Rajan Natarajan]

Hi Ritwik,

I'm not able to find the link of Sean's response for this same question which 
we asked sometime back. So I'm attaching his response once again for you as 
follows:

> Iis there any doc or guide on how to start writing our own annotator?

There are two example annotators in the ctakes-examples project under the ae/ 
directory.  You can look at those, but I recommend that you look at some 
information on Uimafit, which can be used to create new annotators:
https://uima.apache.org/d/uimafit-2.1.0/tools.uimafit.book.pdf
An introduction to creating Analysis Engines (Annotators) is on page 5.

Coding style is individualistic, but below is a rubberstamp that I use to get 
started:

import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;

/**
 * @author SPF , chip-nlp
 * @version %I%
 * @since 9/22/2017
 */
@PipeBitInfo(
  name = "Template",
  description = "For Example.", role = PipeBitInfo.Role.ANNOTATOR
)
final public class Template extends JCasAnnotator_ImplBase {

   static private final Logger LOGGER = Logger.getLogger( "Template" );

   /**
* {@inheritDoc}
*/
   @Override
   public void initialize( final UimaContext context ) throws 
ResourceInitializationException {
  // Always call the super first
  super.initialize( context );
  // place AE initialization code here
   }

   /**
* {@inheritDoc}
*/
   @Override
   public void process( final JCas jCas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Processing ..." );
  // Place AE processing code here
  LOGGER.info( "Finished." );
   }
}



If you use IntelliJ as your ide you can create a file template with these 
parameters:

#if (${PACKAGE_NAME} && ${PACKAGE_NAME} != "")package ${PACKAGE_NAME};#end

import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;

#parse("File Header.java")
@PipeBitInfo(
  name = "${NAME}",
  #if ( ${PROJECT_NAME} != "")description = "For ${PROJECT_NAME}.",#end
  role = PipeBitInfo.Role.ANNOTATOR
)
final public class ${NAME} extends JCasAnnotator_ImplBase {

   static private final Logger LOGGER = Logger.getLogger( "${NAME}" );

   /**
* {@inheritDoc}
*/
   @Override
   public void initialize( final UimaContext context ) throws 
ResourceInitializationException {
  // Always call the super first
  super.initialize( context );
  // place AE initialization code here
   }

   /**
* {@inheritDoc}
*/
   @Override
   public void process( final JCas jCas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Processing ..." );
  // Place AE processing code here
  LOGGER.info( "Finished." );
   }
}

Thanks again Sean.

Regards,
Gandhi

-Original Message-
From: Ritwik Jain [mailto:ritwik.j...@raxa.com]
Sent: Monday, November 27, 2017 3:57 PM
To: dev@ctakes.apache.org
Subject: Having trouble creating the first annotator.

HI,

I am new to C-takes development and i have taken the project in order to 
develop the first annotator using Ctakes. Can someone guide me by sharing the 
examples of the code for building the annotator.

Regards
Ritwik

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

[Gandhi Rajan Natarajan]

Thanks for the detailed explanation Sean. We will have a look at the 
PiperFileReader and try to implement the rest module in similar lines.

Will keep you posted. Thanks again.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to add that code.  There is already a parameter named 
"LookupXml" that can be used.

That being said, I just took a look at the code in github.  To be honest, I 
would not use the DemoServlet class.  It uses a hardcoded pipeline, complete 
with parameter values.  Instead I would write a new one that utilizes the 
PiperFileReader in core.  If you do that then you can start up a demo with any 
pipeline you want - there is no need to create new code for each different type 
of pipeline - e.g. default clinical vs. temporal.  You can set any custom 
parameter values in the piper file.

This is the gist:

 // Add a simple pre-defined existing pipeline from a file or resource
 PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );

// Get a description of the pipeline created from the file
PipelineBuilder builder = reader.getBuilder();
AnalysisEngineDescription pipeline = builder. getAnalysisEngineDesc();

// For each post, create a jcas object.  Consider using a caspool instead.
   JCas jcas = JCasFactory.createJCas();

   // Set the posted text and run the pipeline
 jcas.setDocumentText( TEXT );
 SimplePipeline.runPipeline( jcas, pipeline );

There may be a better way to run than with the SimplePipeline, but the above 
should suffice.

It would be cool if there was an option for response from the HtmlTextWriter, 
but I don't know how quick and easy that would be to implement.

Sean

-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 1:36 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean and Sirisha,

Thanks a lot for the response.

I tried building and deploying the war from the following repo - 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4=kiJMuwmqMs4szLaIFtTi_lAJVc2h5KK5VYAkmN6wJmU=

On server start, it looks for sno_rx_16ab.xml. Not sure what configuration 
exactly you are asking for.

Also as you said we are looking to set the parameter LookupXml dynamically  in 
AbstractJCasTermAnnotator.java file's initialize method as follows:

String _customDescriptorFilePath = System.getenv("CUSTOM_DESC_FILE_PATH");
  if(_customDescriptorFilePath != null) { LOGGER.info( "Using custom 
descriptor file path: " + _customDescriptorFilePath ); _descriptorFilePath = 
_customDescriptorFilePath; }

Is this approach fine?

Regards,
Gandhi



-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 9:32 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to have sno_rx_16ab* .  I don't know exactly how you are 
configured, but if you have another dictionary that you want to use instead of 
the default sno_rx then you just need to create it and then point the custom 
config .xml.  This can be done a couple of ways, but basically set the 
parameter LookupXml to point to your custom xml path.  This needs to be done at 
startup.  Once ctakes is running (i.e. as a service) you cannot change the 
dictionary.

This is briefly explained at the bottom of the wiki page:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4=3NuvXMGraH4F2tk5TDjgza9ie9kIyCuhbyeku-Xu3hI=

Sean

-----Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 10:44 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean,

When we try to deploy cTAKES as web application, it always looks for 
sno_rx_16ab.xml by default on server start. So do you mean we should also have 
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?

Regards,
Gandhi

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 8:42 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sandeep,

Adding a custom dictionary should n

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean and Sirisha,

Thanks a lot for the response.

I tried building and deploying the war from the following repo - 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo

On server start, it looks for sno_rx_16ab.xml. Not sure what configuration 
exactly you are asking for.

Also as you said we are looking to set the parameter LookupXml dynamically  in 
AbstractJCasTermAnnotator.java file's initialize method as follows:

String _customDescriptorFilePath = System.getenv("CUSTOM_DESC_FILE_PATH");
  if(_customDescriptorFilePath != null) {
LOGGER.info( "Using custom descriptor file path: " + _customDescriptorFilePath 
);
_descriptorFilePath = _customDescriptorFilePath;
}

Is this approach fine?

Regards,
Gandhi



-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 9:32 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Gandhi,

You don't need to have sno_rx_16ab* .  I don't know exactly how you are 
configured, but if you have another dictionary that you want to use instead of 
the default sno_rx then you just need to create it and then point the custom 
config .xml.  This can be done a couple of ways, but basically set the 
parameter LookupXml to point to your custom xml path.  This needs to be done at 
startup.  Once ctakes is running (i.e. as a service) you cannot change the 
dictionary.

This is briefly explained at the bottom of the wiki page:
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 10:44 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sean,

When we try to deploy cTAKES as web application, it always looks for 
sno_rx_16ab.xml by default on server start. So do you mean we should also have 
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?

Regards,
Gandhi

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 8:42 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sandeep,

Adding a custom dictionary should never require code modification.

The dictionary creator gui will create a custom dictionary and its .xml 
configuration file and place them in your ctakes resources/ directory.  No code 
changes necessary.

https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=K-fWZaRAkXxJHPoz7nhE5U4rhYmrwSrGwMqji82GLVc=DIMsU-EWm6kc1X-08Z2GlrsKmug3xQCnPgtDAXp3o1s=

If you search the ctakes devlist emails you should find some threads discussing 
custom dictionaries and bsv files.  (bar separated value, aka pipe-delimited).  
For smaller custom dictionaries those can be created.  The emails should 
include information on creating the .xml dictionary configuration files.

Sean

-Original Message-
From: Sandeep Byatha Gururaja rao [mailto:sandeep...@arisglobal.com]
Sent: Tuesday, November 21, 2017 9:40 AM
To: dev@ctakes.apache.org
Subject: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi,

Is there currently any way to use a custom dictionary descriptor file without 
making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast 
jar file.

Regards,
Sandeep
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.
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.
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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

When we try to deploy cTAKES as web application, it always looks for 
sno_rx_16ab.xml by default on server start. So do you mean we should also have 
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?

Regards,
Gandhi

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 8:42 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi Sandeep,

Adding a custom dictionary should never require code modification.

The dictionary creator gui will create a custom dictionary and its .xml 
configuration file and place them in your ctakes resources/ directory.  No code 
changes necessary.

https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI

If you search the ctakes devlist emails you should find some threads discussing 
custom dictionaries and bsv files.  (bar separated value, aka pipe-delimited).  
For smaller custom dictionaries those can be created.  The emails should 
include information on creating the .xml dictionary configuration files.

Sean

-Original Message-
From: Sandeep Byatha Gururaja rao [mailto:sandeep...@arisglobal.com]
Sent: Tuesday, November 21, 2017 9:40 AM
To: dev@ctakes.apache.org
Subject: Use of custom Dictionary Descriptor file [EXTERNAL]

Hi,

Is there currently any way to use a custom dictionary descriptor file without 
making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast 
jar file.

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

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi,

I have attached the patch file for cTAKES Spring upgrade in 
https://issues.apache.org/jira/browse/CTAKES-472  Unfortunately I'm not able to 
assign this issue to me as I don’t have access. Could someone help me out with 
the access?

For time being I have commented out the DataAnnotatorTest failure in the patch.

Could someone test the patch and let us know so that I can commit the changes 
in SVN?

This change will lay the foundation for REST module implementation in cTAKES.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Wednesday, November 01, 2017 8:24 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL]

Alex,

Gandhi covered everything we are working on. Please do mail me if you'd like to 
join in and I can give you some open tasks.

Thanks,

Matthew Vita
www.matthewvita.com

On Mon, Oct 30, 2017 at 8:46 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Alex and Sean,
>
> Thanks for the acknowledgement.
>
> As mentioned earlier in the thread, I have sent the github link -
> https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes
> - SVN-src  that contains changes to be made to upgrade cTAKES to
> Spring4x.
> I have done it on my local sandbox and it works. But as I mentioned
> earlier, I was not able to test ytex module changes as I'm not aware
> of those modules. Matthew is already testing the spring upgrade
> changes and hopefully we will able be close it. If you could test the
> ytex modules, it will be of great help I guess.
>
> Regarding docker works on cTAKES, hats off to Matthew. We can assist
> him if he needs any help out there.
>
> Regarding REST API, we are planning to use Spring REST service as
> introducing Jersey container may be an overhead I feel. Also regarding
> your idea on new module, I too agree with you. But in the new module,
> we can improvise Chei Pen's work in this link -
> https://github.com/healthnlp/
> examples/tree/master/ctakes-temporal-demo and name it as 'ctakes-web'
> or 'ctakes-web-rest' so that the module can be used to build cTAKES as
> both traditional web app as well as expose it as an REST service. It's just a 
> thought from my side which we can discuss upon.
>
> Once the web-rest module is ready, I feel it will take cTAKES to a
> whole new level as you can even plug it with mobile applications that
> can send the clinical text for analysis and get JSON response that can
> be rendered on mobile app UI.
>
> Suggestions are welcome. Cheers.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
> Sent: Monday, October 30, 2017 6:07 PM
> To: Apache cTAKES Dev <dev@ctakes.apache.org>
> Subject: Re: cTAKES as REST service [EXTERNAL]
>
> Gandhi and Matthew, thank you for your hard work.
>
> I was working on upgrading libraries and fixing dependencies too. I
> would love to help with Spring dependency. For that reason, I have created 
> issue:
> "upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472 [1]).
>
> Another great idea is the REST service, for that reason I created
> CTAKES-473 [2]. It was also requested by Chei Pen in CTAKES-188 [3]. I
> would like to know if you settled already to any framework (e.g.
> Jersey vs
> CXF) and if you also manage the dictionaries and different profiles
> through the API.
>
> The last important idea I get is the Dockerfile, which sounds great
> for the community to just test and play with cTAKES without the need
> of building and exploring the source code. I was testing your work
> Matthew, and I think it is a great start.
>
> What is the community practice in code for features that require a
> longer time to be developed? Would it use a branch until it gets
> stable, or it is preferred to have it in trunk for a faster
> integration. The REST API feature, it will require a new module. Does
> the community prefers a name for it (i.e ctakes-rest-api) ?
>
> Alex
>
> [1] - https://issues.apache.org/jira/browse/CTAKES-472
> [2] - https://issues.apache.org/jira/browse/CTAKES-473
> [3] - https://issues.apache.org/jira/browse/CTAKES-188
>
>
> On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com> wrote:
>
> > Matthew,
> >
> > Looking forward to hear from you. Please let me know if there are
> > any changes required to make the rest service more superior and
> > performance effective. Cheers.
> >
> > Regards,
> > Gandhi
> >
> >
> > -Original Message-
> > From: Matthew Vita [mailto:matthewvit...@gmail.com]
> > Sent: Sunday, October 29, 2017 9:30 PM
> > To: dev@ct

RE: YTEX Assistance required RE: Test case failure [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Alex,

I tried out a fresh checkout from SVN and git. Tried a full build in both 
setups and DateAnnotatorTest fails consistently for me. Did you changed build 
order or something in pom to fix it?

Regards,
Gandhi


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 2:47 AM
To: dev@ctakes.apache.org
Subject: RE: YTEX Assistance required RE: Test case failure [EXTERNAL]

Thanks for the info Alex. Will check and keep you posted.

