Remove TODOs from 3.0

[tomas-langer]

Check all instances of TODO 3.0.0-JAKARTA and fix the issues (or remove the TODO if the issue is fixed/works as designed).

[klustria]

Partial resolution was made via PR: #4447 which covers the following:

1. Remove comments in JdbcMetricsHistogram, JdbcMetricsTimer and NoOpMetricImpl as it was reviewed that no extra work needs to be done on them
2. HelidonInboundHeaderProvider was restored to use implements InboundHeadersProvider because org.glassfish.jersey.ext.microprofile:jersey-mp-rest-client dependency was restored back via PR 3884
3. org.jboss.classfilewriter:jboss-classfilewriter dependency is added in integrations/graal/mp-native-image-extension after it was removed from weld-se-core so that internal class ClassFileUtils can be restored in WeldSubstitutions

[klustria]

Other fixes are being worked on by Laird and Tomas:

1. PR Updates persistence.xmls to 3.0. Re-enables JPA tests. Removes eclips… #4446 in progress to fix weaving by @ljnelson
2. @tomas-langer is working on scripts related failures via re-enable native image tests in pipeline on master #4341 and is forecasted to be resolved with new version of parsson dependency

[klustria]

Remaining issues to work on:

1. Some todos related Micronaut: https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L313-L329, https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L351-L356 and https://github.com/oracle/helidon/blob/master/integrations/micronaut/data/src/test/java/io/helidon/integrations/micronaut/cdi/data/MicronautDataCdiExtensionTest.java#L111-L120
2. Find suitable replacement for javax.annotation:javax.annotation-api (because this is an old version of the Java EE API). Tried jakarta.platform:jakarta.jakartaee-api:8.0.0 and works but was advised this is also not a good alternative as it is for the whole profile. The Jakarta specific library which was recommended jakarta.annotation:jakarta.annotation-api:jar:1.3.5 was unfortunately is causing a DependencyConvergence failure because it is also pulling v2.0.0 of this library from other dependencies like helidon-config, helidon-common-service-loader, and helidon-config-hocon:

[WARNING] 
Dependency convergence error for jakarta.annotation:jakarta.annotation-api:2.0.0 paths to dependency are:
+-io.helidon.config:helidon-config-etcd:3.0.0-SNAPSHOT
  +-io.helidon.config:helidon-config:3.0.0-SNAPSHOT
    +-jakarta.annotation:jakarta.annotation-api:2.0.0
and
+-io.helidon.config:helidon-config-etcd:3.0.0-SNAPSHOT
  +-io.helidon.common:helidon-common-media-type:3.0.0-SNAPSHOT
    +-io.helidon.common:helidon-common-service-loader:3.0.0-SNAPSHOT
      +-jakarta.annotation:jakarta.annotation-api:2.0.0
and
+-io.helidon.config:helidon-config-etcd:3.0.0-SNAPSHOT
  +-jakarta.annotation:jakarta.annotation-api:1.3.5
and
+-io.helidon.config:helidon-config-etcd:3.0.0-SNAPSHOT
  +-io.helidon.config:helidon-config-hocon:3.0.0-SNAPSHOT
    +-jakarta.annotation:jakarta.annotation-api:2.0.0

[WARNING] Rule 0: org.apache.maven.plugins.enforcer.DependencyConvergence failed with message:
Failed while enforcing releasability. See above detailed error message.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.336 s
[INFO] Finished at: 2022-06-28T09:42:38-07:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:3.0.0-M1:enforce (enforce-dependencies) on project helidon-config-etcd: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed. -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

[klustria]

For the DependencyConvergence error, I found a way to include jakarta.annotation:jakarta.annotation-api:jar:1.3.5 even if jakarta.annotation:jakarta.annotation-api:jar:2.0.0 is transitively being pulled by other dependencies. This can be done by adding a . at the end of groupId like this:

        <dependency>
            <groupId>jakarta.annotation.</groupId>
            <artifactId>jakarta.annotation-api</artifactId>
            <version>1.3.5</version>
            <scope>provided</scope>
            <optional>true</optional>
        </dependency>

I found this suggestion from: https://stackoverflow.com/questions/24962607/multiple-versions-of-the-same-dependency-in-maven. Somehow a dot in the groupId is translated as a / as mentioned in this doc: https://maven.apache.org/pom.html#maven-coordinates.

