pom.xml

<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">
    <modelVersion>4.0.0</modelVersion>
    <groupId>org.isatools</groupId>
    <artifactId>ISAcreator</artifactId>
    <packaging>bundle</packaging>
    <version>1.7.12</version>
    <name>ISAcreator</name>
    <url>http://www.isa-tools.org</url>

    <developers>

        <developer>
            <id>agbeltran</id>
            <name>Alejandra Gonzalez-Beltran</name>
            <email>alejandra.gonzalez.beltran@gmail.com</email>
            <organization>ISA tools team</organization>
            <organizationUrl>http://isa-tools.org</organizationUrl>
        </developer>

        <developer>
            <id>djcomlab</id>
            <name>David Johnson</name>
            <email>djcomlab@gmail.com</email>
            <organization>ISA tools team</organization>
            <organizationUrl>http://isa-tools.org</organizationUrl>
        </developer>
    </developers>

    <licenses>
        <license>
            <name>CPAL</name>
            <distribution>Version 1.0</distribution>
            <url>https://raw.githubusercontent.com/ISA-tools/ISAcreator/master/LICENSE.txt</url>
        </license>
    </licenses>

    <scm>
        <url>http://www.github.com/ISA-tools/ISAcreator</url>
    </scm>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <repositories>
        <repository>
            <id>oerc</id>
            <url>http://frog.oerc.ox.ac.uk:8080/nexus-2.1.2/content/groups/oerc</url>
        </repository>

        <repository>
            <id>mvnrepository</id>
            <url>http://www.mvnrepository.com/</url>
        </repository>

        <repository>
            <id>atlassian</id>
            <url>https://m2proxy.atlassian.com/repository/public</url>
        </repository>

        <repository>
            <id>java-dev</id>
            <url>http://download.java.net/maven/2/</url>
        </repository>


    </repositories>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.0</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                    <!--<executable>apt</executable>-->
                    <fork>true</fork>
                    <debug>true</debug>

                    <meminitial>128m</meminitial>
                    <maxmem>512m</maxmem>
                </configuration>
            </plugin>


            <plugin>
                <groupId>org.apache.felix</groupId>
                <artifactId>maven-bundle-plugin</artifactId>
                <version>2.2.0</version>
                <extensions>true</extensions>
                <configuration>
                    <instructions>
                        <Bundle-Activator>org.isatools.isacreator.launch.ISAcreatorActivator</Bundle-Activator>
                        <Bundle-Vendor>ISA team, http://isa-tools.org</Bundle-Vendor>
                    </instructions>
                </configuration>
            </plugin>


            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <archive>
                        <manifestFile>src/main/resources/META-INF/MANIFEST.MF</manifestFile>
                        <!--these properties are ignored-->
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                        </manifest>
                    </archive>

                    <archiverConfig>
                        <duplicateBehavior>skip</duplicateBehavior>
                    </archiverConfig>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>

                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <phase>package</phase>
                        <goals>
                            <goal>attached</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-pmd-plugin</artifactId>
                <version>2.3</version>

                <configuration>
                    <targetJdk>1.5</targetJdk>
                </configuration>
            </plugin>


            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>3.0.0</version>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>xmlbeans-maven-plugin</artifactId>
                <version>2.3.3</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>xmlbeans</goal>
                        </goals>
                    </execution>
                </executions>
                <inherited>true</inherited>
                <configuration>
                    <schemaDirectory>${project.basedir}/src/main/resources/xsd</schemaDirectory>
                    <sourceGenerationDirectory>
                        ${project.basedir}/target/generated/xmlbeans
                    </sourceGenerationDirectory>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.jvnet.jax-ws-commons</groupId>
                <artifactId>jaxws-maven-plugin</artifactId>
                <version>2.2</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>wsimport</goal>
                        </goals>
                        <configuration>

