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pom.xml
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pom.xml
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<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>
<groupId>org.bgee</groupId>
<artifactId>bgee-applications</artifactId>
<version>15</version>
</parent>
<artifactId>bgee-pipeline</artifactId>
<packaging>jar</packaging>
<name>bgee-pipeline</name>
<dependencies>
<!-- The API will be used to access he DAOManager and the TransferObjects,
otherwise, the MySQL layer will be used directly. -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>bgee-dao-api</artifactId>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>bgee-dao-api</artifactId>
<type>test-jar</type>
</dependency>
<!-- The pipeline is allowed to access directly the MySQL layer.
Notably, the insertion/update queries are not part of the API. -->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>bgee-dao-sql</artifactId>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>bgee-core</artifactId>
</dependency>
<dependency>
<groupId>org.bgee.log4jdbc-log4j2</groupId>
<artifactId>log4jdbc-log4j2-jdbc4.1</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.bbop</groupId>
<artifactId>OWLTools-all</artifactId>
</dependency>
<dependency>
<groupId>org.bbop</groupId>
<artifactId>OWLTools-ncbi</artifactId>
</dependency>
<dependency>
<groupId>sbc</groupId>
<artifactId>orthoxml</artifactId>
</dependency>
<dependency>
<groupId>net.sf.supercsv</groupId>
<artifactId>super-csv</artifactId>
</dependency>
<dependency>
<groupId>net.sf.supercsv</groupId>
<artifactId>super-csv-dozer</artifactId>
</dependency>
</dependencies>
<build>
<finalName>bgee-pipeline-${project.version}</finalName>
<plugins>
<!-- Define System properties allowing to correctly configure logging levels
for SLF4J SimpleLogger, and for package java.util.logging, during unit tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<systemPropertyVariables>
<java.util.logging.config.file>${basedir}/src/test/resources/jdkLogConfig.properties</java.util.logging.config.file>
<org.slf4j.simpleLogger.defaultLogLevel>warn</org.slf4j.simpleLogger.defaultLogLevel>
</systemPropertyVariables>
</configuration>
</plugin>
<!-- The use of the maven-assembly-plugin has been replaced by
the maven-shade-plugin, because it allows to manage files from the dependencies
included. <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-assembly-plugin</artifactId>
<configuration> <descriptorRefs> <descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs> <archive> <manifest> <mainClass>org.bgee.pipeline.CommandRunner</mainClass>
</manifest> </archive> </configuration> <executions> <execution> <id>make-assembly</id>
<phase>package</phase> <goals> <goal>single</goal> </goals> </execution>
</executions> </plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>with-dependencies</shadedClassifierName>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<file>${project.groupId}:bgee-dao-sql:with-dependencies</file>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>org.bgee.pipeline.CommandRunner</Main-Class>
<!-- in order to be able to modify
logging levels from config files in same directors as the jar, without recompiling -->
<Class-Path>./</Class-Path>
</manifestEntries>
</transformer>
<!-- To be able to configure loggers from
files external to the jar, and to make sure our conf. files are not overridden
by a file with identical name in a dependency. If we didn't exclude these
files from the jar, they would have preeminence over the external files.
Our property files will be exported to the target directory, see end of this
pom.xml. -->
<transformer
implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
<resource>log4j2.xml</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
<resource>log4j.properties</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
<resource>jdkLogConfig.properties</resource>
</transformer>
<!-- If we wanted to put these configuration
files only in the jar, and to make sure they are not overridden by files
with identical name in a dependency, we should do: -->
<!-- <transformer implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<resource>log4j2.xml</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<resource>log4j.properties</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
<resource>jdkLogConfig.properties</resource>
</transformer> -->
<!-- If we needed to merge them instead,
see org.apache.maven.plugins.shade.resource.AppendingTransformer and org.apache.maven.plugins.shade.resource.XmlAppendingTransformer -->
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<!-- In order to export logger configuration files to the target
directory, for easier external configuration. -->
<resources>
<resource>
<directory>src/main/resources</directory>
<targetPath>${project.build.directory}</targetPath>
<includes>
<include>log4j2.xml</include>
<include>log4j.properties</include>
<include>jdkLogConfig.properties</include>
</includes>
</resource>
</resources>
</build>
</project>