[klustria]

After discussing with @tomas-langer, we are not doing above workaround to add dot . at the end of the groupId, but instead stick with the existing javax.annotation:javax.annotation-api dependency library.

[klustria]

Remaining TODO in the micronaut area:

• https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L313-L329
• https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L351-L356

and

• https://github.com/oracle/helidon/blob/master/integrations/micronaut/data/src/test/java/io/helidon/integrations/micronaut/cdi/data/MicronautDataCdiExtensionTest.java#L111-L120

Per discussion with Tomas, the goal is to upgrade to the latest Micronaut libraries with the hope that they have switch to jakarta validation, but looks like this is not the case. The latest micronaut-validation-3.5.2.pom has this:

<dependency>
  <groupId>javax.validation</groupId>
  <artifactId>validation-api</artifactId>
  <version>2.0.1.Final</version>
  <scope>compile</scope>
</dependency>

which means it does not support jakarta validation.

[klustria]

Micronaut 3.5.2 guide https://docs.micronaut.io/3.5.2/guide/index.html#beanValidation and SNAPSHOT guide https://docs.micronaut.io/snapshot/guide/index.html#beanValidation both mentions:

Since Micronaut 1.2, Micronaut has built-in support for validating beans annotated with javax.validation annotations

Created PR: #4476, the goal of which is to use 2.0.2 of jakarta.validation-api instead of 3.0.0 to revert back to the use of javax.validation rather than jakarta.validation which is what even the latest version of micronaut-validation supports.

[klustria]

For the remaining TODO:

• https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L313-L329
• https://github.com/oracle/helidon/blob/master/integrations/micronaut/cdi/src/main/java/io/helidon/integrations/micronaut/cdi/MicronautCdiExtension.java#L351-L356

For this issue, I finally figured out that both bean definitions that was deemed duplicate need to be added after comparing it with v2.5.1 behavior. Here’s what I debugged for what we deemed are duplicate bean definitions:

In Helidon 2.5.1 (We add both):

io.helidon.integrations.micronaut.cdi.MicronautBean@62d0ac62 - io.helidon.integrations.micronaut.cdi.$TestMicronautBeanDefinition
io.helidon.integrations.micronaut.cdi.MicronautBean@3003697 - io.helidon.integrations.micronaut.cdi.$$TestMicronautBeanDefinition$InterceptedDefinition

In Helidon 3.0 (We sort and add only the first one)

io.helidon.integrations.micronaut.cdi.TestMicronautBean - io.helidon.integrations.micronaut.cdi.$TestMicronautBean$Definition$Intercepted$Definition
io.helidon.integrations.micronaut.cdi.TestMicronautBean - io.helidon.integrations.micronaut.cdi.$TestMicronautBean$Definition

The first field in both lists is the MicronautBean.toString() and the next field after the dash is MicronautBean.definitionRef().getBeanDefinitionName(). In Helidon 3, it looks like a duplicate and that is because toString() was overridden to return the bean type while in Helidon 2.5, it returns the object name. I have changed that to add hashCode so it will be unique. Also we don’t need to choose of which to add between the 2 bean definitions that we thought are duplicate, instead we add both just like in v2.5. So the new code will look like the same as the code prior to the Jakarta 3.0 change. PR related to the mentioned change : #4494

[klustria]

List of PRs that complete this task:

1. Updates persistence.xmls to 3.0. Re-enables JPA tests. Removes eclips… #4446
2. Fix code with 'TODO 3.0.0-JAKARTA' comment #4447
3. Re-enable Packaging Tests #4412 (as part of re-enable native image tests in pipeline on master #4341)
4. Removed final from proxied types, these could no longer be proxied. #4489 (as part of re-enable native image tests in pipeline on master #4341)
5. Revert back to using javax.validation as jakarta.validation is not supported by micronaut #4476
6. Load both bean definitions of the same type instead of choosing just one #4494

Searching TODO 3.0.0-JAKARTA in the project does not yield any more result.