Change JAXB implementation for better java version compatibility #996
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- Downgrade jgrapht to maintain java 8 support - Switch JAXB to glassfish implementation for better java 15+ support
josemduarte
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josemduarte
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Thanks! good catch about jgrapht dependency. I think we'll need a new bugfix release soon to keep the java-8 compatibility.
See comments below
| <dependency> | ||
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| </dependency> |
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It looks like biojava-aa-prop did not have an xml dependency before. I think this is not needed here
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I got test failures without it ('No JAXP implementation found'). I think it was serendipitously included before since we were using the com.sun namespace, but that the glassfish implementation needs to be specifically included. I have included it on all modules that import javax.xml.bind.
| <dependency> | ||
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| </dependency> |
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It looks like biojava-core did not have an xml dependency before. I think this is not needed here
| <dependency> | ||
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| </dependency> |
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It looks like biojava-modfinder did not have an xml dependency before. I think this is not needed here
This also works with Java 8
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There was an issue with running CeSymm on java 15+ (rcsb/symmetry#104). I suspect that this issue effected all projects that include biojava with the maven-shade-plugin. I was able to trace the problem back to the old com.sun.xml.bind implementations. Switching these to the glassfish JAXB implementation fixed the problem.