Re: Mastif Zoner is there now [EXTERNAL]

2024-05-02 Thread Finan, Sean
Hi Peter,

I am glad that mastif is now in the distrobution.  Yes, testing the pre-release 
is a little rough, but once released everything is streamlined and -easy-.  
After the release there shouldn't be any of the funny business of cleaning, 
grabbing a tag, installing local jars, etc.

Thanks again,

Sean

From: Peter Abramowitsch 
Sent: Thursday, May 2, 2024 3:11 PM
To: dev@ctakes.apache.org 
Subject: Mastif Zoner is there now [EXTERNAL]

* External Email - Caution *


Hi Sean

I did a clean build, also removing the mastif zoner library from my maven
cache.  It does get into the distribution now.

My git branch got a bit confused when I tried to merge the tag into it.
But by destroying my branch and using switch -c to create a new one off the
5.1.0 tag it seemed to do the right thing.  I guess when 5.1.0 is merged
into main, that won't be an issue

Peter


Mastif Zoner is there now

2024-05-02 Thread Peter Abramowitsch
Hi Sean

I did a clean build, also removing the mastif zoner library from my maven
cache.  It does get into the distribution now.

My git branch got a bit confused when I tried to merge the tag into it.
But by destroying my branch and using switch -c to create a new one off the
5.1.0 tag it seemed to do the right thing.  I guess when 5.1.0 is merged
into main, that won't be an issue

Peter


Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

2024-05-02 Thread Peter Abramowitsch
I'll test it today.  Thanks Sean.

Peter

On Wed, May 1, 2024, 14:05 Finan, Sean
 wrote:

> Hi Peter,
>
> I think that I have the ctakes-mastif-zoner module behavior as desired.
> Let me know if you have any problems with the new candidate.
>
> Sean
> 
> From: Peter Abramowitsch 
> Sent: Friday, April 26, 2024 11:41 PM
> To: dev@ctakes.apache.org 
> Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate
> [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hi Sean,
>
> It all compiles, but one of the jars is missing from the distribution.
> It's the one I added:  ctakes-mastif-zoner which is required if you're
> going to use the Zone Annotator.
>
> It's in the master pom, and in the pom of ctakes-distribution, and the jar
> got built in its projecte, but it's not scooped up into the distribution.
> I'm not sure where else to look.Can you fix it?
>
> Peter
>
>
> On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean
>  wrote:
>
> > Hi all,
> >
> > There is a candidate for version 5.1.0 of Apache cTAKES source code in a
> > staging repository:
> >
> >
> https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZJnsDvVQ$
> >
> > The code is contained within the file:
> > ctakes-5.1.0-source-release.zip<
> >
> https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGbgcnIf3Q$
> > >
> >
> > I welcome you all to test your favorite pipeline(s) and report any
> issues.
> > I am calling a vote from the PMC to finish by 12:nn Eastern time, next
> > Wednesday May 1.  Please report any issues before that time.  If any
> > 'road-block' issues are found they will need to be addressed before a
> > release.
> >
> > Thank you,
> > Sean
> >
> >
> > p.s.
> >
> > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0
> tag:
> >
> https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGYS7mfi0g$
> >
> > The ctakes-5.1.0 tag was made from the 5.1.0 branch:
> >
> https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZACCHJkw$
> >
> > The 5.1.0 branch is a copy of the main branch:
> >
> https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGaoZVS80g$
> > The version number in the 5.1.0 branch is different, but there are no
> code
> > differences between the two branches.
> >
> >
> >
>


Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

2024-05-02 Thread Finan, Sean
Hi Gandhi,


  *   So post release I would be able to run mvn clean
install on web rest module rather than relying on resources in .m2 folder

The opposite.  Pre-release there are no jars on maven central, post-release 
there are.
Running 'mvn package' directly on the ctakes-web-rest project (in its directory)
or
running 'mvn package' on the ctakes -main- project (in the main ctakes root 
directory) with the web-rest-build profile enabled '-Pweb-rest-build'
will build the ctakes-web-rest.war web package.
That profile is defined in the main ctakes pom.
https://github.com/apache/ctakes/blob/main/pom.xml#L1074

I added a little bit to your instructions in the ctakes-web-rest README  
https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README

The lines here indirectly applies to pre-release builds:
https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README#L22

The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on the 5.1.0 
version of ctakes modules (not the SNAPSHOT).
https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml#L14

The pre-release basically contains an equivalent to "changed code or resources" 
in that the code and resources in the pre-release do not exist on maven 
central, which is where a maven build would normally get them.
When maven builds the pre-release it will not be able to find version 5.1.0 of 
any jars through maven central, so it will look for them in your local .m2 
directory.
Maven puts the 5.1.0 jars in your .m2 directory when you run 'mvn install' on 
the main ctakes project.

In summary,
To build ctakes-web-rest to test the pre-release war, one must run 'mvn 
install' on the ctakes main project before they run 'mvn package' on the 
ctakes-web-rest project (or on the main project's web-rest-build profile).
To build ctakes-web-rest once ctakes 5.1.0 has been released, the extra 
preliminary step of running 'mvn install' will not be necessary.


  *   If you have some time this week, we can connect to understand what 
exactly is the problem.

I can meet you tomorrow evening your time (4-7 pm IST) to work with you in the 
SQL problem.  If you'd rather keep your Friday night to yourself, I can work 
with the same time slot any time through next Monday evening.

Before the 6.0.0 release I will put some Release Manager information in the 
wiki.  The maven release process using a GitHub repo requires a little trick 
that took me a long time to figure out, and the pre-release testing deserves 
some recorded documentation.

Sean




From: gandhi rajan 
Sent: Thursday, May 2, 2024 1:42 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

* External Email - Caution *


Hi Sean,

Thanks for the update. So post release I would be able to run mvn clean
install on web rest module rather than relying on resources in .m2 folder
you mean? Infact I was trying to build them on a machine which doesnt have
any historic jars in the .m2 folder and thats why it was failing.
And ytex issue still remains a mystery to me. If you have some time this
week, we can connect to understand what exactly is the problem.

On Thu, 2 May 2024 at 02:32, Finan, Sean
 wrote:

> Hi Gandhi,
>
> I can build the web-rest module.  I should have mentioned that to build
> any of the rest projects you need to run mvn install.  As the rest requires
> 5.1.0 module jars and they don't exist externally (pre-release), maven must
> be able to fetch them from your .m2 directory.
>
> I haven't been able to duplicate the ytex problems that you see and don't
> know what might be causing them.
>
> Sean
>
> 
> From: gandhi rajan 
> Sent: Tuesday, April 30, 2024 11:18 AM
> To: dev@ctakes.apache.org 
> Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate
> [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hi Peter,
>
> Thanks for the response. I dont think the generate test action is trying to
> use mysql but hsql DB. Anyways, I am able to build other modules apart from
> ytex and ytex-uima module.
>
> Sean, did you try building ctakes-web-rest module by any chance? It seems
> to be broken in my case.
>
> On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch 
> wrote:
>
> > Hi Gandhi,  I think the email from Jeff Painter may explain your
> > situation.  It's a question of your version of mysql being new.   The
> > crucial lines in your trace are:
> >
> > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84)
> > [INFO]  [java] Caused by:
> > java.lang.reflect.InaccessibleObjectException: Unable to make protected
> > final java.lang.Class
> > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws
> > java.lang.ClassFormatError accessible: module java.base does not "opens
> > java.lang" to unnamed module @61ca2dfa
> >
> > And this makes it sound like it is expecting a library version where
> > certain classnames or accessibility has changed.   Check Jeff's