Regards,
Gandhi


-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
Sent: Sunday, November 19, 2017 2:29 AM
To: Apache cTAKES Dev <dev@ctakes.apache.org>
Subject: Re: YTEX Assistance required RE: Test case failure [EXTERNAL]

Hi Gandhi,

I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also 
encountered the issue few times, and is very inconsistent, without being able 
to track it down.

It seems that ytexDates.iterator() is empty in certain conditions. I think is 
related to the order of executions and how resources are generated. On the last 
builds I couldn't reproduce it.

So I suggest a full:
mvn clean install

Alex

[1] -
https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex-uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/testParseDate/


On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> Is anybody that was involved with ytex still out there?
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Saturday, November 18, 2017 9:53 AM
> To: dev@ctakes.apache.org
> Subject: Test case failure [EXTERNAL]
>
> Hi All,
>
> I did a fresh check out of cTAKES code from SVN to work on Spring
> upgrade patch. But I have one failed test case in ctakes-ytex-uima
> module. The error trace is as follows,
>
> 
> ---
> Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest
> 
> ---
> Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583
> sec <<< FAILURE!
> testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest
> )
> Time elapsed: 0.547 sec  <<< FAILURE!
> java.lang.AssertionError
> at org.junit.Assert.fail(Assert.java:86)
> at org.junit.Assert.assertTrue(Assert.java:41)
> at org.junit.Assert.assertTrue(Assert.java:52)
> at org.apache.ctakes.ytex.uima.
> annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:62)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.junit.runners.model.FrameworkMethod$1.
> runReflectiveCall(FrameworkMethod.java:47)
> at org.junit.internal.runners.
> model.ReflectiveCallable.run(ReflectiveCallable.java:12)
> at org.junit.runners.model.FrameworkMethod.
> invokeExplosively(FrameworkMethod.java:44)
> at org.junit.internal.runners.statements.InvokeMethod.
> evaluate(InvokeMethod.java:17)
> at org.junit.runners.ParentRunner.runLeaf(
> ParentRunner.java:271)
> at org.junit.runners.BlockJUnit4ClassRunner.runChild(
> BlockJUnit4ClassRunner.java:70)
> at org.junit.runners.BlockJUnit4ClassRunner.runChild(
> BlockJUnit4ClassRunner.java:50)
> at org.junit.runners.ParentRunner$3.run(
> ParentRunner.java:238)
> at org.junit.runners.ParentRunner$1.schedule(
> ParentRunner.java:63)
> at org.junit.runners.ParentRunner.runChildren(
> ParentRunner.java:236)
> at org.junit.runners.ParentRunner.access$000(
> ParentRunner.java:53)
> at org.junit.runners.ParentRunner$2.evaluate(
> ParentRunner.java:229)
> at org.junit.runners.ParentRunner.run(ParentRunner.
> java:309)
> at org.apache.maven.surefire.
> junit4.JUnit4Provider.execute(JUnit4Provider.java:249)
> at org.apache.maven.surefire.junit4.JUnit4Provider.
> executeTestSet(JUnit4Provider.java:142)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.invoke(
> JUnit4Provider.java:113)
> at sun.reflect.NativeMethodAcces

RE: YTEX Assistance required RE: Test case failure [EXTERNAL]

[Gandhi Rajan Natarajan]

Thanks for the info Alex. Will check and keep you posted.

Regards,
Gandhi


-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
Sent: Sunday, November 19, 2017 2:29 AM
To: Apache cTAKES Dev <dev@ctakes.apache.org>
Subject: Re: YTEX Assistance required RE: Test case failure [EXTERNAL]

Hi Gandhi,

I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also 
encountered the issue few times, and is very inconsistent, without being able 
to track it down.

It seems that ytexDates.iterator() is empty in certain conditions. I think is 
related to the order of executions and how resources are generated. On the last 
builds I couldn't reproduce it.

So I suggest a full:
mvn clean install

Alex

[1] -
https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex-uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/testParseDate/


On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> Is anybody that was involved with ytex still out there?
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Saturday, November 18, 2017 9:53 AM
> To: dev@ctakes.apache.org
> Subject: Test case failure [EXTERNAL]
>
> Hi All,
>
> I did a fresh check out of cTAKES code from SVN to work on Spring
> upgrade patch. But I have one failed test case in ctakes-ytex-uima
> module. The error trace is as follows,
>
> 
> ---
> Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest
> 
> ---
> Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583
> sec <<< FAILURE!
> testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest
> )
> Time elapsed: 0.547 sec  <<< FAILURE!
> java.lang.AssertionError
> at org.junit.Assert.fail(Assert.java:86)
> at org.junit.Assert.assertTrue(Assert.java:41)
> at org.junit.Assert.assertTrue(Assert.java:52)
> at org.apache.ctakes.ytex.uima.
> annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:62)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.junit.runners.model.FrameworkMethod$1.
> runReflectiveCall(FrameworkMethod.java:47)
> at org.junit.internal.runners.
> model.ReflectiveCallable.run(ReflectiveCallable.java:12)
> at org.junit.runners.model.FrameworkMethod.
> invokeExplosively(FrameworkMethod.java:44)
> at org.junit.internal.runners.statements.InvokeMethod.
> evaluate(InvokeMethod.java:17)
> at org.junit.runners.ParentRunner.runLeaf(
> ParentRunner.java:271)
> at org.junit.runners.BlockJUnit4ClassRunner.runChild(
> BlockJUnit4ClassRunner.java:70)
> at org.junit.runners.BlockJUnit4ClassRunner.runChild(
> BlockJUnit4ClassRunner.java:50)
> at org.junit.runners.ParentRunner$3.run(
> ParentRunner.java:238)
> at org.junit.runners.ParentRunner$1.schedule(
> ParentRunner.java:63)
> at org.junit.runners.ParentRunner.runChildren(
> ParentRunner.java:236)
> at org.junit.runners.ParentRunner.access$000(
> ParentRunner.java:53)
> at org.junit.runners.ParentRunner$2.evaluate(
> ParentRunner.java:229)
> at org.junit.runners.ParentRunner.run(ParentRunner.
> java:309)
> at org.apache.maven.surefire.
> junit4.JUnit4Provider.execute(JUnit4Provider.java:249)
> at org.apache.maven.surefire.junit4.JUnit4Provider.
> executeTestSet(JUnit4Provider.java:142)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.invoke(
> JUnit4Provider.java:113)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:62)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.apache.maven.surefire.util.ReflectionUtils.
> invokeMethod

Test case failure

[Gandhi Rajan Natarajan]

Hi All,

I did a fresh check out of cTAKES code from SVN to work on Spring upgrade 
patch. But I have one failed test case in ctakes-ytex-uima module. The error 
trace is as follows,

---
Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest
---
Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec <<< 
FAILURE!
testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest)  Time 
elapsed: 0.547 sec  <<< FAILURE!
java.lang.AssertionError
at org.junit.Assert.fail(Assert.java:86)
at org.junit.Assert.assertTrue(Assert.java:41)
at org.junit.Assert.assertTrue(Assert.java:52)
at 
org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at 
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at 
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at 
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at 
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at 
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at 
org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at 
org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at 
org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at 
org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at 
org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249)
at 
org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142)
at 
org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at 
org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
at 
org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
at 
org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104)
at 
org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

Am I missing something or is it broken recently?

Regards,
Gandhi

This email and any files transmitted with it are confidential and intended 
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you are not the named addressee you should not disseminate, distribute or copy 
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RE: cTAKES Jenkins build is successful.

[Gandhi Rajan Natarajan]

Great job Alex. In fact it is a great milestone. Cheers

Regards,
Gandhi


-Original Message-
From: Alexandru Zbarcea [mailto:al...@apache.org]
Sent: Friday, November 17, 2017 6:04 AM
To: Apache cTAKES Dev 
Subject: cTAKES Jenkins build is successful.

Hi,

The job:
https://builds.apache.org/view/C/view/Apache%20cTAKES/job/ctakes-trunk-compiletest/
is successful.

All tests pass.

I think this is an important milestone. For quite some time we didn't have the 
build as successful :-)

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

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

[Gandhi Rajan Natarajan]

ishYy1Jk-o=-PwjGWv5MEFT_1Jui9b27fdgkKfFRa29hts-FMalo8I=


On Nov 13, 2017 10:41, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:

> Thanks Gandhi!
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Monday, November 13, 2017 10:40 AM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi All,
>
> We had a look at ctakes-Ytex module's failing test cases and looks
> like it will not have an impact once we upgrade Spring 4x in cTAKES.
>
> We will have a run through at other modules and check the failing test
> cases if any.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Sandeep Byatha Gururaja rao [mailto:sandeep...@arisglobal.com]
> Sent: Monday, November 13, 2017 6:50 PM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi Sean,
>
> Myself and Gandhi will work on this and try to fix the issues.
>
> Regards,
> Sandeep
>
> 
>
> Hi Gandhi,
>
> Many thanks for volunteering.  I am slammed with work right now, but
> if anybody else can also help out ...
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, November 09, 2017 12:43 AM
> To: dev@ctakes.apache.org
> Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
>
> Hi Sean,
>
> I can take it up if someone is willing to guide me on this.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Wednesday, November 08, 2017 9:45 PM
> To: dev@ctakes.apache.org
> Subject: Disable yTEX and Regression tests on Jenkins
>
> Hi all,
>
> The Jenkins builds have been failing for about a month now because of
> internal Jenkins changes and 'unit' tests in the ctakes-Regression and
> ctakes-yTEX modules.  This is holding up the build for all of our
> primary clinical-pipeline modules.
>
> If anybody can take a look at the problems and fix them please respond
> to this email.  Otherwise I would like to create a jira issue and
> disable them until somebody does have the time to take care of them.
> If you have a good reason for these tests not being disabled (e.g. we
> might forget to fix
> them) please state a case.  I do not intend to act unilaterally on
> this issue.
>
> Please respond by midnight Friday, November 10.
>
> Thank you,
>
> Sean
> 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.
>
> 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.
> 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.
>
This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
you have received this e-mail by mistake and delete this e-mail from your 
system. If you are not the intended recipient you are notified that disclosing, 
copying, distributing or taking any action in reliance on the contents of this 
information is strictly prohibited and against the law.

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi All,

We had a look at ctakes-Ytex module's failing test cases and looks like it will 
not have an impact once we upgrade Spring 4x in cTAKES.

We will have a run through at other modules and check the failing test cases if 
any.

Regards,
Gandhi


-Original Message-
From: Sandeep Byatha Gururaja rao [mailto:sandeep...@arisglobal.com]
Sent: Monday, November 13, 2017 6:50 PM
To: dev@ctakes.apache.org
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi Sean,

Myself and Gandhi will work on this and try to fix the issues.

Regards,
Sandeep



Hi Gandhi,

Many thanks for volunteering.  I am slammed with work right now, but if anybody 
else can also help out ...

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, November 09, 2017 12:43 AM
To: dev@ctakes.apache.org
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi Sean,

I can take it up if someone is willing to guide me on this.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 9:45 PM
To: dev@ctakes.apache.org
Subject: Disable yTEX and Regression tests on Jenkins

Hi all,

The Jenkins builds have been failing for about a month now because of internal 
Jenkins changes and 'unit' tests in the ctakes-Regression and ctakes-yTEX 
modules.  This is holding up the build for all of our primary clinical-pipeline 
modules.

If anybody can take a look at the problems and fix them please respond to this 
email.  Otherwise I would like to create a jira issue and disable them until 
somebody does have the time to take care of them.  If you have a good reason 
for these tests not being disabled (e.g. we might forget to fix them) please 
state a case.  I do not intend to act unilaterally on this issue.

Please respond by midnight Friday, November 10.

Thank you,

Sean
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.

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.
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 
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RE: Disable yTEX and Regression tests on Jenkins

[Gandhi Rajan Natarajan]

Hi Sean,

I can take it up if someone is willing to guide me on this.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 9:45 PM
To: dev@ctakes.apache.org
Subject: Disable yTEX and Regression tests on Jenkins

Hi all,

The Jenkins builds have been failing for about a month now because of internal 
Jenkins changes and 'unit' tests in the ctakes-Regression and ctakes-yTEX 
modules.  This is holding up the build for all of our primary clinical-pipeline 
modules.

If anybody can take a look at the problems and fix them please respond to this 
email.  Otherwise I would like to create a jira issue and disable them until 
somebody does have the time to take care of them.  If you have a good reason 
for these tests not being disabled (e.g. we might forget to fix them) please 
state a case.  I do not intend to act unilaterally on this issue.

Please respond by midnight Friday, November 10.

Thank you,

Sean
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 
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copying, distributing or taking any action in reliance on the contents of this 
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RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Bhagwat,

Glad that you got it working.

Regarding cTAKES functional questions below, I guess Sean or Tim is the right 
person to give more info.

Regards,
Gandhi

-Original Message-
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
Sent: Tuesday, November 07, 2017 3:22 PM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Thanks Gandhi,

I have gone through both the links and able to get the results.

I am interested in finding the context of clinical notes like if any procedure 
is happened or not.
I think TLINKS  values on web API maybe helpful to get the required result, not 
sure though. Please confirm

I am not able to find the code to generate TLINKS, could you please help me 
locate the code.

And also could anybody please guide me to find context out of the note-sentence.

