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Merge pull request #2 from reactome/feature/update-pom
Feature/update pom
2 parents 84a1f20 + 3f84fcd commit e7154e9

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‎.gitignore‎

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/target/
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doisToBeUpdated-*.txt
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logs/
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target/
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# Ignore IntelliJ files
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.idea/
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update-dois.iml

‎bin/.gitignore‎

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‎bin/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"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<?xml version="1.0" encoding="UTF-8"?>
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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">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.reactome.release.updateDOIs</groupId>
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<artifactId>update-dois</artifactId>
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<packaging>jar</packaging>
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<version>1.0.2-SNAPSHOT</version>
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<packaging>jar</packaging>
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<name>update-dois</name>
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<description>
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Updates DOIs of pathways that were updated significantly between releases (these pathways will be tagged as
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needing a value in their doi attribute)
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</description>
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<url>https://reactome.org</url>
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<licenses>
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<license>
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<name>GNU AFFERO GENERAL PUBLIC LICENSE</name>
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<url>https://www.gnu.org/licenses/agpl-3.0.txt</url>
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</license>
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</licenses>
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<developers>
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<developer>
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<name>Justin Cook</name>
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<email>[email protected]</email>
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<organization>Reactome</organization>
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<organizationUrl>https://reactome.org</organizationUrl>
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</developer>
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</developers>
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<scm>
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<connection>scm:git:git://github.com/reactome/release-update-dois.git</connection>
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<developerConnection>scm:git:ssh://github.com/reactome/release-update-dois.git</developerConnection>
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<url>https://github.com/reactome/release-update-dois</url>
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<tag>develop</tag>
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</scm>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<mockito.version>2.18.3</mockito.version>
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</properties>
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<dependencies>
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<!-- Main dependencies -->
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<dependency>
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<groupId>org.reactome.release</groupId>
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<artifactId>release-common-lib</artifactId>
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<version>1.1.1-SNAPSHOT</version>
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<version>1.2.0</version>
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</dependency>
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<!-- Test dependencies -->
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.powermock</groupId>
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<artifactId>powermock-api-mockito</artifactId>
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<version>1.6.5</version>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-core</artifactId>
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<version>${mockito.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-junit-jupiter</artifactId>
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<version>${mockito.version}</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<!-- sets the Java compiler version targeted by Maven -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.7.0</version>
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<version>3.8.1</version>
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<configuration>
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<source>1.8</source>
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<target>1.8</target>
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</configuration>
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</plugin>
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<!--
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allows 'mvn clean compile assembly:single' command to create a jar with dependencies
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execution section also allows 'mvn clean package' command to create two jars - with/without dependencies
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-->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>3.2.0</version>
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<configuration>
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<archive>
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<manifest>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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</configuration>
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<executions>
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<execution>
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<id>make-assembly</id> <!-- this is used for inheritance merges -->
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<phase>package</phase> <!-- bind to the packaging phase -->
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<!--
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allows 'mvn release' command to create a new release of the project
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https://maven.apache.org/maven-release/maven-release-plugin/
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-->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-release-plugin</artifactId>
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<version>2.5.3</version>
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<configuration>
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<autoVersionSubmodules>true</autoVersionSubmodules>
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<useReleaseProfile>false</useReleaseProfile>
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<releaseProfiles>release</releaseProfiles>
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<goals>deploy</goals>
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<tagNameFormat>v@{project.version}</tagNameFormat>
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</configuration>
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</plugin>
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<!--
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checks the POM file has the order specified by the POM Code Convention
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http://maven.apache.org/developers/conventions/code.html#POM_Code_Convention
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-->
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>tidy-maven-plugin</artifactId>
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<version>1.1.0</version>
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<executions>
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<execution>
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<id>validate</id>
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<phase>validate</phase>
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<goals>
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<goal>check</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>

‎src/test/java/org/reactome/release/updateDOIs/AppTest.java‎

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