                            <wsdlUrls>
                                <wsdlUrl>https://www.ebi.ac.uk/europepmc/webservices/soap?wsdl</wsdlUrl>
                            </wsdlUrls>
                            <packageName>uk.ac.ebi.cdb.client</packageName>
                            <sourceDestDir>target/generated/citexplore</sourceDestDir>
                            <!-- Without this, multiple WSDLs won't be processed :( -->
                            <staleFile>${project.build.directory}/jaxws/stale/wsdl.cdb.done</staleFile>
                        </configuration>
                    </execution>

                </executions>

                <dependencies>

                    <dependency>
                        <groupId>com.sun.xml.ws</groupId>
                        <artifactId>jaxws-tools</artifactId>
                        <version>2.1.7</version>
                        <exclusions>
                            <exclusion>
                                <groupId>org.jvnet.staxex</groupId>
                                <artifactId>stax-ex</artifactId>
                            </exclusion>
                        </exclusions>
                    </dependency>

                    <dependency>
                        <groupId>org.jvnet.staxex</groupId>
                        <artifactId>stax-ex</artifactId>
                        <version>1.2</version>
                        <exclusions>
                            <exclusion>
                                <groupId>javax.xml.stream</groupId>
                                <artifactId>stax-api</artifactId>
                            </exclusion>
                        </exclusions>
                    </dependency>

                </dependencies>

            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>1.5</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <!--<artifactSet>-->
                                <!--<excludes>-->
                                    <!--<exclude>org.apache.lucene:lucene-core</exclude>-->
                                    <!--<exclude>lucene:*</exclude>-->
                                <!--</excludes>-->
                            <!--</artifactSet>-->
                            <createDependencyReducedPom>false</createDependencyReducedPom>
                            <transformers>
                                <transformer
                                        implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.eluder.coveralls</groupId>
                <artifactId>coveralls-maven-plugin</artifactId>
                <version>4.3.0</version>
            </plugin>

            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.7.6.201602180812</version>
                <executions>
                    <execution>
                        <id>prepare-agent</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

        </plugins>

        <resources>
            <!-- defines the files to be filtered -->
            <resource>
                <directory>${project.basedir}/src/main/resources</directory>
                <filtering>true</filtering>
                <includes>
                    <include>**/*.properties</include>
                </includes>
            </resource>
            <!--   defines the files to copy unaltered  -->
            <resource>
                <directory>${project.basedir}/src/main/resources</directory>
                <filtering>false</filtering>
                <excludes>
                    <exclude>**/*.properties</exclude>
                </excludes>
            </resource>
        </resources>

    </build>

    <dependencyManagement>
        <dependencies>

            <dependency>
                <groupId>net.java.dev.fuse</groupId>
                <artifactId>fuse-core</artifactId>
                <version>0.4</version>
            </dependency>

            <dependency>
                <groupId>commons-net</groupId>
                <artifactId>commons-net</artifactId>
                <version>2.0</version>
            </dependency>

            <dependency>
                <groupId>commons-io</groupId>
                <artifactId>commons-io</artifactId>
                <version>2.7</version>
            </dependency>

            <dependency>
                <groupId>net.sourceforge.collections</groupId>
                <artifactId>collections-generic</artifactId>
                <version>4.01</version>
            </dependency>

            <dependency>
                <groupId>net.sf.opencsv</groupId>
                <artifactId>opencsv</artifactId>
                <version>2.1</version>
            </dependency>

            <dependency>
                <groupId>prefuse</groupId>
                <artifactId>prefuse</artifactId>
                <version>1.0.1</version>
            </dependency>

            <dependency>
                <groupId>org.profusians</groupId>
                <artifactId>profusians</artifactId>
                <version>beta-20080629</version>
            </dependency>

            <dependency>
                <groupId>net.minidev</groupId>
                <artifactId>json-smart</artifactId>
                <version>2.0-RC3</version>
            </dependency>

            <dependency>
                <groupId>commons-lang</groupId>
                <artifactId>commons-lang</artifactId>
                <version>2.4</version>
            </dependency>

            <dependency>
                <groupId>javax.xml.ws</groupId>
                <artifactId>jaxws-api</artifactId>
                <version>2.2.5</version>
            </dependency>

            <dependency>
                <groupId>javax.activation</groupId>
                <artifactId>activation</artifactId>
                <version>1.1</version>
            </dependency>

