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

2024-05-14 Thread Finan, Sean 
Ah - are you just running the class within intellij?  If so, you need to set 
the classpath in the run configuration to be ctakes-examples.  Otherwise the 
classpath doesn't contain anything from modules outside ctakes-gui and 
ctakes-core.

Alternatively, run the maven compile step with the "runPiperGui" profile 
selected.  That will also run the piper file submitter gui with the correct 
classpath.

Using a binary build, after running bin/getUmlsDictionary, running 
bin/runPiperSubmitter also works.

I don't want to do it for 5.1.0, but I should make names of the class, profile 
and script match.

I will check the wiki instructions and make sure that -exact- details are in 
there.

Sean


From: Miller, Timothy 
Sent: Tuesday, May 14, 2024 12:55 PM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

* External Email - Caution *


I can check out and build successfully with mvn from the command line. I can 
successfully open in intellij and run the piper file submitter. I get an error 
trying to run the default fast pipeline piper file:

Loading Piper File DefaultTokenizerPipeline ...


Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle 
java.util.PropertyResourceBundle, key No Analysis Component found for 
ContextDependentTokenizerAnnotator



It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator.

Tim



From: Miller, Timothy 
Date: Tuesday, May 14, 2024 at 9:25 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *


What would you recommend for testing? Download the release tag to a clean 
system and try to do mvn compile and run some tests?
Tim


From: Finan, Sean 
Date: Thursday, May 2, 2024 at 6:57 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS]
* External Email - Caution *


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://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$

I added a little bit to your instructions in the ctakes-web-rest README  
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$

The lines here indirectly applies to pre-release builds:

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

2024-05-14 Thread Finan, Sean 
Hi Tim,

Thanks for testing, I'll look into this.

Sean

From: Miller, Timothy 
Sent: Tuesday, May 14, 2024 12:55 PM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

* External Email - Caution *


I can check out and build successfully with mvn from the command line. I can 
successfully open in intellij and run the piper file submitter. I get an error 
trying to run the default fast pipeline piper file:

Loading Piper File DefaultTokenizerPipeline ...


Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle 
java.util.PropertyResourceBundle, key No Analysis Component found for 
ContextDependentTokenizerAnnotator



It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator.

Tim



From: Miller, Timothy 
Date: Tuesday, May 14, 2024 at 9:25 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *


What would you recommend for testing? Download the release tag to a clean 
system and try to do mvn compile and run some tests?
Tim


From: Finan, Sean 
Date: Thursday, May 2, 2024 at 6:57 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS]
* External Email - Caution *


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://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$

I added a little bit to your instructions in the ctakes-web-rest README  
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$

The lines here indirectly applies to pre-release builds:
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$

The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on

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

2024-05-14 Thread Miller, Timothy 
I can check out and build successfully with mvn from the command line. I can 
successfully open in intellij and run the piper file submitter. I get an error 
trying to run the default fast pipeline piper file:

Loading Piper File DefaultTokenizerPipeline ...


Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle 
java.util.PropertyResourceBundle, key No Analysis Component found for 
ContextDependentTokenizerAnnotator



It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator.

Tim



From: Miller, Timothy 
Date: Tuesday, May 14, 2024 at 9:25 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *


What would you recommend for testing? Download the release tag to a clean 
system and try to do mvn compile and run some tests?
Tim


From: Finan, Sean 
Date: Thursday, May 2, 2024 at 6:57 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS]
* External Email - Caution *


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://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$

I added a little bit to your instructions in the ctakes-web-rest README  
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$

The lines here indirectly applies to pre-release builds:
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$

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).

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

2024-05-14 Thread Miller, Timothy 
What would you recommend for testing? Download the release tag to a clean 
system and try to do mvn compile and run some tests?
Tim


From: Finan, Sean 
Date: Thursday, May 2, 2024 at 6:57 AM
To: dev@ctakes.apache.org 
Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] 
[SUSPICIOUS]
* External Email - Caution *


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://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$

I added a little bit to your instructions in the ctakes-web-rest README  
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$

The lines here indirectly applies to pre-release builds:
https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$

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://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$

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

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