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pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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/maven-v4_0_0.xsd">
<properties>
<bundle.symbolicName>org.bridgedb.cytoscape</bundle.symbolicName>
<bundle.namespace>org.bridgedb.cytoscape</bundle.namespace>
<cytoscape.api.version>3.1.0</cytoscape.api.version>
<bridgedb.version>2.3.0</bridgedb.version>
</properties>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bridgedb</groupId>
<artifactId>bridgedb.cytoscape.app</artifactId>
<version>1.2.0</version>
<name>BridgeDb</name>
<packaging>bundle</packaging>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/main/lib</directory>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<executions>
<execution>
<id>default-testCompile</id>
<phase>test-compile</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>default-compile</id>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
<configuration>
<source>1.8</source>
<target>1.8</target>
<optimize>true</optimize>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
<compilerArguments>
<Xmaxwarns>10000</Xmaxwarns>
<Xmaxerrs>10000</Xmaxerrs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7.1</version>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
</plugin>
<!-- Generates the OSGi metadata based on the osgi.bnd file. -->
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.2.0</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
<Export-Package>${bundle.namespace}</Export-Package>
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
<Bundle-Activator>${bundle.namespace}.internal.BridgeDbApp</Bundle-Activator>
<!--<Embed-Dependency>groupId=org.bridgedb;scope=compile|runtime;inline=true</Embed-Dependency>-->
<!--embed all dependencies except the ones with scpe provided-->
<Embed-Dependency>*;scope=!provided</Embed-Dependency>
<Embed-Transitive>true</Embed-Transitive>
<Import-Package>*;resolution:=optional</Import-Package>
<Bundle-Name>BridgeDb</Bundle-Name>
<!--
<Embed-Dependency>*;scope=!provided;type=!pom;inline=true</Embed-Dependency>
<Import-Package>javax.crypto,javax.crypto.interfaces,jav
ax.crypto.spec,javax.jws,javax.management,javax.naming,javax.naming.dir
ectory,javax.naming.spi,javax.net,javax.net.ssl,javax.security.auth,jav
ax.sql,javax.swing,javax.swing.border,javax.swing.event,javax.swing.pla
f,javax.swing.table,javax.swing.tree,javax.xml.bin
d.annotation,javax.xml.datatype,javax.xml.namespace,javax.xml.parsers,j
avax.xml.transform,javax.xml.transform.dom,javax.xml.transform.stream,j
avax.xml.ws,javax.xml.ws.soap,org.cytoscape.application;version="[3.1
,4)",org.cytoscape.application.swing;version="[3.1,4)",org.cytoscape.fi
lter.model;version="[3.1,4)",org.cytoscape.model;version="[3.1,4)",org.
cytoscape.model.subnetwork;version="[3.1,4)",org.cytoscape.property;ver
sion="[3.1,4)",org.cytoscape.service.util;version="[3.1,4)",org.cytosca
pe.session;version="[3.1,4)",org.cytoscape.util.swing;version="[3.1,4)"
,org.cytoscape.view.model;version="[3.1,4)",org.cytoscape.view.presenta
tion;version="[3.1,4)",org.cytoscape.view.vizmap;version="[3.1,4)",org.
cytoscape.work;version="[3.1,4)",org.cytoscape.work.swing;version="[3.1
,4)",org.cytoscape.work.util;version="[3.1,4)",org.osgi.framework;versi
on="[1.5,2)",org.slf4j;version="[1.5,2)",org.w3c.dom,org.xml.sax,*;resolution:=optional
</Import-Package>
-->
</instructions>
<archive>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<!-- Links to the Cytoscape Maven repositories. -->
<repositories>
<repository>
<id>cytoscape_snapshots</id>
<snapshots>
</snapshots>
<releases>
<enabled>false</enabled>
</releases>
<name>Cytoscape Snapshots</name>
<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
</repository>
<repository>
<id>cytoscape_releases</id>
<snapshots>
<enabled>false</enabled>
</snapshots>
<releases>
</releases>
<name>Cytoscape Releases</name>
<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
</repository>
<repository>
<id>apache-repo-releases</id>
<url>https://repository.apache.org/content/repositories/</url>
<releases>
<enabled>true</enabled>
</releases>
</repository>
<repository>
<id>com.springsource.repository.bundles.release</id>
<name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Releases</name>
<url>http://repository.springsource.com/maven/bundles/release</url>
</repository>
<repository>
<id>com.springsource.repository.bundles.external</id>
<name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name>
<url>http://repository.springsource.com/maven/bundles/external</url>
</repository>
<!-- <repository> -->
<!-- <id>repo</id> -->
<!-- <releases> -->
<!-- <enabled>true</enabled> -->
<!-- <checksumPolicy>ignore</checksumPolicy> -->
<!-- </releases> -->
<!-- <snapshots> -->
<!-- <enabled>false</enabled> -->
<!-- </snapshots> -->
<!-- <url>file://${project.basedir}/repo</url> -->
<!-- </repository> -->
</repositories>
<!-- Dependencies needed to compile this project. -->
<dependencies>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
<version>4.2.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>service-api</artifactId>
<version>${cytoscape.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
<version>${cytoscape.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
<version>${cytoscape.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-util-api</artifactId>
<version>${cytoscape.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
<!-- Logging -->
<dependency>
<groupId>org.ops4j.pax.logging</groupId>
<artifactId>pax-logging-api</artifactId>
<version>1.5.2</version>
<scope>provided</scope>
</dependency>
<!-- <dependency>
<groupId>org.bridgedb</groupId>
<artifactId>bridgedb</artifactId>
<version>2.0.0</version>
<optional>true</optional>
<scope>system</scope>
<systemPath>${project.basedir}/localRepo/org.bridgedb.jar</systemPath>
</dependency>
-->
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.bio</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb.construct</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb.webservice</groupId>
<artifactId>org.bridgedb.webservice.bridgerest</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb.webservice</groupId>
<artifactId>org.bridgedb.webservice.biomart</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb.webservice</groupId>
<artifactId>org.bridgedb.webservice.picr</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb.webservice</groupId>
<artifactId>org.bridgedb.webservice.synergizer</artifactId>
<version>${bridgedb.version}</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>synergizer-client</artifactId>
<version>1.1.0</version>
<optional>true</optional>
<scope>system</scope>
<systemPath>${project.basedir}/localRepo/synergizer-client-1.1.0.jar</systemPath>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>10.5.3.0_1</version>
</dependency>
</dependencies>
</project>