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  
> 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
> 
> 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


 -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

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

[Sandeep Byatha Gururaja rao]

Hi,

Great job Matthew !!!

Regards,
Sandeep

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.

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

[Matthew Vita]

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