On 3 November 2017 at 19:44, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Bhagwat,
>
> I'm not sure if it will help you. But I extended the code available in
> https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
> to get the XML output and parsed the required mentions for me like
> Procedure, Disorder etc.
>
> You can look at the code here - https://github.com/
> gandhirajan/cTAKES/tree/master/cTakes-Rest-Service/
> src/main/java/com/ctakes/nlp and see if it helps. Cheers.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
> Sent: Friday, November 03, 2017 7:39 PM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS]
>
> Thank you Sean and Tim for your support.
>
> I have followed the links given by Sean and overview by Tim  which is
> pretty helpful to get the better understanding of source code.
>
> I have run ctakes-example project that internally executes
> ClinicalPipelineFactory.getDefaultPipeline() method. This has given
> results like POS tag, Polarity, etc.
> Now, I am more interested in finding Procedure, Medication, Drug, etc.
> Could you please point me to the code file or help with code snippet
> to capture above terms.
>
>
>
> On 30 October 2017 at 19:36, Finan, Sean
> <sean.fi...@childrens.harvard.edu
> >
> wrote:
>
> > Hi Bhagwat,
> >
> > If you are interested in the default clinical pipeline, you can look
> > at the wiki here:
> > https://cwiki.apache.org/confluence/display/CTAKES/
> > Default+Clinical+Pipeline
> > For a visual representation of what Tim described.
> >
> > The AEs used for the ctakes 4.0 default clinical pipeline are shown
> > at the bottom of this wiki page: https://cwiki.apache.org/
> > confluence/display/CTAKES/Piper+Files
> > The Class names are shown, but not the packages.  If you have a
> > decent IDE they should be easy to find - for Intellij press CTRL-N
> > and type the name of the class.
> >
> > Another option is to use the Simple Pipeline Fabricator gui to look
> > at the available readers and AEs and see what they do (and their
> > required inputs).  Check the wiki at: https://cwiki.apache.org/
> > confluence/display/CTAKES/Simple+Pipeline+Fabricator+GUI
> > If you launch the gui and let it gather information, you can look at
> > the pipe bit names and descriptions (reader, AE).  If it interests
> > you, click the "add" button (big '+') and on the right you will see
> > the path to the source code for that bit of the pipeline.  Not all
> > AEs
> are described ...
> > calling all community ...  but I think that most are.
> >
> > Sean
> >
> >
> > -Original Message-
> > From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> > Sent: Monday, October 30, 2017 9:48 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS]
> >
> > cTAKES is based on Apache UIMA, which is a pipeline-building tool.
> > So the output you see in the CVD is the result of many different
> > pieces of the pipeline run in succession, and they are each in
> > different modules of cTAKES. ctakes-core has the most basic elements
> > that will run for every pipeline -- tokens, sentences, etc.
> > ctakes-dictionary-lookup-fast is what maps text spans to UMLS concepts.
> ctakes-assertion finds negation status.
> > ctakes-chunker creates syntactic chunks and ctakes-pos-tagger finds
> > part-of-speech tags for tokens. There are many others but I think
> > this covers the basics. In general, if you see a type in the CVD
> > that you find interesting, your best bet is to grep the code f

RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Bhagwat,

I'm not sure if it will help you. But I extended the code available in 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo to get 
the XML output and parsed the required mentions for me like Procedure, Disorder 
etc.

You can look at the code here - 
https://github.com/gandhirajan/cTAKES/tree/master/cTakes-Rest-Service/src/main/java/com/ctakes/nlp
 and see if it helps. Cheers.

Regards,
Gandhi


-Original Message-
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
Sent: Friday, November 03, 2017 7:39 PM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

Thank you Sean and Tim for your support.

I have followed the links given by Sean and overview by Tim  which is pretty 
helpful to get the better understanding of source code.

I have run ctakes-example project that internally executes
ClinicalPipelineFactory.getDefaultPipeline() method. This has given results 
like POS tag, Polarity, etc.
Now, I am more interested in finding Procedure, Medication, Drug, etc.
Could you please point me to the code file or help with code snippet to capture 
above terms.



On 30 October 2017 at 19:36, Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:

> Hi Bhagwat,
>
> If you are interested in the default clinical pipeline, you can look
> at the wiki here: https://cwiki.apache.org/confluence/display/CTAKES/
> Default+Clinical+Pipeline
> For a visual representation of what Tim described.
>
> The AEs used for the ctakes 4.0 default clinical pipeline are shown at
> the bottom of this wiki page: https://cwiki.apache.org/
> confluence/display/CTAKES/Piper+Files
> The Class names are shown, but not the packages.  If you have a decent
> IDE they should be easy to find - for Intellij press CTRL-N and type
> the name of the class.
>
> Another option is to use the Simple Pipeline Fabricator gui to look at
> the available readers and AEs and see what they do (and their required
> inputs).  Check the wiki at: https://cwiki.apache.org/
> confluence/display/CTAKES/Simple+Pipeline+Fabricator+GUI
> If you launch the gui and let it gather information, you can look at
> the pipe bit names and descriptions (reader, AE).  If it interests
> you, click the "add" button (big '+') and on the right you will see
> the path to the source code for that bit of the pipeline.  Not all AEs are 
> described ...
> calling all community ...  but I think that most are.
>
> Sean
>
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Monday, October 30, 2017 9:48 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS]
>
> cTAKES is based on Apache UIMA, which is a pipeline-building tool. So
> the output you see in the CVD is the result of many different pieces
> of the pipeline run in succession, and they are each in different
> modules of cTAKES. ctakes-core has the most basic elements that will
> run for every pipeline -- tokens, sentences, etc.
> ctakes-dictionary-lookup-fast is what maps text spans to UMLS concepts. 
> ctakes-assertion finds negation status.
> ctakes-chunker creates syntactic chunks and ctakes-pos-tagger finds
> part-of-speech tags for tokens. There are many others but I think this
> covers the basics. In general, if you see a type in the CVD that you
> find interesting, your best bet is to grep the code for that type and
> see where it is being created (if you don't want to wait for an email from 
> the list).
> Pipeline components are known as "Analysis Engines" (AEs) in UIMA
> lingo and as a result are often in a package ending in .ae.
> Hope this helps you navigate the code!
> Tim
>
> 
> From: Bhagwat Posane <bhagwat.pos...@gmail.com>
> Sent: Monday, October 30, 2017 7:24 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
>
> Thanks Gandhi, for the quick response.
>
> I have source code of cTAKES which is available under
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.
> apache.org_repos_asf_ctakes_trunk=DwIBaQ=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=Efsfuj37pWNoR_
> 6AidMyWm4ab03VgFjoRDFcJxdS9k0=ZquL0hWuNhJGyujJCmNBTCENaERN6B
> U3zisHhnM18Wo=. I see there are many projects in it.
>
> I am checking user version using \CTAKES_HOME\bin\runctakesCVD.bat,
> this opens an UI. I could run analysis engine for a clinical note
> according to the guidelines in the user-install guide..
> It gives me descent result in the left pane of the UI.
> Now I am looking for the source-code that gives this result fo

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Alex and Sean,

Thanks for the acknowledgement.

As mentioned earlier in the thread, I have sent the github link - 
https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes-SVN-src  
that contains changes to be made to upgrade cTAKES to Spring4x. I have done it 
on my local sandbox and it works. But as I mentioned earlier, I was not able to 
test ytex module changes as I'm not aware of those modules. Matthew is already 
testing the spring upgrade changes and hopefully we will able be close it. If 
you could test the ytex modules, it will be of great help I guess.

Regarding docker works on cTAKES, hats off to Matthew. We can assist him if he 
needs any help out there.

Regarding REST API, we are planning to use Spring REST service as introducing 
Jersey container may be an overhead I feel. Also regarding your idea on new 
module, I too agree with you. But in the new module, we can improvise Chei 
Pen's work in this link - 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo and name 
it as 'ctakes-web' or 'ctakes-web-rest' so that the module can be used to build 
cTAKES as both traditional web app as well as expose it as an REST service. 
It's just a thought from my side which we can discuss upon.

Once the web-rest module is ready, I feel it will take cTAKES to a whole new 
level as you can even plug it with mobile applications that can send the 
clinical text for analysis and get JSON response that can be rendered on mobile 
app UI.

Suggestions are welcome. Cheers.

Regards,
Gandhi


-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
Sent: Monday, October 30, 2017 6:07 PM
To: Apache cTAKES Dev <dev@ctakes.apache.org>
Subject: Re: cTAKES as REST service [EXTERNAL]

Gandhi and Matthew, thank you for your hard work.

I was working on upgrading libraries and fixing dependencies too. I would love 
to help with Spring dependency. For that reason, I have created issue:
"upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472 [1]).

Another great idea is the REST service, for that reason I created
CTAKES-473 [2]. It was also requested by Chei Pen in CTAKES-188 [3]. I would 
like to know if you settled already to any framework (e.g. Jersey vs
CXF) and if you also manage the dictionaries and different profiles through the 
API.

The last important idea I get is the Dockerfile, which sounds great for the 
community to just test and play with cTAKES without the need of building and 
exploring the source code. I was testing your work Matthew, and I think it is a 
great start.

What is the community practice in code for features that require a longer time 
to be developed? Would it use a branch until it gets stable, or it is preferred 
to have it in trunk for a faster integration. The REST API feature, it will 
require a new module. Does the community prefers a name for it (i.e 
ctakes-rest-api) ?

Alex

[1] - https://issues.apache.org/jira/browse/CTAKES-472
[2] - https://issues.apache.org/jira/browse/CTAKES-473
[3] - https://issues.apache.org/jira/browse/CTAKES-188


On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Matthew,
>
> Looking forward to hear from you. Please let me know if there are any
> changes required to make the rest service more superior and
> performance effective. Cheers.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Sunday, October 29, 2017 9:30 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL]
>
> Sean,
>
> Ghandi and I have met and we both agreed that his solution is superior
> to the one I was working on. Therefore, I will be helping to see this
> project through to the end so we can get it into the codebase!
>
> Here are the remaining work items that I will be spending time on:
>
>1. Get it running (I'm using Linux Mint)
>2. Test it out (including stress tests)
>3. Automate it to run in Docker (just need UMLS credentials)
>4. Make a call to
>https://github.com/GoTeamEpsilon/cTAKES-Concept-Mention-Parser to get a
>nice JSON payload that is easy to traverse (this can be an optional
> switch,
>of course - I believe it may be best to rewrite this in Java should
> this be
>included with the solution)
>5. Test the output in my web viewer:
>https://github.com/GoTeamEpsilon/cTAKES-Friendly-Web-UI
>6. Work on preparing the solution for the cTAKES core codebase. I will
>prepare it with a very rich README.
>
> I will provide my updates over the coming days.
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Gandhi,
> >
> > Thank you for the ad

RE: source code of user installation of cTakes.

[Gandhi Rajan Natarajan]

Sorry to say that I don’t have much idea on this. But you can setup the cTAKES 
source code and debug the complete flow if you want.

Else you will have wait for the experts like Sean or Tim to answer this.

Regards,
Gandhi


-Original Message-
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
Sent: Monday, October 30, 2017 4:54 PM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes.

Thanks Gandhi, for the quick response.

I have source code of cTAKES which is available under 
https://svn.apache.org/repos/asf/ctakes/trunk. I see there are many projects in 
it.

I am checking user version using \CTAKES_HOME\bin\runctakesCVD.bat, this opens 
an UI. I could run analysis engine for a clinical note according to the 
guidelines in the user-install guide..
It gives me descent result in the left pane of the UI.
Now I am looking for the source-code that gives this result for a clinical 
note. Could you please point me to the project, where can I see to it in the 
ctakes-trunk or so.



On 30 October 2017 at 16:36, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Bhagwat,
>
> The source code of cTAKES is available under
> https://svn.apache.org/repos/ asf/ctakes/trunk
>
> Regarding the resources to start off, cTAKES official site
> documentations should be fine.
>
> I also feel, mailing list is the one stop shop for all your other
> detailed queries.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
> Sent: Monday, October 30, 2017 4:30 PM
> To: dev@ctakes.apache.org
> Subject: source code of user installation of cTakes.
>
> Hello,
>
> I have seen the results of user installation of cTakes , the output is
> pretty interesting.
>
> Can anybody point to the source code of the same?
>
> I have just started exploring this project if anybody point me to good
> resources to understand it thoroughly that will be great help!!
>
> I have downloaded the developer installation too.
>
> --
> Thanks,
> Bhagwat Posane
> 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.
>



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

RE: source code of user installation of cTakes.

[Gandhi Rajan Natarajan]

Hi Bhagwat,

The source code of cTAKES is available under 
https://svn.apache.org/repos/asf/ctakes/trunk

Regarding the resources to start off, cTAKES official site documentations 
should be fine.

I also feel, mailing list is the one stop shop for all your other detailed 
queries.

Regards,
Gandhi


-Original Message-
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
Sent: Monday, October 30, 2017 4:30 PM
To: dev@ctakes.apache.org
Subject: source code of user installation of cTakes.

Hello,

I have seen the results of user installation of cTakes , the output is pretty 
interesting.

Can anybody point to the source code of the same?

I have just started exploring this project if anybody point me to good 
resources to understand it thoroughly that will be great help!!

I have downloaded the developer installation too.

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

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Matthew,

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

Regards,
Gandhi


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

Sean,

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

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

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

I will provide my updates over the coming days.

Thanks,

Matthew Vita
www.matthewvita.com

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

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

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

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

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

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

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

Regards,
Gandhi


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

Hi Gandhi,

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

Sean

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

Hi Sean,

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

To brief it, I did the following changes:

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

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

 Hope it helps someone.

Regards,
Gandhi

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

Hi Sean,

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

Regards,
Gandhi


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

Hi Gandhi,

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

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

Thanks,
Sean

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

Hi All,

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

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

Please advise.

Regards,
Gandhi

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

RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

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

To brief it, I did the following changes:

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

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

 Hope it helps someone.

