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Java - GeoLite2 database corruption when creating .jar in Gradle

Recently I have been using GeoLite2 City database in my application to get information on the user location using their IP. The database works fine in my local machine, but when I compile it to a .jar using ./gradlew -Pprod clean bootJar I get this error when trying to access a component that uses the database:
InvalidDatabaseException
Could not find a MaxMind DB metadata marker in this file (<InputStream>). Is this a valid MaxMind DB file?
Searching for this error, I found this thread on StackOveflow that explained the need to disable resource filtering for binary files in Maven. Thing is, I'm using gradle, which as far as I know, does not have this resource and should not be facing this problem.
Regardless, I tried searching for a solution and tried implementing something based on this thread to fix the issue. I ended up adding this to my build.gradle:
processResources {
from('src/main/resources/data') {
include '**/*.mmdb'
}
}
That, however, also did not work. It seems like this should be a simple issue, but I have not been able to solve it and neither did I find someone with the same issue so far. Any help would be appreaciated!

You could try this (note: I did not test it)
processResources {
filesNotMatching("**/*.mmdb") {
}
}

Jar hell for missing classes folder when running ESRestTestCase

So I'm running into a Jar hell problem when trying to run individual integration tests, using -Dtest=, that runs as a ESRestTestCase (ESTestCase). The issue here seems to be that some elasticsearch classpath validation class requires target/classes to exist. However, this project is only for testing so that requirement doesn't make sense.
This happened with Elasticsearch 7.0.0 and Java 1.8.0.251. Not sure if this is a problem with later versions.
java.lang.RuntimeException: found jar hell in test classpath
at org.elasticsearch.bootstrap.BootstrapForTesting.<clinit>(BootstrapForTesting.java:98)
at org.elasticsearch.test.ESTestCase.<clinit>(ESTestCase.java:229)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at com.carrotsearch.randomizedtesting.RandomizedRunner$2.run(RandomizedRunner.java:623)
Caused by: java.nio.file.NoSuchFileException: <MY PROJECT FOLDER PATH HERE>/target/classes
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(UnixFileAttributeViews.java:55)
at sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:144)
at java.nio.file.Files.readAttributes(Files.java:1737)
at java.nio.file.FileTreeWalker.getAttributes(FileTreeWalker.java:219)
at java.nio.file.FileTreeWalker.visit(FileTreeWalker.java:276)
at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:322)
at java.nio.file.Files.walkFileTree(Files.java:2662)
at java.nio.file.Files.walkFileTree(Files.java:2742)
at org.elasticsearch.bootstrap.JarHell.checkJarHell(JarHell.java:199)
at org.elasticsearch.bootstrap.JarHell.checkJarHell(JarHell.java:86)
at org.elasticsearch.bootstrap.BootstrapForTesting.<clinit>(BootstrapForTesting.java:96)
... 4 more

At first I tried various methods for making sure the classes folder was still created. I ran into new problems that seemed fixed in later versions so I upgraded to Elasticsearch 7.6.2 (And lucene 8.4.0). Upgrading seemed to remove the need for the folder to exist but triggered other issues (similar to this). I worked around such issues with -Dtests.security.manager=false. Then I got thread leak issues which I "solved" by setting #ThreadLeakScope(ThreadLeakScope.Scope.NONE) on the test class.
Then finally it seemed to work when running maven in command line for individual tests. But when trying to run the maven task with debugger in Intellij the debugger does not seem to attach.
So I try to run it as JUnit templated test in Intellij. Here I get jar hell when running it but it works to debug. The jar hell was later solved by setting idea.no.launcher=true in idea.properties.
Alright, good enough for now. These workarounds are far from ideal but it works for my current purposes. A lot of things will change before moving into mainline anyway. And maybe this will help someone else. Hopefully I can post a better solution later.

Adding new aggregate function in Presto fails

I am trying to build custom aggregate functions for presto. I have created a FAT Jar and deployed the jar into the plugin directory. When I restart presto, it is always giving me this error :
java.lang.AbstractMethodError
at com.facebook.presto.server.PluginManager.installPlugin(PluginManager.java:183)
at com.facebook.presto.server.PluginManager.loadPlugin(PluginManager.java:175)
at com.facebook.presto.server.PluginManager.loadPlugin(PluginManager.java:158)
Unfortunately, I do not see any verbose error message which will give me a clue on what is actually missing here. I used presto-ml plugin as an example and implemented getFunctions() in plugin implementation. Is there a way to figure out what is missing?
I did check the source code of PLuginManager.java. I am just looking for a way to debug this in a better way.

