+1 from me. -Dennis ________________________________ From: Savova, Guergana <guergana.sav...@childrens.harvard.edu.INVALID> Sent: Wednesday, May 15, 2024 2:26 PM To: dev@ctakes.apache.org <dev@ctakes.apache.org> Subject: RE: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution * +1 from me. --Guergana -----Original Message----- From: Finan, Sean <sean.fi...@childrens.harvard.edu.INVALID> Sent: Wednesday, May 15, 2024 1:32 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Tim! ________________________________ From: Miller, Timothy <timothy.mil...@childrens.harvard.edu.INVALID> Sent: Wednesday, May 15, 2024 11:38 AM To: dev@ctakes.apache.org <dev@ctakes.apache.org> Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean <sean.fi...@childrens.harvard.edu.INVALID> Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org <dev@ctakes.apache.org> Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * 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 <timothy.mil...@childrens.harvard.edu.INVALID> Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org <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 <timothy.mil...@childrens.harvard.edu.INVALID> Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org <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 <sean.fi...@childrens.harvard.edu.INVALID> Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org <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$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e%3e> 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$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e%3e> 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$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3e%3e> 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$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$%3e%3e> 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 <gandhiraja...@gmail.com> Sent: Thursday, May 2, 2024 1:42 AM To: dev@ctakes.apache.org <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 <sean.fi...@childrens.harvard.edu.invalid> 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 <gandhiraja...@gmail.com> > Sent: Tuesday, April 30, 2024 11:18 AM > To: dev@ctakes.apache.org <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 > <pabramowit...@gmail.com> > 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 > > <gandhiraja...@gmail.com> > > 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.<init>(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(Acces > sorInjector.java:83) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(O > ptimizedAccessorFactory.java:176) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize( > Accessor.java:282) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>( > SingleElementNodeProperty.java:94) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstan > ce0(Native > > > Method) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstan > ce(NativeConstructorAccessorImpl.java:77) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newIn > stance(DelegatingConstructorAccessorImpl.java:45) > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Construc > tor.java:499) > > > [INFO] [java] at > > > > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:4 > 80) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFa > ctory.java:128) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl > .java:181) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImp > l.java:509) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.jav > a:326) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.jav > a:141) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(J > AXBContextImpl.java:1163) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:1 > 45) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:2 > 36) > > > [INFO] [java] at > > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Na > > > tive > > > Method) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeM > ethodAccessorImpl.java:77) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Del > egatingMethodAccessorImpl.java:43) > > > [INFO] [java] at > > > java.base/java.lang.reflect.Method.invoke(Method.java:568) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:171) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:129) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.find(ContextFinder.java:307) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:478) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:435) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:336) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.