Regards,
Gandhi

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

Hi Sean,

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

Regards,
Gandhi


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

Hi Gandhi,

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

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

Thanks,
Sean

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

Hi All,

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

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

Please advise.

Regards,
Gandhi

This email and any files transmitted with it are confidential and intended 
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you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
you have received this e-mail by mistake and delete this e-mail from your 
system. If you are not the intended recipient you are notified that disclosing, 
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information is strictly prohibited and against the law.

RE: cTAKES as REST service

[Gandhi Rajan Natarajan]

Hi Matthew,

Big thanks for the response. Actually in our case we are trying to integrate 
cTAKES with our application and it's our application which will invoke the rest 
calls and get back the response for further processing.

Also I have not worked on Docker before but would love to. So if you feel I may 
be of some help in your project, please keep me posted. As you said I would be 
more than happy to contribute for the open source. Cheers.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Wednesday, October 25, 2017 9:57 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service

Gandhi,

I am actually working on a series of Docker containers that expose an HTTP 
endpoint to send clinical text to and then it POSTs the results back to your 
application's HTTP endpoint in JSON. Please let me know if this approach 
interests you and we can schedule a Google Hangouts to talk about what work is 
left (I estimate that I will be done in a month and a half).

Please do note that this solution is 100% free/open source :)


Thanks,

Matthew Vita
www.matthewvita.com

On Wed, Oct 25, 2017 at 6:20 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi All,
>
> We have extended the cTAKES web application available under
> https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
> and added our custom annotator. We have tested the same and it works
> fine with CVD. But we are facing problems while trying to expose this
> as rest service.
>
> cTAKES uses Spring 3.1.2 version internally which don't have out of
> the box support for rest controller. Can we go ahead and update the
> spring version to 4x in cTAKES? Will it have any impact in the cTAKES 
> behavior?
> Also is there a better way to expose cTAKES as rest service apart from
> spring?
>
> Please advise.
>
> Regards,
> Gandhi
>
> This email and any files transmitted with it are confidential and
> intended solely for the use of the individual or entity to whom they are 
> addressed.
> If you are not the named addressee you should not disseminate,
> distribute or copy this e-mail. Please notify the sender or system
> manager by email immediately if you have received this e-mail by
> mistake and delete this e-mail from your system. If you are not the
> intended recipient you are notified that disclosing, copying,
> distributing or taking any action in reliance on the contents of this
> information is strictly prohibited and against the law.
>
This email and any files transmitted with it are confidential and intended 
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you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
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RE: cTAKES as REST service [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

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

Regards,
Gandhi


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

Hi Gandhi,

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

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

Thanks,
Sean

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

Hi All,

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

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

Please advise.

Regards,
Gandhi

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

cTAKES as REST service

[Gandhi Rajan Natarajan]

Hi All,

We have extended the cTAKES web application available under 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo and 
added our custom annotator. We have tested the same and it works fine with CVD. 
But we are facing problems while trying to expose this as rest service.

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

Please advise.

Regards,
Gandhi

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

RE: false positive

[Gandhi Rajan Natarajan]

Hi Abilash,

I'm not sure how much it will make sense. But in our custom annotator we wrote 
on top of cTAKES, we resolved this false positives to an extent by using 
commonly used English words metadata available from OpenNLP.

Regards,
Gandhi

-Original Message-
From: abilash.mat...@cognizant.com [mailto:abilash.mat...@cognizant.com]
Sent: Wednesday, October 25, 2017 3:57 PM
To: dev@ctakes.apache.org
Subject: false positive

Hi all,

We are seeing some false positives identified by CTAKES after we tested couple 
of medical records samples. Can anyone help us on how to ignore these words 
from tagging incorrectly?

Word

Finding

test

Procedure

Page

Procedure

treatment

Procedure

medicine

Drug

medication

Drug

attachments

Procedure

RELEASE

Procedure

reconstruction

Procedure

DOB

Drug

Procedure

Procedure

Division

Procedure


Thanks,
Abilash Mathew
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RE: Queries on custom annotators [EXTERNAL]

[Gandhi Rajan Natarajan]

Will check it out Sean. Thanks for your prompt response as always.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, October 16, 2017 8:25 PM
To: dev@ctakes.apache.org
Subject: RE: Queries on custom annotators [EXTERNAL]

Hi Gandhi,

For 1)  Just to be sure, you are running your pipeline using xml descriptor 
files?
For 2)  Consider using FileLocator.getAsStream(..).

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, October 14, 2017 3:52 AM
To: dev@ctakes.apache.org
Subject: Queries on custom annotators [EXTERNAL]

Hi All,

We have wrote a custom annotation to identify the pharma company names, 
integrated it with cTAKES and it works fairly well with CVD. But when I tried 
integrating the same in my extended  web application that uses 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=Zbg2DrUy1YNQ0FBNuKWzx8i2dSCVUWvyJ57O_iO6jKY=c3NWc2Ah1memb3jrupIa1tTA7IWwKooyllOwrQ8zlq8=
  as base, I face few issues.


1)  We have defined certain mandatory parameter for the annotator. The JAVA 
code and XML config for passing the parameters is as follows:

public static final String PARAM_JDBC_DRIVER = "JdbcDriver"; public static 
final String PARAM_JDBC_URL = "JdbcUrl"; public static final String 
PARAM_JDBC_USER = "JdbcUser"; public static final String PARAM_JDBC_PASS = 
"JdbcPass"; @ConfigurationParameter(name = PARAM_JDBC_DRIVER, mandatory = 
false, description = "JDBC Driver") private String jdbcDriver;

@ConfigurationParameter(name = PARAM_JDBC_URL, mandatory = false, description = 
"JDBC URL") private String jdbcUrl;

@ConfigurationParameter(name = PARAM_JDBC_USER, mandatory = false, description 
= "JDBC User") private String jdbcUser ;

@ConfigurationParameter(name = PARAM_JDBC_PASS, mandatory = false, description 
= "JDBC Pass") private String jdbcPass;





JdbcDriver
JdbcDriver
String
false
false
  


JdbcUrl
JdbcUrl
String
false
false
  


JdbcUser
JdbcUser
String
false
false
  


JdbcPass
JdbcPass
String
false
false
  



  
JdbcDriver

  com.mysql.jdbc.Driver

  

  
JdbcUrl

  
jdbc:mysql://127.0.0.1:3306/umls?useUnicode=truecharacterEncoding=utf8useSSL=false

  

  
JdbcUser

  root

  

  
JdbcPass

  admin123

  


If I change the mandate attribute from 'false' to 'true', while trying to use 
this annotator, I get an error stating that the mandatory parameter is not 
passed. I'm not sure what other configuration is required to make this work and 
pass mandatory values. Any help on this?


2)  Currently in the 'initialize' method of the annotator, I'm loading few 
metadata resources using the following code,


InputStream inputStream = annotCtx.getResourceAsStream(fileName);

But when this line is executed, it gives a following warning message in the 
console,

"13-Oct-2017 15:54:50.141 WARNING [localhost-startStop-1] 
org.apache.uima.impl.ChildUimaContext_impl.getResourceAsStream The unmanaged 
resource ORG.txt was accessed.This feature is deprecated, and support may be 
removed in future versions."

Could someone throw some light on how to resolve this warning and loaded the 
resource in a best way?

Regards,
Gandhi

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RE: steps to upgrade to the latest version of umls and snomed

[Gandhi Rajan Natarajan]

Hi Rajeev,

All you got to do is to use latest dictionary generator GUI to generate snomed 
2017 scripts. We tried this and loaded to MySQL DB and it works. For more info 
you can check the recent thread on 'HSQLDB out of memory with custom 
dictionary' under 
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201710.mbox/browser

Regards,
Gandhi


-Original Message-
From: rajeevxmy...@gmail.com [mailto:rajeevxmy...@gmail.com]
Sent: Sunday, October 15, 2017 12:40 AM
To: dev@ctakes.apache.org
Subject: steps to upgrade to the latest version of umls and snomed

Hello,

As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for 
dictionary lookup.

Did anyone try to upgrade? What should be the approach to upgrade db scripts to 
latest umls 2017ab, snomed 2017? Any automation procedure available?


Thanks
Regards
Rajeev


Sent from Mail for Windows 10

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RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sirisha,

I tried executing this in my windows machine and it works fine. The execution 
also creates the output folder itself. So as Sean suggested this could be an 
issue with file permissions or folder creation permissions.

Regards,
Gandhi

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 11, 2017 9:24 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Can you, as the user running ctakes, do a "touch /output/TestSample1.xml.xmi" ?

-Original Message-
From: Sirisha Pulivarthi [mailto:sirisha_pulivar...@horizonblue.com.INVALID]
Sent: Wednesday, October 11, 2017 11:22 AM
To: dev@ctakes.apache.org
Subject: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Hi,

I'm working on doing a POC using Ctakes 4.0.0 - below is what I'm trying to do 
"Ingest a CDA document containing free form text, run it through a Clinical 
Document processing pipeline and spit out a converted result".

I have downloaded and installed user guide, tried below command with one of the 
test document bin/runClinicalPipeline.sh  -i /testdata  --xmiOut  /output  
--user xxx  --pass xxx

However, I'm running into below exception

Oct 11, 2017 9:40:24 AM 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl 
processAndOutputNewCASes(273)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException
at 
org.apache.ctakes.core.cc.AbstractOutputFileWriter.process(AbstractOutputFileWriter.java:84)
at 
org.apache.uima.analysis_component.CasAnnotator_ImplBase.process(CasAnnotator_ImplBase.java:56)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.(ASB_impl.java:412)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.(ASB_impl.java:412)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
at 
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
at 
org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:150)
at org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:293)
at org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:81)
Caused by: java.io.IOException: java.io.FileNotFoundException: 
/output/TestSample1.xml.xmi (No such file or directory) at 
org.apache.ctakes.core.cc.FileTreeXmiWriter.writeFile(FileTreeXmiWriter.java:45)
at 
org.apache.ctakes.core.cc.AbstractOutputFileWriter.process(AbstractOutputFileWriter.java:82)
... 15 more
Caused by: java.io.FileNotFoundException: /output/TestSample1.xml.xmi (No such 
file or directory) at java.io.FileOutputStream.open0(Native Method) at 
java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.(FileOutputStream.java:213)
Activity

I have created CTAKES-466 this morning. Would appreciate your help on this.

Thank you
Sirisha

***

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and permanently delete this message.

***
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this e-mail. Please notify the sender or system manager by email immediately if 
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RE: HSQLDB out of memory with custom dictionary

[Gandhi Rajan Natarajan]

Hi Matthew,

Please check out my response to Kathy. If feel that has the required info to 
start off. Please let me know if you are looking for any specific additional 
info.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Wednesday, October 11, 2017 11:00 AM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary

Hi Kathy and Gandhi,

I started to put together a more formal solution for this here:
https://github.com/GoTeamEpsilon/cTAKES-HSQLDB-to-MySQL-Dictionary - It is not 
perfect but it makes things a bit easier. I was able to load in millions of 
records into MySQL, which is awesome!

*If you have a non-trivial dictionary, chances are you will exhaust HSQLDB's 
capabilities. By using this solution, you will have a MySQL schema filled up 
with what would have been the HSQLDB data.*

*This solution uses lazy lists and streams to keep memory usage low when the 
script files are huge.*

I have not got it working with the XML jdbc configuration yet so if you (or 
anyone else) could share an example that would be amazing.

Thanks,

Matthew Vita
www.matthewvita.com

On Tue, Oct 10, 2017 at 9:57 PM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Kathy,
>
> Good to hear from you. Please find the response below.
>
> NOTE: This is based on my experience with cTAKES so far. Please
> correct me if someone find the answers to be wrong.
>
> 1. Does it matter what the name of the database?
>
> Name of the database really don’t matter. But the name you have
> created should be mapped in the Dictionary GUI generated XML file's 'jdbcurl'
> property.
>
> 2. What configuration file do I change to switch to use the new database?
>
> If you are using the example downloaded from
> https://github.com/healthnlp/
> examples/tree/master/ctakes-temporal-demo , then in Pipeline.java you
> gotta map the XML file name generated using the Dictionary GUI instead of 
> 'sno_rx_16ab.xml'
>
> If you want to use the new database for CVD, then you got to change '
> DEFAULT_DICT_DESC_PATH' to point to the new XML file in
> JCasTermAnnotator.java and rebuild ctakes-dictionary-lookup-fast
> module and use the jar file.
>
> 3) Do you think I can use SQL server instead of MySQL?  My SQL seems
> to run faster.
>
> This choice is user specific and I can't comment on performance
> comparison as I have no clue on this.
>
>
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Kathy Ferro [mailto:healthcare1...@gmail.com]
> Sent: Tuesday, October 10, 2017 9:26 PM
> To: dev@ctakes.apache.org
> Subject: Re: HSQLDB out of memory with custom dictionary
>
> Gandhi,
>
> My name is Kathy Ferro.
>
> Matthew and I are trying to accomplish the thing.  I got the scripts
> loaded into both SQL server and MySQL.  I did it in two ways.
> 1. Manually modifier the scripts for DB specific and run them in query
> analyzer window as you described.  Works find if the data is small enough.
> For bigger file, it looks up.
> 2. I wrote c# program to read the scripts and insert records one by
> one I re-load them.
>
> My question for you are:
>
> 2. What configuration file do I change to switch to use the new database?
> 3. Do you think I can use SQL server instead of MySQL?  My SQL seems
> to run faster.
>
> Thank
> Kathy
>
>
>
>
> On Tue, Oct 10, 2017 at 2:34 AM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com> wrote:
>
> > Hi Matthew,
> >
> > The SQLs looks fine. The only additional table I'm using apart from
> > the tables mentioned below is MDR table (MEDDRA related) and I don’t
> > use AIR table.
> >
> > Do you really think you need a JAVA program to convert those insert
> > statements to work with MySQL? I just opened the script file in text
> > editor like Editplus and did a find for `[\)]\n` and replaced it
> > with `);\n` using find and replace all option with REGEX and we are
> > done with
> the scripts.
> >
> > But only thing is you can load the data in parallel by splitting the
> > script files as mentioned earlier which saves times for you and may
> > be you can write a JAVA program to split the file. This is the
> > easiest approach I feel.
> >
> > Regards,
> > Gandhi
> >
> >
> > -Original Message-
> > From: Matthew Vita [mailto:matthewvit...@gmail.com]
> > Sent: Tuesday, October 10, 2017 10:47 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: HSQLDB out of memory with custom dictionary
> >
> > Gandhi,
> >
> > I really appreciate this information. I have started working out the
> > schema and plan on writing a pr

RE: HSQLDB out of memory with custom dictionary

[Gandhi Rajan Natarajan]

Hi Kathy,

Good to hear from you. Please find the response below.

