Migrate onto Java21

[averyniceday]

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

• complete migration to Java21
• Review Manda's 3 PRs

Technical Description (How are we going to achieve the above)

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes

[mandawilson]

PRs (but update them with the latest cbioportal before merging them):

• Upgrade to java 21 genome-nexus/genome-nexus-annotation-pipeline#272
• Upgrade to Java 21 cmo-pipelines#1100
• https://github.com/knowledgesystems/pipelines/pull/460

[mandawilson]

CMO pipelines (though some of these applied to pipelines and/or genome-nexus-annotation-pipeline):

Upgrade to Spring 5.3.31
:
Spring JDK version support
https://github.com/spring-projects/spring-framework/wiki/Spring-Framework-Versions#
Spring Framework 5.3.x: JDK 8-21 (as of 5.3.26)

Upgrade to Spring boot 2.7.18:
Looks like spring boot is 2.3.3.RELEASE, but that according to this:
https://spring.io/blog/2023/11/16/spring-framework-5-3-31-and-6-0-14-available-now/
Spring Framework 5.3.31 comes with Spring Boot 2.7.18

Switch to mysql.com mysql-connector-j Only needed for cmo-pipelines. Pipelines didn't need this update but we did it anyway:
[ERROR] 'dependencies.dependency.version' for mysql:mysql-connector-java:jar is missing. @ line 51, column 17

Update to 3.5.1 for the maven shade plugin:
Unable to parse configuration of mojo org.apache.maven.plugins:maven-shade-plugin:2.3:shade for parameter transformers: Cannot load implementation hint 'org.springframework.boot.maven.PropertiesMergingResourceTransformer': org/apache/maven/plugins/shade/resource/ReproducibleResourceTransformer: org.apache.maven.plugins.shade.resource.ReproducibleResourceTransformer

This says to update to latest version of plugin: https://stackoverflow.com/questions/55748745/unable-to-parse-configuration-of-mojo-org-apache-maven-pluginsmaven-shade-plugi

[mandawilson]

genome-nexus-annotation-pipeline:

Updating byte-buddy + mockito because of this:
Caused by: java.lang.IllegalArgumentException: Java 21 (65) is not supported by the current version of Byte Buddy which officially supports Java 20 (64) - update Byte Buddy or set net.bytebuddy.experimental as a VM property
Solution here:
raphw/byte-buddy#1396

I had trouble using a updated genome-nexus-java-api-client because I had to use a fork of the library we use to compile to code in order to compile with Java 21, and then it was throwing exceptions in the genome-nexus-annotation-pipeline because fields defined as non-optional/required in the GN swagger were not being returned to us on API calls.

[mandawilson]

We were getting this error compiling:
[ERROR] Failed to execute goal on project importer: Could not resolve dependencies for project org.mskcc.cbio:importer:jar:1.0-SNAPSHOT: Failed to collect dependencies at com.github.cbioportal.cbioportal:core:jar:d4b0655 -> com.github.cbioportal.cbioportal:security-spring:jar:d4b0655 -> com.github.cbioportal:spring-social-live:jar:40100de1ad80e2865c834f2b64b32bb6c2b368ce -> org.springframework.social:spring-social-security:jar:1.1.0.M4: Failed to read artifact descriptor for org.springframework.social:spring-social-security:jar:1.1.0.M4: Could not transfer artifact org.springframework.social:spring-social-security:pom:1.1.0.M4 from/to maven-default-http-blocker (http://0.0.0.0/): Blocked mirror for repositories: [spring-milestones (http://repo.spring.io/milestone, default, releases), org.springframework.maven.release (http://maven.springframework.org/release, default, releases), org.springframework.maven.milestone (http://maven.springframework.org/milestone, default, releases)] -> [Help 1]

We manually downloaded the jar and pom from here: https://repo.spring.io/ui/native/plugins-release/org/springframework/social/spring-social-security/1.1.0.M4/

mvn install:install-file -Dfile=spring-social-security-1.1.0.M4.jar -DpomFile=spring-social-security-1.1.0.M4.pom

We have done this for spring-social-security, spring-social-core, and spring-social-web.

mvn install:install-file -Dfile=spring-social-core-1.1.0.M4.jar -DpomFile=spring-social-core-1.1.0.M4.pom

We manually unpacked the jar in /home/wilson/.m2/repository/batik/batik/1.5/ and corrected the MANIFEST.MF file. We also had to for batik-rasterizer-1.5.jar.

DON'T DO A mvn -U clean install

jar xf batik-rasterizer-1.5.jar

jar cf batik-rasterizer-1.5.jar .

If there are other jar files then use 0 as an option.

• We pass "noteColumn=false" to the annotator POST method (a new parameter). We need to figure out if that is the correct thing to do.

[sheridancbio]

we moved the "deploy jars into production and update pipelines3 to a java21 jvm" type of tasks to the card for integrating pipelines with the new "cbioportal-core" repository.

[sheridancbio]

As things stand, both the cmo-pipelines repository and the pipelines repository have been compiled and tested (at least unit tests) under a java21 jvm. Bringing both codebases into accord with the latest version of the cbioportal codebase now requires integration with the externalized core module which is available now here: https://github.com/cBioPortal/cbioportal-core

In the current build, we are using these somewhat out of date timepoints:

cmo-pipelines

This PR knowledgesystems/cmo-pipelines#1100 builds off of the head of the master branch of cmo-pipelines. It links in dependency genome-nexus-annotation-pipeline at commit hash 0f4e72e5902e309f082083068b17bffaf2a86565 which was merged on (2023_10_11 via pr genome-nexus/genome-nexus-annotation-pipeline#267). That in turn has dependency on cbioportal at commit hash ee5802d836c05ed846d7d1ea3f584febdc07ffa8 which was merged on (2023_10_10).
So this development is about 3 months out of currency, and requires adding the new cbioportal-core repository to be made current.

pipelines

This PR https://github.com/knowledgesystems/pipelines/pull/460 builds off of the head of the master branch of pipelines. It links in dependency genome-nexus-annotation-pipeline at commit hash efd80bbbee60826dabfab1a8a26b1e2969a90508 which is part of a pending PR to genome-nexus-annotation-pipeline genome-nexus/genome-nexus-annotation-pipeline#272 which is built off the head of master. That in turn has dependency on cbioportal at commit hash ee5802d836c05ed846d7d1ea3f584febdc07ffa8 which was merged on (2023_10_10). A second direct dependency is present in pipelines on that same point in the history of cbioportal (ee5802d836c05ed846d7d1ea3f584febdc07ffa8)
So this development is also about 3 months out of currency, and requires adding the new cbioportal-core repository to be made current.

[mandawilson]

The genome-nexus-annotation-pipeline also compiles and runs tests under the Java 21 jvm.