<init>(ObjectFac > toryBind.java:43) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getObjectFactory > Mapping(ObjectFactoryUtil.java:41) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJAXBElementBy > SrcXml(ObjectFactoryUtil.java:49) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getConnTypeBySrc > Xml(ObjectFactoryUtil.java:86) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJdbcTypeBySrc > Xml(ObjectFactoryUtil.java:64) > > > [INFO] [java] at > > > org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:80) > > > [INFO] [java] at > > > 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 > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(Acc > essibleObject.java:354) > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(Acc > essibleObject.java:297) > > > [INFO] [java] at > > > > java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:1 > 99) > > > [INFO] [java] at > > > java.base/java.lang.reflect.Method.setAccessible(Method.java:193) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:1 > 77) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:1 > 72) > > > [INFO] [java] at > > > > > > > > > java.base/java.security.AccessController.doPrivileged(AccessController > .java:318) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.jav > a:172) > > > [INFO] [java] ... 34 more > > > > > > On Mon, 29 Apr 2024 at 21:21, Peter Abramowitsch < > > pabramowit...@gmail.com> > > > wrote: > > > > > > > I think this is the class where Java is exiting with 1 > > > > /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.jav > > > > a > > > > > > > > btw my environment is MacOS and I notice yours is Windows, so > > > > the > root > > > > cause why this class is giving you trouble is something I > > > > wouldn't be > > > able > > > > to help you with. But some debug statements rather than asserts > would > > > tell > > > > you, I think. > > > > > > > > Peter > > > > > > > > On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch < > > > > pabramowit...@gmail.com> > > > > wrote: > > > > > > > > > Hi Gandhi > > > > > This project is an odd one in the sense that when you tell it > > > > > to > skip > > > the > > > > > tests, it still goes through the effort in building up the db > > > environment > > > > > that the tests would use. But in any case, for me it does > > > > > build > > either > > > > > way. In the attached log, I've run a maven clean before doing > > > > > the > > > build > > > > > without tests. > > > > > > > > > > However, check my previous email about your issue. Whereas > > > > > you'd > > > > narrowed > > > > > it down to a script, I found a line in your email which showed > > > > > the > > > error > > > > > within that script's execution: A java program: jdl running > > > > > as > > > App.Main > > > > > threw an assertion on one of the tasks connected with the > > > > > mysql > > > database > > > > it > > > > > was trying to configure. You could put some debugging > > > > > statements > in > > > > there > > > > > to see which one. > > > > > > > > > > Peter > > > > > > > > > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan < > > gandhiraja...@gmail.com> > > > > > wrote: > > > > > > > > > >> Thanks for the insights Peter. I dint make it clear that I > > > > >> did ran > > the > > > > >> install on ytex module with test case execution toggled off. > > > > >> I > used > > > the > > > > >> following command - "mvn -e clean install -Dmaven.test.skip=true" > > and > > > I > > > > >> still hit the same error. > > > > >> > > > > >> On digging deep, I could find that the build process is > > > > >> trying to > > > > execute > > > > >> "<ant antfile="build-setup.xml" dir="scripts" > target="test.setup">" > > in > > > > >> build-main.xml which in turn is trying to invoke the > > > > >> following > > target > > > in > > > > >> build.setup.xml: > > > > >> > > > > >> <target name="test.setup" description="setup properties and > database > > > for > > > > >> unit tests" > > > > >> > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > > > >> <ant dir="data" target="all" inheritAll="true"/> </target> > > > > >> > > > > >> Did you try running this on a fresh setup Peter? > > > > >> > > > > >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch < > > > > pabramowit...@gmail.com > > > > >> > > > > > >> wrote: > > > > >> > > > > >> > Hi Gandhi > > > > >> > Your error appears to be at this line > > > > >> > > > > > >> > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > > > >> Java > > > > >> > returned: 1 > > > > >> > > > > > >> > A test application being run here: AppMain is in charge of > > loading > > > a > > > > >> > temporary mysqldb that is used to test that part of ytex. For > me > > > it > > > > is > > > > >> > working, but if you can find a way to run that surefire > > > > >> > test in > > the > > > > >> > debugger, you can find out why it's failing on one of the > > > assertions. > > > > >> > Otherwise you can take this shortcut > > > > >> > > > > > >> > mvn <goal> -Dmaven.test.skip=true > > > > >> > > > > > >> > To build the project without running any tests. > > > > >> > > > > > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan < > > > gandhiraja...@gmail.com > > > > > > > > > >> > wrote: > > > > >> > > > > > >> > > Hi Sean, > > > > >> > > > > > > >> > > When I tried to build the complete ctakes suite, i get > > > > >> > > build > > > failure > > > > >> for > > > > >> > > ctakes-ytex module with the following error: > > > > >> > > > > > > >> > > [ERROR] Failed to execute goal > > > > >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > > > >> > > (generate-test-config) on project ctakes-ytex: An Ant > > > BuildException > > > > >> has > > > > >> > > occured: The following error occurred while executing > > > > >> > > this > line: > > > > >> > > [ERROR] > > > > >> > > > > > > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > > > >> > Java > > > > >> > > returned: 1 > > > > >> > > [ERROR] around Ant part ...