NOTE: This is based on my experience with cTAKES so far. Please correct me if 
someone find the answers to be wrong.

1. Does it matter what the name of the database?

Name of the database really don’t matter. But the name you have created should 
be mapped in the Dictionary GUI generated XML file's 'jdbcurl' property.

2. What configuration file do I change to switch to use the new database?

If you are using the example downloaded from 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo , then 
in Pipeline.java you gotta map the XML file name generated using the Dictionary 
GUI instead of 'sno_rx_16ab.xml'

If you want to use the new database for CVD, then you got to change ' 
DEFAULT_DICT_DESC_PATH' to point to the new XML file in  JCasTermAnnotator.java 
and rebuild ctakes-dictionary-lookup-fast module and use the jar file.

3) Do you think I can use SQL server instead of MySQL?  My SQL seems to run 
faster.

This choice is user specific and I can't comment on performance comparison as I 
have no clue on this.



Regards,
Gandhi


-Original Message-
From: Kathy Ferro [mailto:healthcare1...@gmail.com]
Sent: Tuesday, October 10, 2017 9:26 PM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary

Gandhi,

My name is Kathy Ferro.

Matthew and I are trying to accomplish the thing.  I got the scripts loaded 
into both SQL server and MySQL.  I did it in two ways.
1. Manually modifier the scripts for DB specific and run them in query analyzer 
window as you described.  Works find if the data is small enough.
For bigger file, it looks up.
2. I wrote c# program to read the scripts and insert records one by one I 
re-load them.

My question for you are:

2. What configuration file do I change to switch to use the new database?
3. Do you think I can use SQL server instead of MySQL?  My SQL seems to run 
faster.

Thank
Kathy




On Tue, Oct 10, 2017 at 2:34 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Matthew,
>
> The SQLs looks fine. The only additional table I'm using apart from
> the tables mentioned below is MDR table (MEDDRA related) and I don’t
> use AIR table.
>
> Do you really think you need a JAVA program to convert those insert
> statements to work with MySQL? I just opened the script file in text
> editor like Editplus and did a find for `[\)]\n` and replaced it with
> `);\n` using find and replace all option with REGEX and we are done with the 
> scripts.
>
> But only thing is you can load the data in parallel by splitting the
> script files as mentioned earlier which saves times for you and may be
> you can write a JAVA program to split the file. This is the easiest
> approach I feel.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Tuesday, October 10, 2017 10:47 AM
> To: dev@ctakes.apache.org
> Subject: Re: HSQLDB out of memory with custom dictionary
>
> Gandhi,
>
> I really appreciate this information. I have started working out the
> schema and plan on writing a program that will automatically prepare a
> script to work with MySQL. Work in progress. Can you do a quick review
> of my MySQL schema so far?
>
> CREATE SCHEMA CTAKES_DATA;
>
> use CTAKES_DATA;
>
> CREATE TABLE CUI_TERMS (
>   CUI BIGINT NOT NULL,
>   RINDEX INT(128) NOT NULL,
>   TCOUNT INT(128) NOT NULL,
>   TEXT VARCHAR(255) NOT NULL,
>   RWORD VARCHAR(48) NOT NULL
> );
> CREATE INDEX IDX_CUI_TERMS ON CUI_TERMS (RWORD);
>
> CREATE TABLE TUI (
>   CUI BIGINT NOT NULL,
>   TUI INT(128) NOT NULL
> );
> CREATE INDEX IDX_TUI ON TUI (CUI);
>
> CREATE TABLE PREFTERM (
>   CUI BIGINT NOT NULL,
>   PREFTERM VARCHAR(511) NOT NULL
> );
> CREATE INDEX IDX_PREFTERM ON PREFTERM (CUI);
>
> CREATE TABLE RXNORM (
>   CUI BIGINT NOT NULL,
>   RXNORM BIGINT NOT NULL
> );
> CREATE INDEX IDX_RXNORM ON RXNORM (CUI);
>
> CREATE TABLE SNOMEDCT_US (
>   CUI BIGINT NOT NULL,
>   SNOMEDCT_US BIGINT NOT NULL
> );
> CREATE INDEX IDX_SNOMEDCT_US ON SNOMEDCT_US (CUI);
>
> Quick question: do you use the AIR table?
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Mon, Oct 9, 2017 at 1:14 AM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com> wrote:
>
> > Hi Mathew,
> >
> > First I would like to tell you that even I m a newbie in cTAKES.
> > Unfortunately I don’t find any documentation on this. I have
> > followed a crude way to accomplish as this is an one time activity.
> > This is what
> I did:
> >
> > 1) Used dictionary generator GUI to generate Snomed, RxNorm and
> > MEDDRA dictionary data that resulted in '.script' f

RE: HSQLDB out of memory with custom dictionary

[Gandhi Rajan Natarajan]

Hi Mathew,

First I would like to tell you that even I m a newbie in cTAKES. Unfortunately 
I don’t find any documentation on this. I have followed a crude way to 
accomplish as this is an one time activity. This is what I did:

1) Used dictionary generator GUI to generate Snomed, RxNorm and MEDDRA 
dictionary data that resulted in '.script' file under my 
\resources\org\apache\ctakes\dictionary\lookup\fast\ 
folder
2) The '.script' file has HSQLDB specific queries. I have removed the unwanted 
statements for me pertaining to HSQLDB from the file and converted them to 
mysql specific queries manually.
3) I have added semicolons at the end of each line in the script using text 
editor and splitted the file in to five parts. Then I ran those five sctipr 
files  in five different mysql command lines. It took me approximately 4 hours 
to pump all the data in to MySQL DB.

I'm not sure whether it is the right way to proceed as I mentioned earlier. But 
with no documentation available for MySQL DB with  cTAKES, this is the 
approached that worked for me. Hope it will be helpful.

Regards,
Gandhi


-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Monday, October 09, 2017 10:41 AM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary

Gandhi,

Thank you for the reply. Do you have any documentation on how to accomplish 
this?

Thanks,

Matthew Vita
www.matthewvita.com

On Sun, Oct 8, 2017 at 3:14 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Mathew,
>
> I feel using MySQL Db would be better idea than using in-memory
> HSQLDB. In fact, this also comes handy when you are planning to deploy
> ctakes as a web application as in our case.
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Sunday, October 08, 2017 6:02 AM
> To: dev@ctakes.apache.org
> Subject: HSQLDB out of memory with custom dictionary
>
> Hi Sean, Tim, cTAKES Community,
>
> I have put together what I am considering a pretty standard dictionary
> with sources from the following:
>
>
>-
>
>MEDLINEPLUS
>-
>
>MSH
>-
>
>NCI
>-
>
>NDFRT
>-
>
>CHV
>-
>
>CSP
>-
>
>ICPC2P
>-
>
>MEDCIN
>-
>
>SNOMED
>-
>
>RXNORM
>-
>
>ICD10
>
>
> However, when copied over to cTAKES (handled by the handy Dictionary
> Creator GUI) HSQLDB runs out of memory.
>
> This is my first experience with HSQLDB so you’ll have to excuse my
> limited knowledge here. I do understand that it can run either
> in-memory and on disk, but I’m not sure how to configure this.
>
> Here is how I am connecting to it:
>
>
>   
>
>
> sno_rx_16abTerms
>
>  >org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDicti
> >on
> >ary implementationName>
>
> 
>
>   
>
>"jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/
> lookup/fast/sno_rx_16ab/sno_rx_16ab"
> />
>
>   
>
>   
>
>   
>
>   https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser; />
>
>   
>
>   
>
>   
>
> 
>
>   
>
>   
>
>
>
> Can I configure HSQLDB to be used on disk? If this is not a good
> approach, can I spin up MySQL in its place?
>
>
> Sorry if this has asked before.
>
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
> 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.
>
This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. If 
you are not the named addressee you should not disseminate, distribute or copy 
this e-mail. Please notify the sender or system manager by email immediately if 
you have received this e-mail by mistake and delete this e-mail from your 
system. If you are not the intended recipient you are notified that disclosing, 
copying, distributing or taking any action in reliance on the contents of this 
information is strictly prohibited and against the law.

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi James,

Thanks for the response. As you said its definitely not a showstopper. We 
encountered this measurement in the narratives we were testing and thought of 
fixing this. That’s the whole idea. Also as per the code, 'fslashCondition' 
added before 2nd token should avoid false positives is what I feel. Anyways I 
will let the experts like you to decide on this. Thanks for the consideration 
again.

Regards,
Gandhi


-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Tuesday, October 03, 2017 10:05 PM
To: dev@ctakes.apache.org
Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

FWIW, I started taking a look at the patch. (It's in code that I'm not that
familiar with, so a quick glance isn't sufficient for me.)
I did a search in UMLS for m2 in the terminologies commonly used by cTAKES
to see if adding m2 could result in marking something as a measurement when
it's not - and I did find many terms in the UMLS that contain m2. There are
plenty of other measurement abbreviations that also appear within other
terms, so it's not a showstopper - but is a consideration.

I haven't tested the patch yet to see if the way the patch is implemented -
checking for 2 tokens - avoids that issue.  Not sure if I'll get a chance
to look more this week. if you end up picking up looking at it Sean, at
least you know what I've done.

-- James


On Tue, Oct 3, 2017 at 12:25 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> Hi Gandhi,
>
> Ctakes is a purely volunteer effort, so there are never any guarantees ...
> If nobody looks at the value and unit jira and patch this week then I will
> try to get to it asap.
>
> Thanks for letting us use your example note!
>
> Sean
>
> -----Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Tuesday, October 03, 2017 12:21 PM
> To: dev@ctakes.apache.org
> Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
> [SUSPICIOUS]
>
> Hi Sean,
>
>
>
> Will this JIRA issue - https://urldefense.proofpoint.
> com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-
> 2D459=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=EPRi2YznX0T5F4yYV0y2OmCxU0Q_
> Gx24B_omGRWF8kg=fhwLqbd8Tgg6z-jFe9Z7t0baNz2YgNwM-SCSeTnrZes=   be
> looked up by someone as Tim mentioned?
>
>
>
> The paragraph we sent earlier can be in the example notes provided the
> protocol number is masked/modified.
>
>
>
> Regards,
>
> Gandhi
>
>
>
>
>
> -Original Message-
>
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
>
> Sent: Tuesday, October 03, 2017 7:27 PM
>
> To: dev@ctakes.apache.org
>
> Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
> [SUSPICIOUS]
>
>
>
> Hi Gandhi,
>
>
>
> Thank you for asking.  There is no action item for you concerning the
> coreference output that you see.   However, if you would like to help the
> community understand how the module works (input and output), maybe you
> could do something like run the pipeline on your original sentence, then
> that sentence plus another (before), then that sentence plus another
> (after) ... and see how the output changes with the input.  If you take
> screenshots or something then we could put them on the wiki.  Also, would
> you mind if the paragraph you sent became one of the example notes in
> ctakes?  That means that it would be redistributed with the code.
>
>
>
> Sean
>
>
>
> -Original Message-
>
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
>
> Sent: Tuesday, October 03, 2017 4:26 AM
>
> To: dev@ctakes.apache.org
>
> Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
> [SUSPICIOUS]
>
>
>
> Hi Tim/Sean,
>
>
>
>
>
>
>
> Is this an action item on us? If yes, Could someone give us some valid
> inputs to test the same? Is someone else going to review this again?
>
>
>
>
>
>
>
> Regards,
>
>
>
> Gandhi
>
>
>
>
>
>
>
>
>
>
>
> -Original Message-
>
>
>
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
>
>
>
> Sent: Monday, October 02, 2017 8:06 PM
>
>
>
> To: dev@ctakes.apache.org
>
>
>
> Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL]
> [SUSPICIOUS]
>
>
>
>
>
>
>
> My bad, I didn't read too closely and thought this was going to be a
> coreference patch. I don't know this FSM code that well, so I am not an
> expert. My biggest concern at a glance is that these addition

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Sean, Completely agree with you on this. Thanks for your support.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, October 03, 2017 9:56 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

Ctakes is a purely volunteer effort, so there are never any guarantees ...
If nobody looks at the value and unit jira and patch this week then I will try 
to get to it asap.

Thanks for letting us use your example note!

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 12:21 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Sean,



Will this JIRA issue - 
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D459=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=EPRi2YznX0T5F4yYV0y2OmCxU0Q_Gx24B_omGRWF8kg=fhwLqbd8Tgg6z-jFe9Z7t0baNz2YgNwM-SCSeTnrZes=
   be looked up by someone as Tim mentioned?



The paragraph we sent earlier can be in the example notes provided the protocol 
number is masked/modified.



