Updated to Jakarta JAXB and Java 17 (ref: #1075)#1076
Updated to Jakarta JAXB and Java 17 (ref: #1075)#1076josemduarte merged 3 commits intobiojava:masterfrom
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I didn't test it, because I assumed it would be a major release branch. I ran it on Java 19 with a target level of 17. I can do it when I get back to the office on Tuesday. Note that I also changed the release in the POM. If you want to reject the pull. I can change the version back to 7.0.3-SNAPSHOT, and test against Java 11, and create a new pull request. That might be the better way. |
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I installed JDK on my local machine and ran |
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Thanks so much. Jaxb has been quite a headache as new versions of java rolled out. Hopefully this should give us some time to breathe.
See comments about pom.
| <version>2.3.1</version> | ||
| <groupId>jakarta.xml.bind</groupId> | ||
| <artifactId>jakarta.xml.bind-api</artifactId> | ||
| <version>4.0.0</version> |
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I think versions should be declared in this top pom.xml only (note this is the dependencyManagement section) and not in the modules. Then we have centralised version management.
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Removed explicit versions and scope from POM as required.
biojava-structure/pom.xml
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| <artifactId>jaxb-api</artifactId> | ||
| <groupId>jakarta.xml.bind</groupId> | ||
| <artifactId>jakarta.xml.bind-api</artifactId> | ||
| <version>4.0.0</version> |
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Please remove version here. It should be only in dependencyManagement in top pom.xml
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Removed explicit versions and scope from POM as required.
biojava-structure/pom.xml
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| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| <version>4.0.3</version> | ||
| <scope>runtime</scope> |
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-protein-disorder/pom.xml
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| <artifactId>jaxb-api</artifactId> | ||
| <groupId>jakarta.xml.bind</groupId> | ||
| <artifactId>jakarta.xml.bind-api</artifactId> | ||
| <version>4.0.0</version> |
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Please remove version here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-protein-disorder/pom.xml
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| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| <version>4.0.3</version> | ||
| <scope>runtime</scope> |
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-modfinder/pom.xml
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| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| <version>4.0.3</version> | ||
| <scope>runtime</scope> |
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-core/pom.xml
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| <artifactId>jaxb-api</artifactId> | ||
| <groupId>jakarta.xml.bind</groupId> | ||
| <artifactId>jakarta.xml.bind-api</artifactId> | ||
| <version>4.0.0</version> |
There was a problem hiding this comment.
Please remove version here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-core/pom.xml
Outdated
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| <version>4.0.3</version> | ||
| <scope>runtime</scope> |
There was a problem hiding this comment.
Please remove version and scope here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-aa-prop/pom.xml
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| <artifactId>jaxb-api</artifactId> | ||
| <groupId>jakarta.xml.bind</groupId> | ||
| <artifactId>jakarta.xml.bind-api</artifactId> | ||
| <version>4.0.0</version> |
There was a problem hiding this comment.
Please remove version here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
biojava-aa-prop/pom.xml
Outdated
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| <version>4.0.3</version> | ||
| <scope>runtime</scope> |
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Please remove version and scope here. It should be only in dependencyManagement in top pom.xml
There was a problem hiding this comment.
Removed explicit versions and scope from POM as required.
… dependencyManagement section in the POM. Reran unit tests with no errors.
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Removed explicit scope and version, except in the dependency management section of the POM. Re-compiled and ran unit tests with no error. |
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It appears that openchart was removed from the JBoss Maven repository. I looked and it isn't on Maven Central, either. I Googled around and can't seem to find any mention of it. |
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I took a look at my local repository, and openchart was there on May 26, 2023 when I first compiled biojava. I looked inside the jar, and it was compiled November 28, 2008, so it appears to not be an active project. |
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Thanks for the changes! LGTM
Thanks also for checking the openchart dependency. I was fearing it would disappear one day from jboss repo. Since you've tested already, I think we can merge this for now and see how to get rid of the openchart dependency in another PR.
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I changed the version in the POM to v8, since another issue indicated that the change would be a version change. Other than that, I just used the Intellij IDEA Refactor/Migrate... to change the package names and updated the POMs accordingly. No other functional code changes were made. The unit tests passed.