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

[gandhi rajan]

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 pull
> > requests and see if that fixes your problem.
> >
> > Another quick trick is maven  -fae (Fail at end)  It will go
> > through the rest of the build and only show failures then
> > Peter
> >
> > On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan 
> > wrote:
> >
> > > HI Peter,
> > >
> > > Thanks for the insights. I tried to debug from AppMain.java and it
> > > eventually fails in
> > >
> > >
> >
> "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.(ObjectFactoryBind.java:43)"
> > >
> > > Attaching the complete stacktrace for reference:
> > >
> > >
> > > [INFO]  [java] invoking method
> > > [INFO]  [java] Exception in thread "main"
> > > java.lang.ExceptionInInitializerError
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.(SingleElementNodeProperty.java:94)
> > > [INFO]  [java]  at
> > >
> > >
> >
> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > > Method)
> > > [INFO]  [java]  at
> > >
> > >
> >
> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
> > > [INFO]  [java]  at
> > >
> > >
> >
> java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> > > [INFO]  [java]  at
> > >
> > >
> >
> java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
> > > [INFO]  [java]  at
> > >
> java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:181)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:326)
> > > [INFO]  [java]  at
> > >
> > >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:141)
> > > [INFO]  [java]  at
> > >
> > >
> >
> 

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

[Finan, Sean]

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]

[Finan, Sean]

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 pull
> requests and see if that fixes your problem.
>
> Another quick trick is maven  -fae (Fail at end)  It will go
> through the rest of the build and only show failures then
> Peter
>
> On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan 
> wrote:
>
> > HI Peter,
> >
> > Thanks for the insights. I tried to debug from AppMain.java and it
> > eventually fails in
> >
> >
> "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.(ObjectFactoryBind.java:43)"
> >
> > Attaching the complete stacktrace for reference:
> >
> >
> > [INFO]  [java] invoking method
> > [INFO]  [java] Exception in thread "main"
> > java.lang.ExceptionInInitializerError
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.(SingleElementNodeProperty.java:94)
> > [INFO]  [java]  at
> >
> >
> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > Method)
> > [INFO]  [java]  at
> >
> >
> java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
> > [INFO]  [java]  at
> >
> >
> java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> > [INFO]  [java]  at
> >
> >
> java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
> > [INFO]  [java]  at
> > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:181)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:326)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:141)
> > [INFO]  [java]  at
> >
> >
> com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1163)
> > [INFO]  [java]  at
> > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145)
> > [INFO]  [java]  at
> > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:236)
> > [INFO]  [java]  at
> > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native
> > Method)
> > [INFO]  [java]  at
> >
> >
> java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
> > [INFO]  [java]  at
> >
> >
> java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> > [INFO]  [java]  at
> > java.base/java.lang.reflect.Method.invoke(Method.java:568)

Fw: Please test the Apache cTAKES 5.1.0 release candidate

[Finan, Sean]

Hi all,

As you may have seen, the last 5.1.0 candidate had some issues.

I have created a new 5.1.0 candidate, available here:
https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/

As before, individual module jars up two levels and in associated 
subdirectories.

Hopefully this candidate fares better.  Please report any findings before next 
Monday,  May 6th.

Thank you,

Sean

p.s.
If you test build any of the rest projects (e.g. ctakes-web-rest) or build an 
installation with Dockhand, you must first run mvn install.  Those builds 
require ctakes module jars to exist where they can be fetched, and as ctakes 
5.1.0 will not be available through maven central before a release, the jars 
must be in your .m2 directory.






From: Finan, Sean
Sent: Friday, April 26, 2024 11:58 AM
To: dev@ctakes.apache.org 
Subject: Please test the Apache cTAKES 5.1.0 release candidate

Hi all,

There is a candidate for version 5.1.0 of Apache cTAKES source code in a 
staging repository:
https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/

The code is contained within the file:
ctakes-5.1.0-source-release.zip

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://github.com/apache/ctakes/releases/tag/ctakes-5.1.0

The ctakes-5.1.0 tag was made from the 5.1.0 branch:
https://github.com/apache/ctakes/tree/5.1.0

The 5.1.0 branch is a copy of the main branch:
https://github.com/apache/ctakes/tree/main
The version number in the 5.1.0 branch is different, but there are no code 
differences between the two branches.