Change JAXB implementation for better java version compatibility #996
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,80 +1,88 @@ | ||
| <?xml version="1.0"?> | ||
| <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <parent> | ||
| <artifactId>biojava</artifactId> | ||
| <groupId>org.biojava</groupId> | ||
| <version>6.0.1-SNAPSHOT</version> | ||
| </parent> | ||
| <artifactId>biojava-modfinder</artifactId> | ||
| <name>biojava-modfinder</name> | ||
| <url>http://www.biojava.org</url> | ||
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| <licenses> | ||
| <license> | ||
| <name>GNU LGPL v2</name> | ||
| <url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url> | ||
| <distribution>repo</distribution> | ||
| </license> | ||
| </licenses> | ||
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| <properties> | ||
| <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> | ||
| <project.build.targetEncoding>UTF-8</project.build.targetEncoding> | ||
| </properties> | ||
| <dependencies> | ||
| <dependency> | ||
| <groupId>junit</groupId> | ||
| <artifactId>junit</artifactId> | ||
| <scope>test</scope> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.biojava</groupId> | ||
| <artifactId>biojava-structure</artifactId> | ||
| <version>6.0.1-SNAPSHOT</version> | ||
| <type>jar</type> | ||
| <scope>compile</scope> | ||
| </dependency> | ||
| <!-- logging dependencies (managed by parent pom, don't set versions or scopes here) --> | ||
| <dependency> | ||
| <groupId>org.slf4j</groupId> | ||
| <artifactId>slf4j-api</artifactId> | ||
| </dependency> | ||
| <!-- binding for log4j2, scope=runTime set in parent pom --> | ||
| <dependency> | ||
| <groupId>org.apache.logging.log4j</groupId> | ||
| <artifactId>log4j-slf4j-impl</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.apache.logging.log4j</groupId> | ||
| <artifactId>log4j-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.apache.logging.log4j</groupId> | ||
| <artifactId>log4j-core</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>javax.xml.bind</groupId> | ||
| <artifactId>jaxb-api</artifactId> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>org.glassfish.jaxb</groupId> | ||
| <artifactId>jaxb-runtime</artifactId> | ||
| </dependency> | ||
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Contributor
There was a problem hiding this comment. It looks like biojava-modfinder did not have an xml dependency before. I think this is not needed here |
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| </dependencies> | ||
| <build> | ||
| <plugins> | ||
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| <!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 --> | ||
| <plugin> | ||
| <groupId>org.apache.maven.plugins</groupId> | ||
| <artifactId>maven-jar-plugin</artifactId> | ||
| <configuration> | ||
| <excludes> | ||
| <exclude>demo/**</exclude> | ||
| </excludes> | ||
| </configuration> | ||
| </plugin> | ||
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| <plugin> | ||
| <groupId>org.apache.maven.plugins</groupId> | ||
| <artifactId>maven-compiler-plugin</artifactId> | ||
| <configuration> | ||
| <debug>true</debug> | ||
| </configuration> | ||
| </plugin> | ||
| </plugins> | ||
| </build> | ||
| </project> | ||
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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.