Regards,

Gandhi





-Original Message-

From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]

Sent: Tuesday, October 03, 2017 7:27 PM

To: dev@ctakes.apache.org

Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]



Hi Gandhi,



Thank you for asking.  There is no action item for you concerning the 
coreference output that you see.   However, if you would like to help the 
community understand how the module works (input and output), maybe you could 
do something like run the pipeline on your original sentence, then that 
sentence plus another (before), then that sentence plus another (after) ... and 
see how the output changes with the input.  If you take screenshots or 
something then we could put them on the wiki.  Also, would you mind if the 
paragraph you sent became one of the example notes in ctakes?  That means that 
it would be redistributed with the code.



Sean



-Original Message-

From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]

Sent: Tuesday, October 03, 2017 4:26 AM

To: dev@ctakes.apache.org

Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]



Hi Tim/Sean,







Is this an action item on us? If yes, Could someone give us some valid inputs 
to test the same? Is someone else going to review this again?







Regards,



Gandhi











-Original Message-



From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]



Sent: Monday, October 02, 2017 8:06 PM



To: dev@ctakes.apache.org



Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]







My bad, I didn't read too closely and thought this was going to be a 
coreference patch. I don't know this FSM code that well, so I am not an expert. 
My biggest concern at a glance is that these additions help find more true 
positives (as in your examples), can we verify that they won't create false 
positives?



Tim











On Fri, 2017-09-29 at 06:25 +, Gandhi Rajan Natarajan wrote:



> Hi Sean,



>



> Thanks again for the response. I guess its mistake from my side that I



> dint send the complete text. Did you mean that with the text I sent,



> the co-reference superscript-1 will be lost?



>



> Also as per your advice, We have created an issue  - 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefen=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=sGlpzaOnKKPgjhHkkpfELXpFFGvJtj1Ib-9t3JrGbpQ=STDKsvR9fK6KZuwRjRT3q1gZI8T7ptaKlVWVumKi5dc=



> se.proofpoint.com/v2/url?u=https-



> 3A__issues.apache.org_jira_browse_CTAKES-



> 2D459=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-



> IbsIg9Q1TPOylpP9FE4GTK-



> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g



> nqCIxz6hOzUUQ=Tihsi1dyNHsqsYbwyClGANfqk2Ov2nfQL2YuIV1L0CI=   for



> measurement FSM changes and attached the modified file changes. Could



> someone have a look and know your thoughts please?



>



> Regards,



> Gandhi



>



>



> -Original Message-



> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]



> Sent: Thursday, September 28, 2017 8:21 PM



> To: dev@ctakes.apache.org



> Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu>



> Subject: RE: Enabling drugner pipeline and identifying dates



> [EXTERNAL] [SUSPICIOUS]



>



> Hi Gandhi,



>



> I don't recall you sending me that entire snippet of text.  I think



> that I only had your single example sentence.



> You have discovered

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Thanks for the update Sean. Please keep us posted so that we can test the same 
once your fix is ready.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, October 03, 2017 10:04 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,
I have one discovery pertaining to the coref items so far.
Your first coreference (#1) is not appearing in the html because it consists 
only of a "generic" item: "this patient".
Coreference: This patient , This patient , This patient , this patient , this 
patient , this patient , this patient
This is a bug in the html writer that I will need to fix.
Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 4:26 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Tim/Sean,



Is this an action item on us? If yes, Could someone give us some valid inputs 
to test the same? Is someone else going to review this again?



Regards,

Gandhi





-Original Message-

From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]

Sent: Monday, October 02, 2017 8:06 PM

To: dev@ctakes.apache.org

Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]



My bad, I didn't read too closely and thought this was going to be a 
coreference patch. I don't know this FSM code that well, so I am not an expert. 
My biggest concern at a glance is that these additions help find more true 
positives (as in your examples), can we verify that they won't create false 
positives?

Tim





On Fri, 2017-09-29 at 06:25 +, Gandhi Rajan Natarajan wrote:

> Hi Sean,

>

> Thanks again for the response. I guess its mistake from my side that I

> dint send the complete text. Did you mean that with the text I sent,

> the co-reference superscript-1 will be lost?

>

> Also as per your advice, We have created an issue  - 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefen=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=sGlpzaOnKKPgjhHkkpfELXpFFGvJtj1Ib-9t3JrGbpQ=STDKsvR9fK6KZuwRjRT3q1gZI8T7ptaKlVWVumKi5dc=

> se.proofpoint.com/v2/url?u=https-

> 3A__issues.apache.org_jira_browse_CTAKES-

> 2D459=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-

> IbsIg9Q1TPOylpP9FE4GTK-

> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g

> nqCIxz6hOzUUQ=Tihsi1dyNHsqsYbwyClGANfqk2Ov2nfQL2YuIV1L0CI=   for

> measurement FSM changes and attached the modified file changes. Could

> someone have a look and know your thoughts please?

>

> Regards,

> Gandhi

>

>

> -Original Message-

> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]

> Sent: Thursday, September 28, 2017 8:21 PM

> To: dev@ctakes.apache.org

> Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu>

> Subject: RE: Enabling drugner pipeline and identifying dates

> [EXTERNAL] [SUSPICIOUS]

>

> Hi Gandhi,

>

> I don't recall you sending me that entire snippet of text.  I think

> that I only had your single example sentence.

> You have discovered one of the quirks of software: "change the data,

> change the result."

> Ctakes is a system with many moving parts.  Things that precede or

> follow your original example sentence will change the evaluation of

> that sentence.

> With the pipeline you are using and the full note, you should see a

> number (mine is 4) next to the first "thalomid" in the original

> example sentence.  If you click that number you should see (to the

> right) 4 instances of "thalomid".

> Tim can correct me here, but maybe the coreference module ranked the

> links between "thalomid" as much higher than the rank between "study

> treatment of thalomid 200mg" and "the treatment of hepatocellular

> carcinoma" and discarded the encapsulating treatment texts from

> markables?  It is probably more complex than that.

>

> >

> > we have also made some code changes in MeasurementFSM.java to

> > identify certain measurements like '20 mg/m2' which was not

> > identified out of the box.  Should we send the code changes to you

> > so that you can consider the same to be productized ? Please

> > advise."

> I don't know if you've noticed the recent emails on the dev list

> involving Alexandru Zbarcea.  Alex has been creating or commenting on

> Jira items and attaching code for  fixes and enhancements.  This is a

> widely used process and is fairly easy to follow.   I think that the

> 

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Sean,

Will this JIRA issue - https://issues.apache.org/jira/browse/CTAKES-459  be 
looked up by someone as Tim mentioned?

The paragraph we sent earlier can be in the example notes provided the protocol 
number is masked/modified.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, October 03, 2017 7:27 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

Thank you for asking.  There is no action item for you concerning the 
coreference output that you see.   However, if you would like to help the 
community understand how the module works (input and output), maybe you could 
do something like run the pipeline on your original sentence, then that 
sentence plus another (before), then that sentence plus another (after) ... and 
see how the output changes with the input.  If you take screenshots or 
something then we could put them on the wiki.  Also, would you mind if the 
paragraph you sent became one of the example notes in ctakes?  That means that 
it would be redistributed with the code.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 4:26 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Tim/Sean,



Is this an action item on us? If yes, Could someone give us some valid inputs 
to test the same? Is someone else going to review this again?



Regards,

Gandhi





-Original Message-

From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]

Sent: Monday, October 02, 2017 8:06 PM

To: dev@ctakes.apache.org

Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]



My bad, I didn't read too closely and thought this was going to be a 
coreference patch. I don't know this FSM code that well, so I am not an expert. 
My biggest concern at a glance is that these additions help find more true 
positives (as in your examples), can we verify that they won't create false 
positives?

Tim





On Fri, 2017-09-29 at 06:25 +, Gandhi Rajan Natarajan wrote:

> Hi Sean,

>

> Thanks again for the response. I guess its mistake from my side that I

> dint send the complete text. Did you mean that with the text I sent,

> the co-reference superscript-1 will be lost?

>

> Also as per your advice, We have created an issue  - 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefen=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=sGlpzaOnKKPgjhHkkpfELXpFFGvJtj1Ib-9t3JrGbpQ=STDKsvR9fK6KZuwRjRT3q1gZI8T7ptaKlVWVumKi5dc=

> se.proofpoint.com/v2/url?u=https-

> 3A__issues.apache.org_jira_browse_CTAKES-

> 2D459=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-

> IbsIg9Q1TPOylpP9FE4GTK-

> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g

> nqCIxz6hOzUUQ=Tihsi1dyNHsqsYbwyClGANfqk2Ov2nfQL2YuIV1L0CI=   for

> measurement FSM changes and attached the modified file changes. Could

> someone have a look and know your thoughts please?

>

> Regards,

> Gandhi

>

>

> -Original Message-

> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]

> Sent: Thursday, September 28, 2017 8:21 PM

> To: dev@ctakes.apache.org

> Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu>

> Subject: RE: Enabling drugner pipeline and identifying dates

> [EXTERNAL] [SUSPICIOUS]

>

> Hi Gandhi,

>

> I don't recall you sending me that entire snippet of text.  I think

> that I only had your single example sentence.

> You have discovered one of the quirks of software: "change the data,

> change the result."

> Ctakes is a system with many moving parts.  Things that precede or

> follow your original example sentence will change the evaluation of

> that sentence.

> With the pipeline you are using and the full note, you should see a

> number (mine is 4) next to the first "thalomid" in the original

> example sentence.  If you click that number you should see (to the

> right) 4 instances of "thalomid".

> Tim can correct me here, but maybe the coreference module ranked the

> links between "thalomid" as much higher than the rank between "study

> treatment of thalomid 200mg" and "the treatment of hepatocellular

> carcinoma" and discarded the encapsulating treatment texts from

> markables?  It is probably more complex than that.

>

> >

> > we have also made some code changes in MeasurementFSM.java to

> > identify certain measurements like '20 mg/m2' which was not

> > identified out of the box.  Should we send the code changes to you

> > so that you can con

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

as suffering worsening fatigue and got 
tired getting out of his chair.  On 25Aug02, this patient died due to disease 
progression.  The investigator assessed the death as not related to study 
treatment and expected"




-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Monday, October 02, 2017 10:36 AM
To: dev@ctakes.apache.org
Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS]

My bad, I didn't read too closely and thought this was going to be a

coreference patch. I don't know this FSM code that well, so I am not an

expert. My biggest concern at a glance is that these additions help

find more true positives (as in your examples), can we verify that they

won't create false positives?

Tim





On Fri, 2017-09-29 at 06:25 +, Gandhi Rajan Natarajan wrote:

> Hi Sean,

>

> Thanks again for the response. I guess its mistake from my side that

> I dint send the complete text. Did you mean that with the text I

> sent, the co-reference superscript-1 will be lost?

>

> Also as per your advice, We have created an issue  - 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefen=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=CGnNaO_ZfECB0wIfj3upr01l4w_rNBG8no_VN9cFxhs=ikLBvXRXENiHoTgailnfsVrB-sy2hMgKCTVIO8iUeNE=

> se.proofpoint.com/v2/url?u=https-

> 3A__issues.apache.org_jira_browse_CTAKES-

> 2D459=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-

> IbsIg9Q1TPOylpP9FE4GTK-

> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g

> nqCIxz6hOzUUQ=Tihsi1dyNHsqsYbwyClGANfqk2Ov2nfQL2YuIV1L0CI=   for

> measurement FSM changes and attached the modified file changes. Could

> someone have a look and know your thoughts please?

>

> Regards,

> Gandhi

>

>

> -Original Message-

> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]

> Sent: Thursday, September 28, 2017 8:21 PM

> To: dev@ctakes.apache.org

> Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu>

> Subject: RE: Enabling drugner pipeline and identifying dates

> [EXTERNAL] [SUSPICIOUS]

>

> Hi Gandhi,

>

> I don't recall you sending me that entire snippet of text.  I think

> that I only had your single example sentence.

> You have discovered one of the quirks of software: "change the data,

> change the result."

> Ctakes is a system with many moving parts.  Things that precede or

> follow your original example sentence will change the evaluation of

> that sentence.

> With the pipeline you are using and the full note, you should see a

> number (mine is 4) next to the first "thalomid" in the original

> example sentence.  If you click that number you should see (to the

> right) 4 instances of "thalomid".

> Tim can correct me here, but maybe the coreference module ranked the

> links between "thalomid" as much higher than the rank between "study

> treatment of thalomid 200mg" and "the treatment of hepatocellular

> carcinoma" and discarded the encapsulating treatment texts from

> markables?  It is probably more complex than that.

>

> >

> > we have also made some code changes in MeasurementFSM.java to

> > identify certain measurements like '20 mg/m2' which was not

> > identified out of the box.  Should we send the code changes to you

> > so that you can consider the same to be productized ? Please

> > advise."

> I don't know if you've noticed the recent emails on the dev list

> involving Alexandru Zbarcea.  Alex has been creating or commenting on

> Jira items and attaching code for  fixes and enhancements.  This is a

> widely used process and is fairly easy to follow.   I think that the

> following links are relevant:

> Working with issues:  https://urldefense.proofpoint.com/v2/url?u=http

> s-3A__confluence.atlassian.com_jiracoreserver073_working-2Dwith-

> 2Dissues-

> 2D861257307.html=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe

> FU=Heup-IbsIg9Q1TPOylpP9FE4GTK-

> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g

> nqCIxz6hOzUUQ=Fo-LGlsEfYJpgYcWvrDmor0B3YGxx5brZLelntVMxrU=

> Creating patches:   https://urldefense.proofpoint.com/v2/url?u=https-

> 3A__confluence.atlassian.com_crucible_creating-2Dpatch-2Dfiles-2Dfor-

> 2Dpre-2Dcommit-2Dreviews-

> 2D298977458.html=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe

> FU=Heup-IbsIg9Q1TPOylpP9FE4GTK-

> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=0kLxqu0Xu_2pjzCrVwxC4cd_1ubh_g

> nqCIxz6hOzUUQ=wVhEQCU73iEplHm34bO2AtgaDUpjAvrFe4GFx5b6pYo=

> Attaching files:   https://urldefense.proofpoint.com/v2/url?u=https-3

> A__confluence.atlassian.com_jiracorecloud_attach

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Sean,

Thanks again for the response. I guess its mistake from my side that I dint 
send the complete text. Did you mean that with the text I sent, the 
co-reference superscript-1 will be lost?