<ant antfile="build-setup.xml" > > > > >> dir="scripts" > > > > >> > > target="test.setup">... @ 5:70 in > > > > >> > > > > > > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-mai > > > n.xml > > > > >> > > > > > > >> > > Is this expected Sean? > > > > >> > > > > > > >> > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > > > >> > > <sean.fi...@childrens.harvard.edu.invalid> 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/repo > sitories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_! > tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuER > Idgo__Owtxkd2ysxNkgAWbqNXsKw$<https://urldefense.com/v3/__https:/repos > 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SRgmXffKQuERIdgo__Owtxkd2ysxNkgAWbqNXsKw$%3e%3chttps:/urldefense.com/v > 3/__https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apac__;!!NZvER7FxgEiBAiR_!o44IuOECO_gSQdbYYobd1aOfwXM1X_o_PVdd3GqTaKaySKqhOvZ_ISFgs9VKtfMe_DiXAkMLCvIkp_1cOnspYHjQxDwQ7wWG7f_0pZ37eBLR1x7cRDpUUG8tOQ$ > he/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhp > cQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAWbqNX > sKw$%3chttps:/urldefense.com/v3/__https:/repository.apache.org/content > /repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiB > AiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXff > KQuERIdgo__Owtxkd2ysxNkgAWbqNXsKw$%3e%3e> > > > > >> > > > > > > > >> > > > The code is contained within the file: > > > > >> > > > ctakes-5.1.0-source-release.zip< > > > > >> > > > > > > > >> > > > > > > >> > > > > > >> > > > > > > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repo > sitories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-re > lease.zip__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28Pkc > ylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAUTMj5tmQ$<https://urldefense.com/v3/__https://u__;!!NZvER7FxgEiBAiR_!o44IuOECO_gSQdbYYobd1aOfwXM1X_o_PVdd3GqTaKaySKqhOvZ_ISFgs9VKtfMe_DiXAkMLCvIkp_1cOnspYHjQxDwQ7wWG7f_0pZ37eBLR1x7cRDpSXm4kUA$ > rldefense.com/v3/__https://urldefense.com/v3/__https://repository.apache.org/content/repositories/s__;!!NZvER7FxgEiBAiR_!o44IuOECO_gSQdbYYobd1aOfwXM1X_o_PVdd3GqTaKaySKqhOvZ_ISFgs9VKtfMe_DiXAkMLCvIkp_1cOnspYHjQxDwQ7wWG7f_0pZ37eBLR1x7cRDqvFvsi-w$ > taging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip_ > _;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nv > 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ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAi > R_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQ > uERIdgo__Owtxkd2ysxNkgAUTMj5tmQ$%3e><https://urldefense.com/v3/__https > :/repository.apache.org/content/repositories/staging/org/apache/ctakes > /ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!tcp > xrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdg > o__Owtxkd2ysxNkgAUTMj5tmQ$%3chttps:/urldefense.com/v3/__https:/reposit > ory.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5 > .1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D > 8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd > 2ysxNkgAUTMj5tmQ$%3e%3chttps:/urldefense.com/v3/__https:/repository.ap > ache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/c > takes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsL > y0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNk > gAUTMj5tmQ$%3chttps:/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_!tcpxrhYwLK6D8VsrsLy0QyKhpcQ > bTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAUTMj5tm > Q$%3e%3e> > > > > >> > > > > > > > > >> > > > > > > > >> > > > I welcome you all to test your favorite pipeline(s) and > report > > > any > > > > >> > > issues. > > > > >> > > > I am calling a vote from the PMC to finish by 12:nn > > > > >> > > > Eastern > > > time, > > > > >> next > > > > >> > > > Wednesday May 1. 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d2ysxNkgAU4h58rOQ$%3chttps:/urldefense.com/v3/__https:/github.com/apac > he/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbT > XjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAU4h58rOQ$ > %3e%3e> > > > > >> > > > The version number in the 5.1.0 branch is different, > > > > >> > > > but > there > > > are > > > > >> no > > > > >> > > code > > > > >> > > > differences between the two branches. > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > >> > > -- > > > > >> > > Regards, > > > > >> > > Gandhi > > > > >> > > > > > > >> > > "The best way to find urself is to lose urself in the > > > > >> > > service > of > > > > >> others > > > > >> > > !!!" > > > > >> > > > > > > >> > > > > > >> > > > > >> > > > > >> -- > > > > >> Regards, > > > > >> Gandhi > > > > >> > > > > >> "The best way to find urself is to lose urself in the service > > > > >> of > > > others > > > > >> !!!" > > > > >> > > > > > > > > > > > > > > > > > > -- > > > Regards, > > > Gandhi > > > > > > "The best way to find urself is to lose urself in the service of > > > others !!!" > > > > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of > others !!!" > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
