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(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$FieldReflection.optimize(Accessor.java:282) [INFO] [java] at com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>(SingleElementNodeProperty.java:94) [INFO] [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [INFO] [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) [INFO] [java] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [INFO] [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) [INFO] [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) [INFO] [java] at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128) [INFO] [java] at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:181) [INFO] [java] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509) [INFO] [java] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:326) [INFO] [java] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:141) [INFO] [java] at com.sun.xml.bind.v2.runtime.JAXBContextImpl$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) [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>(ObjectFactoryBind.java:43) [INFO] [java] at org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getObjectFactoryMapping(ObjectFactoryUtil.java:41) [INFO] [java] at org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJAXBElementBySrcXml(ObjectFactoryUtil.java:49) [INFO] [java] at org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getConnTypeBySrcXml(ObjectFactoryUtil.java:86) [INFO] [java] at org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJdbcTypeBySrcXml(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(AccessibleObject.java:354) [INFO] [java] at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) [INFO] [java] at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199) [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:177) [INFO] [java] at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:172) [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.java: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.java > > 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-main.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://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< > >> > > > > >> > > > >> > > >> > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/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. > >> > > > > >> > > > > >> > > > > >> > > > >> > > -- > >> > > 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 !!!"