NoSuchMethodError with Camel RouteDefinition class

I am trying to debug a Java / Maven project with a lot of depencies on various libraries.
When I run it on a Linux server the program starts up fine, but when I try to run it in Eclipse it throws the following exception:
Exception in thread "main" java.lang.NoSuchMethodError: org.apache.camel.model.RouteDefinition.getErrorHandlerBuilder()Lorg/apache/camel/ErrorHandlerFactory;
at org.apache.camel.spring.spi.SpringTransactionPolicy.wrap(SpringTransactionPolicy.java:69)
at org.apache.camel.model.PolicyDefinition.createProcessor(PolicyDefinition.java:133)
at org.apache.camel.model.ProcessorDefinition.makeProcessor(ProcessorDefinition.java:437)
at org.apache.camel.model.ProcessorDefinition.addRoutes(ProcessorDefinition.java:183)
at org.apache.camel.model.RouteDefinition.addRoutes(RouteDefinition.java:817)
at org.apache.camel.model.RouteDefinition.addRoutes(RouteDefinition.java:165)
at org.apache.camel.impl.DefaultCamelContext.startRoute(DefaultCamelContext.java:697)
at org.apache.camel.impl.DefaultCamelContext.startRouteDefinitions(DefaultCamelContext.java:1654)
at org.apache.camel.impl.DefaultCamelContext.doStartCamel(DefaultCamelContext.java:1441)
at org.apache.camel.impl.DefaultCamelContext.doStart(DefaultCamelContext.java:1338)
at org.apache.camel.impl.ServiceSupport.start(ServiceSupport.java:67)
at org.apache.camel.impl.ServiceSupport.start(ServiceSupport.java:54)
at org.apache.camel.impl.DefaultCamelContext.start(DefaultCamelContext.java:1316)
Now, I can see that the RouteDefinition class is in the camel-core-2.9.3,jar and I can see that this library is imported. So how come it doesn't see that method?
How do I go about debugging this?
Could I get info from the process running on the Linux server? For example can I get the list of Jars that are imported and the order in which they are imported?
Many thanks!

The error that you're getting is caused by Maven pulling in the wrong version. Try deleting all versions out of your local repo, add it explicitly to your pom, clean out all of your builds, pray to the eclipse gods, etc. If it still gives you the error, check your local repo to see which wrong versions it pulled in, figure out what depends on them, and add explicit ignores for them while keeping the explicit include.

Publish failed using Ant publisher (Eclipse/datanucleus)

I am being driven mad the following (apparently hard) error from eclipse.
Publish failed using Ant publisher
Resource is out of sync with the file system: '/MyServlet/build/classes/com/inver/hotzones/database/BaseNetworkData.class'.
I have seen comments on similar errors where refreshing eclipses view of the project helps but it is not helping me. Have tried cleaning the project, removing it from the webserver, deleting war files but cant seem to clear it. I have reset my TMPDIR variable so that it uses a directory on the same filesystem as that appeared to be another possible cause.
The error occurs on classes which have been enhanced by datanuculeus. I have auto-enhance on the project. The other references to this problem indicate that it is due to Eclipses view of the project being out of step with the filesystem, and I am guessing that this has something to do with thedata nucleus enhancement.
Any ideas?
Thanks.
I am using Eclipse 3.5.2 with latest datanucleus pluggins.
Stack trace
org.eclipse.core.runtime.CoreException: Resource is out of sync with the file system: '/MyServlet/build/classes/com/inver/hotzones/database/BaseNetworkData.class'.
at org.eclipse.jst.server.generic.core.internal.publishers.AbstractModuleAssembler.copyModule(AbstractModuleAssembler.java:172)
at org.eclipse.jst.server.generic.core.internal.publishers.WarModuleAssembler.assemble(WarModuleAssembler.java:31)
at org.eclipse.jst.server.generic.core.internal.publishers.AntPublisher.assembleModule(AntPublisher.java:167)
at org.eclipse.jst.server.generic.core.internal.publishers.AntPublisher.publish(AntPublisher.java:128)
at org.eclipse.jst.server.generic.core.internal.GenericServerBehaviour.publishModule(GenericServerBehaviour.java:82)
at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publishModule(ServerBehaviourDelegate.java:949)
at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publishModules(ServerBehaviourDelegate.java:1039)
at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:872)
at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:708)
at org.eclipse.wst.server.core.internal.Server.publishImpl(Server.java:2731)
at org.eclipse.wst.server.core.internal.Server$PublishJob.run(Server.java:278)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)