Also as per your advice, We have created an issue  - 
https://issues.apache.org/jira/browse/CTAKES-459  for measurement FSM changes 
and attached the modified file changes. Could someone have a look and know your 
thoughts please?

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 28, 2017 8:21 PM
To: dev@ctakes.apache.org
Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu>
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

I don't recall you sending me that entire snippet of text.  I think that I only 
had your single example sentence.
You have discovered one of the quirks of software: "change the data, change the 
result."
Ctakes is a system with many moving parts.  Things that precede or follow your 
original example sentence will change the evaluation of that sentence.
With the pipeline you are using and the full note, you should see a number 
(mine is 4) next to the first "thalomid" in the original example sentence.  If 
you click that number you should see (to the right) 4 instances of "thalomid".
Tim can correct me here, but maybe the coreference module ranked the links 
between "thalomid" as much higher than the rank between "study treatment of 
thalomid 200mg" and "the treatment of hepatocellular carcinoma" and discarded 
the encapsulating treatment texts from markables?  It is probably more complex 
than that.

> we have also made some code changes in MeasurementFSM.java to identify 
> certain measurements like '20 mg/m2' which was not identified out of the box. 
>  Should we send the code changes to you so that you can consider the same to 
> be productized ? Please advise."

I don't know if you've noticed the recent emails on the dev list involving 
Alexandru Zbarcea.  Alex has been creating or commenting on Jira items and 
attaching code for  fixes and enhancements.  This is a widely used process and 
is fairly easy to follow.   I think that the following links are relevant:
Working with issues:  
https://confluence.atlassian.com/jiracoreserver073/working-with-issues-861257307.html
Creating patches:   
https://confluence.atlassian.com/crucible/creating-patch-files-for-pre-commit-reviews-298977458.html
Attaching files:   
https://confluence.atlassian.com/jiracorecloud/attaching-files-and-screenshots-to-issues-765593805.html

I don't know if you have a jira account and permissions for the ctakes project. 
 An administrator may need to set that up for you.

Thanks,
Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, September 28, 2017 4:09 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Sean,

Thanks for the response. I was able to see the co-reference superscript using 
the html file that you sent. Interestingly even I was able to generate the 
sample HTML using  piper GUI by  having only that single line - " The patient 
started study treatment of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 
(days 1, 8, and 15) on 06/07/02 for the treatment of hepatocellular carcinoma. 
" in the input file.

But when I change the input file content with the following lines:

"This patient is participating in a Non-IND study; Protocol CG-000424: "Phase 
I/II of Thalidomide and Epirubicin in Patients with Unresectable or Metastatic 
Hepatocellular Carcinoma".Information has been received from the investigator 
regarding an 82 year-old male patient who had gastrointestinal bleeding while 
on Thalomid, Epirubicin, and Coumadin. He had a past medical history of 
diverticulosis in 03/02 and a right atrial clot from intraventricular catheter 
(IVC) for which he was started on Coumadin. During the hospitalization for a 
right atrial clot in 03/02 hepatocellular carcinoma was first noted and he was 
referred to an oncologist.  The patient started study treatment of Thalomid 
200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for 
the treatment of hepatocellular carcinoma.  He was concomitantly receiving 
Cardura, Ambien (for insomnia), Megace, Coumadin, and Oxycodone. This patient 
presented to the emergency room with the chief complaint of hematochezia. He 
reported noticing bright red blood and small clots mixed in with his stool. On 
07/13/02, he was admitted due to gastrointestinal bleed.  The physician ordered 
2 large bore intravenous lines and planned to transfuse for hematocrit less 
than 30%. Due to the  INR (international normalized ratio) level of 3.0, 
Coumadin was held. He was also noted to have bilate

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

 measurements like '20 mg/m2' which was not identified out of the box.  
Should we send the code changes to you so that you can consider the same to be 
productized ? Please advise.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, September 22, 2017 6:54 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

You don't need to add BackwardsTimeAnnotator to your piper.  It is added by the 
TemporalSubPipe.piper.  The  error that you are seeing regarding training is 
very strange, but you can try adding this line to the top of the file:
set isTraining=false

Can you run a sample file with your piper and send me the log statements?  It 
might help me figure out what is going on.

> is there any doc or guide on how to start writing our own annotator.
There are two example annotators in the ctakes-examples project under the ae/ 
directory.  You can look at those, but I recommend that you look at some 
information on Uimafit, which can be used to create new annotators:
https://uima.apache.org/d/uimafit-2.1.0/tools.uimafit.book.pdf
An introduction to creating Analysis Engines (Annotators) is on page 5.

Coding style is individualistic, but below is a rubberstamp that I use to get 
started:

import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;

/**
 * @author SPF , chip-nlp
 * @version %I%
 * @since 9/22/2017
 */
@PipeBitInfo(
  name = "Template",
  description = "For Example.", role = PipeBitInfo.Role.ANNOTATOR
)
final public class Template extends JCasAnnotator_ImplBase {

   static private final Logger LOGGER = Logger.getLogger( "Template" );

   /**
* {@inheritDoc}
*/
   @Override
   public void initialize( final UimaContext context ) throws 
ResourceInitializationException {
  // Always call the super first
  super.initialize( context );
  // place AE initialization code here
   }

   /**
* {@inheritDoc}
*/
   @Override
   public void process( final JCas jCas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Processing ..." );
  // Place AE processing code here
  LOGGER.info( "Finished." );
   }
}



If you use IntelliJ as your ide you can create a file template with these 
parameters:

#if (${PACKAGE_NAME} && ${PACKAGE_NAME} != "")package ${PACKAGE_NAME};#end

import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;

#parse("File Header.java")
@PipeBitInfo(
  name = "${NAME}",
  #if ( ${PROJECT_NAME} != "")description = "For ${PROJECT_NAME}.",#end
  role = PipeBitInfo.Role.ANNOTATOR
)
final public class ${NAME} extends JCasAnnotator_ImplBase {

   static private final Logger LOGGER = Logger.getLogger( "${NAME}" );

   /**
* {@inheritDoc}
*/
   @Override
   public void initialize( final UimaContext context ) throws 
ResourceInitializationException {
  // Always call the super first
  super.initialize( context );
  // place AE initialization code here
   }

   /**
* {@inheritDoc}
*/
   @Override
   public void process( final JCas jCas ) throws AnalysisEngineProcessException 
{
  LOGGER.info( "Processing ..." );
  // Place AE processing code here
  LOGGER.info( "Finished." );
   }
}





-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Friday, September 22, 2017 2:23 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Sean,

Thanks again for the detailed response.

I still couldn't manage to get superscript-1 co-reference in piper GUI.  Also 
I'm not able to use "BackwardsTimeAnnotator" in piper GUI as it gives me the 
below error:

org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class "org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator" failed.  
(Descriptor: )
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
Caused by: java.lang.IllegalArgum

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

[Gandhi Rajan Natarajan]

Hi Sean,

Thanks again for the detailed response.

I still couldn't manage to get superscript-1 co-reference in piper GUI.  Also 
I'm not able to use "BackwardsTimeAnnotator" in piper GUI as it gives me the 
below error:

org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class "org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator" failed.  
(Descriptor: )
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
Caused by: java.lang.IllegalArgumentException: Please specify PARAM_IS_TRAINING 
- unable to infer it from context
at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:109)

Somewhere in old mails it's mentioned that it's because of missing dependencies 
so I tried adding ClearTkAnnotator with no luck yet. My piper file is as 
follows:

load AdvancedTokenizerPipeline.piper
add ContextDependentTokenizerAnnotator
add POSTagger
load ChunkerSubPipe.piper
load DictionarySubPipe.piper
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
load AttributeCleartkSubPipe.piper
load RelationSubPipe.piper
load TemporalSubPipe.piper
load CorefSubPipe.piper
add org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
add pretty.html.HtmlTextWriter
add FileTreeXmiWriter

Any suggestion on this? Also I'm using all the latest 4.0.1 cTAKES Jars. 
Regarding the identification of Names, will dig deep on what you have mentioned.

Sorry to ask this as you already mentioned that there are no detailed docs for 
cTAKES. But is there any doc or guide on how to start writing our own annotator 
if required? It not, Is there any simple annotator that you would suggest us to 
look into to get better understanding on annotators for us to proceed further.  
Thanks in advance.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 21, 2017 7:59 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

> We guess we are missing out on something as we could not find co-references 
> for "200mg". Should we add anymore piper for this?
The piper commands that I sent has everything to obtain coreferences.  I use it 
regularly - it is what I used on your example sentence to get the coreferences 
that I mentioned.

> Also the change mentioned in the thread ...
That is a very old thread and I don't think that it applies to what you are 
trying to do.

> We also have a requirement to identify the patient names and sex
As James said, ctakes isn't really meant to do this.  Ctakes is catered toward 
extracting clinical data, and to this point names have not fallen into that 
category.  It is more a task for general nlp.  There is an opennlp model that 
can identify names and a few others (I used to see names using GATE).  ctakes 
has wrapped opennlp for other tasks and you should be able to do the same to 
adapt an engine for names into ctakes.

> cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or 06 / 07 / 
> 02 or 27Aug2002
As Chen mentioned, the BackwardTimeAnnotator module uses an ML model trained on 
gold data.  It isn't perfect.  You can add another time annotator on top of 
this to get some of the more simply formatted date mentions - there are a lot 
of them out there.  Personally I have used jchronic as it can be easily tweaked 
to recognize medically-relevant temporal expressions relating to surgery, 
pharmacology, etc.

Sean


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 20, 2017 8:50 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 
[SUSPICIOUS]

Hi Gandhi,

I don't have time to go through all of this right now, but I will try to get to 
it soon.

Make sure that you are running the latest version in trunk.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, September 20, 2017 7:03 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi, Could someone help me out on the below queries please?

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, September 19, 2017 8:51 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Sean,

Thanks again for the detailed and prompt response. We were able to run the 
piper GUI as per your advice. But in the output (The patient started study 
treatment of Thalomid 200mg ( days 1 - 21 ) , and Epirubicin ,20 mg / m2 ( days 
1 , 8 , and 15 ) on 06 / 07 / 02 for the t

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi James & Sean, Thanks for your support.

Regarding  point-1,  We don’t have any database or metadata to get the name or 
sex information. Is it not possible to achieve in cTAKES by any other names?  
If yes, what other approach will be feasible to implement this along with 
cTAKES as we need this info very much for our requirement.

Regarding  point-2, I will have a check on what you have suggested. But dates 
analysis is not part of temporal module?  Do you mean to say that if we use 
drug ner module, ContextDependentTokenizerAnnotator will be overwritten for 
date identifications?  Also while using piper GUI to run the analysis, we could 
see the following message in the console:
21 Sep 2017 00:08:04  INFO EventTimeRelationAnnotator - Starting processing ...
Null value found in Feature(, )

Could someone brief on this error and how to overcome it?


Regards,
Gandhi


-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Wednesday, September 20, 2017 8:41 PM
To: dev@ctakes.apache.org
Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL]

1) I would typically not use cTAKES for extracting patient names or sex. is 
there any database or metadata that you can get that information from?

2) Dates are found by the ContextDependentTokenizerAnnotator, which uses  
DateFSM.java in package org.apache.ctakes.core.fsm.machine.
I believe drug ner uses DateParser in org.apache.ctakes.core.util to interpret 
the date annotations. So you might need to modify both DateFSM and DateParser.



On Tue, Sep 19, 2017 at 11:20 AM, Gandhi Rajan Natarajan < 
gandhi.natara...@arisglobal.com> wrote:

> Hi Sean,
>
> Thanks again for the detailed and prompt response. We were able to run
> the piper GUI as per your advice. But in the output (The patient
> started study treatment of Thalomid 200mg ( days 1 - 21 ) , and
> Epirubicin ,20 mg / m2 ( days 1 , 8 , and 15 ) on 06 / 07 / 02 for the
> treatment of hepatocellular carcinoma.), we were not able to find
> superscript-1 as you mentioned earlier but could find superscript-2, 3
> etc.  We guess we are missing out on something as we could not find
> co-references for "200mg". Should we add anymore piper for this?
>
> Also the change mentioned in the thread - http://mail-archives.apache.
> org/mod_mbox/ctakes-user/201403.mbox/%3CCAL6WimrJ_mm1+
> xyggbzv62diyuwp0sca9vev8mnhgwe4hsn...@mail.gmail.com%3E is required
> for the drug-ner module to identify drug-ner annotations.
>
> 1) We also have a requirement to identify the patient names and sex
> available in narrative texts. Please let us know how to achieve the
> same as its not identifying the proper nouns and the relationship with the 
> patient?
> Eg. "This male patient named Tom Hardy aged 35 years is participating
> in a Non-IND study"
>
> 2) cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or
> 06 / 07 / 02 or 27Aug2002 as in the below example. Please let us know
> how to enhance the system to identify such date patterns.
> E.g " On 20Aug02, the investigator noted that this patient was
> suffering worsening fatigue and got tired getting out of his chair"
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Monday, September 18, 2017 10:02 PM
> To: dev@ctakes.apache.org
> Subject: RE: Enabling drugner pipeline and identifying dates
> [EXTERNAL]
>
> Hi Gandhi,
>
> > So in this case will be able to see drug attributes in the output XML?
> As long as you have the DrugMentionAnnotator in your pipeline you
> should be able to find drug attributes in the xml output file.
>
> > we also saw some code changes needs to be done to use drug-ner module.
> Is it still valid?
> As far as I know there aren't any necessary code changes to get drug
> ner running.  However, I do not normally use drugner so I can't say for 
> certain.
>
> > Also you mentioned that the drun-ner module is out of date
> It can still be used and will produce annotations.  All that I meant
> was that there may not be many people out there using it.  It is not
> part of the default pipeline.
>
>   > You also mentioned that when you run the sentence, the date was
> identified. Where and how exactly did you ran it so that we can check
> the same?
> I run the following in a piper file because I am interested in a lot
> of modules (I added drugner just for you):
>
> // Advanced Tokenization: Regex sectionization, BIO Sentence Detector
> (lumper), Paragraphs, Lists load AdvancedTokenizerPipeline.piper add
> ContextDependentTokenizerAnnotator
> add POSTagger
> // Chunkers
> load ChunkerSubPipe.piper
> // Default fast dictionary lookup
> load DictionarySubPipe.piper
> add org

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

[Gandhi Rajan Natarajan]

Thanks for the response Sean. Your help is really appreciated.

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 20, 2017 6:20 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Gandhi,

I don't have time to go through all of this right now, but I will try to get to 
it soon.

Make sure that you are running the latest version in trunk.

Sean

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, September 20, 2017 7:03 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi, Could someone help me out on the below queries please?

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, September 19, 2017 8:51 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Sean,

Thanks again for the detailed and prompt response. We were able to run the 
piper GUI as per your advice. But in the output (The patient started study 
treatment of Thalomid 200mg ( days 1 - 21 ) , and Epirubicin ,20 mg / m2 ( days 
1 , 8 , and 15 ) on 06 / 07 / 02 for the treatment of hepatocellular 
carcinoma.), we were not able to find superscript-1 as you mentioned earlier 
but could find superscript-2, 3 etc.  We guess we are missing out on something 
as we could not find co-references for "200mg". Should we add anymore piper for 
this?

Also the change mentioned in the thread - 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Duser_201403.mbox_-253CCAL6WimrJ-5Fmm1-2BXyggBZv62diYuWP0ScA9VEV8mNHGWe4hSNHQg-40mail.gmail.com-253E=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JoUDRZHu91gGMslwknPzTQC_UG2LEBLyOfXR3ikwOL0=GzhvIkBu4cgyzYN9n6VLe2rz4sJhJzMxDcWyB0BkqAc=
  is required for the drug-ner module to identify drug-ner annotations.

1) We also have a requirement to identify the patient names and sex available 
in narrative texts. Please let us know how to achieve the same as its not 
identifying the proper nouns and the relationship with the patient?
Eg. "This male patient named Tom Hardy aged 35 years is participating in a 
Non-IND study"

2) cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or 06 / 07 
/ 02 or 27Aug2002 as in the below example. Please let us know how to enhance 
the system to identify such date patterns.
E.g " On 20Aug02, the investigator noted that this patient was suffering 
worsening fatigue and got tired getting out of his chair"

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 18, 2017 10:02 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Gandhi,

> So in this case will be able to see drug attributes in the output XML?
As long as you have the DrugMentionAnnotator in your pipeline you should be 
able to find drug attributes in the xml output file.

> we also saw some code changes needs to be done to use drug-ner module. Is it 
> still valid?
As far as I know there aren't any necessary code changes to get drug ner 
running.  However, I do not normally use drugner so I can't say for certain.

> Also you mentioned that the drun-ner module is out of date
It can still be used and will produce annotations.  All that I meant was that 
there may not be many people out there using it.  It is not part of the default 
pipeline.

  > You also mentioned that when you run the sentence, the date was identified. 
Where and how exactly did you ran it so that we can check the same?
I run the following in a piper file because I am interested in a lot of modules 
(I added drugner just for you):

// Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), 
Paragraphs, Lists load AdvancedTokenizerPipeline.piper add 
ContextDependentTokenizerAnnotator
add POSTagger
// Chunkers
load ChunkerSubPipe.piper
// Default fast dictionary lookup
load DictionarySubPipe.piper
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
// Cleartk Entity Attributes
load AttributeCleartkSubPipe.piper
// Relations
load RelationSubPipe.piper
// Temporal
load TemporalSubPipe.piper
// Coreferences
load CorefSubPipe.piper
// Html output
add pretty.html.HtmlTextWriter

For information on piper files, see 
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFiles=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=JoUDRZHu91gGMslwknPzTQC_UG2LEBLyOfXR3ikwOL0=9ueuHYwEywok8byBXEkVjmTWiChmaIY3ryB4Pi6ajRo=
I run it in my IDE with:
org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G -p .piper 
-i org/ap

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi, Could someone help me out on the below queries please?

Regards,
Gandhi

-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, September 19, 2017 8:51 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Sean,

Thanks again for the detailed and prompt response. We were able to run the 
piper GUI as per your advice. But in the output (The patient started study 
treatment of Thalomid 200mg ( days 1 - 21 ) , and Epirubicin ,20 mg / m2 ( days 
1 , 8 , and 15 ) on 06 / 07 / 02 for the treatment of hepatocellular 
carcinoma.), we were not able to find superscript-1 as you mentioned earlier 
but could find superscript-2, 3 etc.  We guess we are missing out on something 
as we could not find co-references for "200mg". Should we add anymore piper for 
this?

Also the change mentioned in the thread - 
http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3ccal6wimrj_mm1+xyggbzv62diyuwp0sca9vev8mnhgwe4hsn...@mail.gmail.com%3E
 is required for the drug-ner module to identify drug-ner annotations.

1) We also have a requirement to identify the patient names and sex available 
in narrative texts. Please let us know how to achieve the same as its not 
identifying the proper nouns and the relationship with the patient?
Eg. "This male patient named Tom Hardy aged 35 years is participating in a 
Non-IND study"

2) cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or 06 / 07 
/ 02 or 27Aug2002 as in the below example. Please let us know how to enhance 
the system to identify such date patterns.
E.g " On 20Aug02, the investigator noted that this patient was suffering 
worsening fatigue and got tired getting out of his chair"

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 18, 2017 10:02 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Gandhi,

> So in this case will be able to see drug attributes in the output XML?
As long as you have the DrugMentionAnnotator in your pipeline you should be 
able to find drug attributes in the xml output file.

> we also saw some code changes needs to be done to use drug-ner module. Is it 
> still valid?
As far as I know there aren't any necessary code changes to get drug ner 
running.  However, I do not normally use drugner so I can't say for certain.

> Also you mentioned that the drun-ner module is out of date
It can still be used and will produce annotations.  All that I meant was that 
there may not be many people out there using it.  It is not part of the default 
pipeline.

  > You also mentioned that when you run the sentence, the date was identified. 
Where and how exactly did you ran it so that we can check the same?
I run the following in a piper file because I am interested in a lot of modules 
(I added drugner just for you):

// Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), 
Paragraphs, Lists load AdvancedTokenizerPipeline.piper add 
ContextDependentTokenizerAnnotator
add POSTagger
// Chunkers
load ChunkerSubPipe.piper
// Default fast dictionary lookup
load DictionarySubPipe.piper
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
// Cleartk Entity Attributes
load AttributeCleartkSubPipe.piper
// Relations
load RelationSubPipe.piper
// Temporal
load TemporalSubPipe.piper
// Coreferences
load CorefSubPipe.piper
// Html output
add pretty.html.HtmlTextWriter

For information on piper files, see 
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
I run it in my IDE with:
org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G -p .piper 
-i org/apache/ctakes/examples/notes -o  --user  --pass 
 You can run it by command line by substituting 
"org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G" with 
"bin/runPiperFile".
You can also run it through a ctakes 4.01 (trunk) gui.  See 
https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI

> I'm not able to see any clickable option in HTML output
You must have the HtmlTextWriter at the end of your pipeline to produce html 
files.  To keep the xml file output, place "add FileTreeXmiWriter" at the end 
of the piper.

> Apologizes for too many
No worries, we are happy to have your interest!

Sean


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, September 16, 2017 7:01 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Sean,

Thanks again for the prompt response. Appreciate your input on adding 
DrugMentionAnnotator. Actually, we are relying on pretty printer output just to 
understand the analysis. Our logic to extract disorders and findings are based 
on the XML file generated by 
https://urldefense.p

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

Thanks again for the detailed and prompt response. We were able to run the 
piper GUI as per your advice. But in the output (The patient started study 
treatment of Thalomid 200mg ( days 1 - 21 ) , and Epirubicin ,20 mg / m2 ( days 
1 , 8 , and 15 ) on 06 / 07 / 02 for the treatment of hepatocellular 
carcinoma.), we were not able to find superscript-1 as you mentioned earlier 
but could find superscript-2, 3 etc.  We guess we are missing out on something 
as we could not find co-references for "200mg". Should we add anymore piper for 
this?

Also the change mentioned in the thread - 
http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3ccal6wimrj_mm1+xyggbzv62diyuwp0sca9vev8mnhgwe4hsn...@mail.gmail.com%3E
 is required for the drug-ner module to identify drug-ner annotations.

1) We also have a requirement to identify the patient names and sex available 
in narrative texts. Please let us know how to achieve the same as its not 
identifying the proper nouns and the relationship with the patient?
Eg. "This male patient named Tom Hardy aged 35 years is participating in a 
Non-IND study"

2) cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or 06 / 07 
/ 02 or 27Aug2002 as in the below example. Please let us know how to enhance 
the system to identify such date patterns.
E.g " On 20Aug02, the investigator noted that this patient was suffering 
worsening fatigue and got tired getting out of his chair"

Regards,
Gandhi


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 18, 2017 10:02 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Gandhi,

> So in this case will be able to see drug attributes in the output XML?
As long as you have the DrugMentionAnnotator in your pipeline you should be 
able to find drug attributes in the xml output file.

> we also saw some code changes needs to be done to use drug-ner module. Is it 
> still valid?
As far as I know there aren't any necessary code changes to get drug ner 
running.  However, I do not normally use drugner so I can't say for certain.

> Also you mentioned that the drun-ner module is out of date
It can still be used and will produce annotations.  All that I meant was that 
there may not be many people out there using it.  It is not part of the default 
pipeline.

  > You also mentioned that when you run the sentence, the date was identified. 
Where and how exactly did you ran it so that we can check the same?
I run the following in a piper file because I am interested in a lot of modules 
(I added drugner just for you):

// Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), 
Paragraphs, Lists load AdvancedTokenizerPipeline.piper add 
ContextDependentTokenizerAnnotator
add POSTagger
// Chunkers
load ChunkerSubPipe.piper
// Default fast dictionary lookup
load DictionarySubPipe.piper
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
// Cleartk Entity Attributes
load AttributeCleartkSubPipe.piper
// Relations
load RelationSubPipe.piper
// Temporal
load TemporalSubPipe.piper
// Coreferences
load CorefSubPipe.piper
// Html output
add pretty.html.HtmlTextWriter

For information on piper files, see 
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
I run it in my IDE with:
org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G -p .piper 
-i org/apache/ctakes/examples/notes -o  --user  --pass 
 You can run it by command line by substituting 
"org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G" with 
"bin/runPiperFile".
You can also run it through a ctakes 4.01 (trunk) gui.  See 
https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI

> I'm not able to see any clickable option in HTML output
You must have the HtmlTextWriter at the end of your pipeline to produce html 
files.  To keep the xml file output, place "add FileTreeXmiWriter" at the end 
of the piper.

> Apologizes for too many
No worries, we are happy to have your interest!

Sean


-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, September 16, 2017 7:01 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

Hi Sean,

Thanks again for the prompt response. Appreciate your input on adding 
DrugMentionAnnotator. Actually, we are relying on pretty printer output just to 
understand the analysis. Our logic to extract disorders and findings are based 
on the XML file generated by 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_blob_master_ctakes-2Dtemporal-2Ddemo_src_main_java_org_apache_ctakes_web_client_servlet_DemoServlet.java=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=_MJKBj93YJdd5aa84dBvqtg6o-BKBn7UcbfF660CEBI=g8UzBHR

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

[Gandhi Rajan Natarajan]

Hi Sean,

Thanks again for the prompt response. Appreciate your input on adding 
DrugMentionAnnotator. Actually, we are relying on pretty printer output just to 
understand the analysis. Our logic to extract disorders and findings are based 
on the XML file generated by 
https://github.com/healthnlp/examples/blob/master/ctakes-temporal-demo/src/main/java/org/apache/ctakes/web/client/servlet/DemoServlet.java
  So in this case will be able to see drug attributes in the output XML?

In one of the old post 
(http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3ccal6wimrj_mm1+xyggbzv62diyuwp0sca9vev8mnhgwe4hsn...@mail.gmail.com%3E
 ) we also saw some code changes needs to be done to use drug-ner module. Is it 
still valid? Also you mentioned that the drun-ner module is out of date which 
means it cannot be used or it may not provide accurate analysis? Also what 
changes needs to be done to bring it up to date so that we can try the same if 
you can assist?

You also mentioned that when you run the sentence, the date was identified. 
Where and how exactly did you ran it so that we can check the same? Also 
regarding you explanation on corefernce, I'm not able to see any clickable 
option in HTML output. So wanted to understand how can we run and check that 
too.

Apologizes for too many questions as we are just a week old in NLP and cTAKES. 
Thanks in advance.

Regards,
Gandhi

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