            <dependency>
                <groupId>javax.xml.bind</groupId>
                <artifactId>jaxb-api</artifactId>
                <version>2.2.3</version>
            </dependency>

            <dependency>
                <groupId>javax.jws</groupId>
                <artifactId>jsr181-api</artifactId>
                <version>1.0-MR1</version>
            </dependency>

            <dependency>
                <groupId>xml-apis</groupId>
                <artifactId>xml-apis</artifactId>
                <version>1.3.02</version>
            </dependency>

            <dependency>
                <groupId>stax</groupId>
                <artifactId>stax-api</artifactId>
                <version>1.0.1</version>
            </dependency>

            <dependency>
                <groupId>net.sourceforge.jexcelapi</groupId>
                <artifactId>jxl</artifactId>
                <version>2.6.3</version>
                <exclusions>
                    <exclusion>
                        <artifactId>log4j</artifactId>
                        <groupId>log4j</groupId>
                    </exclusion>
                </exclusions>
            </dependency>

            <dependency>
                <groupId>org.apache.xmlbeans</groupId>
                <artifactId>xmlbeans</artifactId>
                <version>3.0.0</version>
            </dependency>

            <dependency>
                <groupId>log4j</groupId>
                <artifactId>log4j</artifactId>
                <version>2.17.2</version>
            </dependency>

            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.13.1</version>
                <scope>test</scope>
            </dependency>

            <dependency>
                <groupId>org.isatools</groupId>
                <artifactId>ISAtabErrorReporter</artifactId>
                <version>0.6</version>
            </dependency>

            <dependency>
                <groupId>com.explodingpixels</groupId>
                <artifactId>scroller</artifactId>
                <version>0.1</version>
            </dependency>

            <dependency>
                <groupId>uk.ac.ebi</groupId>
                <artifactId>jutils</artifactId>
                <version>1.4</version>

                <exclusions>
                    <exclusion>
                        <artifactId>slf4j-api</artifactId>
                        <groupId>org.slf4j</groupId>
                    </exclusion>

                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-log4j12</artifactId>
                    </exclusion>
                </exclusions>

            </dependency>

            <dependency>
                <groupId>org.apache.felix</groupId>
                <artifactId>org.apache.felix.main</artifactId>
                <version>4.2.1</version>
            </dependency>

            <dependency>
                <groupId>org.apache.felix</groupId>
                <artifactId>org.apache.felix.framework</artifactId>
                <version>4.2.1</version>
            </dependency>

            <dependency>
                <groupId>org.isatools</groupId>
                <artifactId>import_layer</artifactId>
                <version>1.6.8</version>
                <exclusions>
                    <exclusion>
                        <groupId>uk.ac.ebi</groupId>
                        <artifactId>ols</artifactId>
                    </exclusion>

                    <exclusion>
                        <groupId>uk.ac.ebi</groupId>
                        <artifactId>jutils</artifactId>
                    </exclusion>

                    <exclusion>
                        <groupId>cpdetector</groupId>
                        <artifactId>cpdetector</artifactId>
                    </exclusion>

                    <exclusion>
                        <groupId>org.isatools</groupId>
                        <artifactId>ISAtabErrorReporter</artifactId>
                    </exclusion>

                </exclusions>
            </dependency>


            <!-- Dependencies for GS code -->
            <dependency>
                <groupId>genomespace</groupId>
                <artifactId>cdk</artifactId>
                <version>1.0</version>
            </dependency>

            <dependency>
                <groupId>genomespace</groupId>
                <artifactId>dm-messages</artifactId>
                <version>1.0</version>
            </dependency>

            <dependency>
                <groupId>com.google.zxing</groupId>
                <artifactId>core</artifactId>
                <version>2.1</version>
            </dependency>

            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
                <version>3.1.0</version>
                <exclusions>
                    <exclusion>
                        <artifactId>
                            com.springsource.org.apache.commons.codec
                        </artifactId>
                        <groupId>org.apache.commons</groupId>
                    </exclusion>


                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-api</artifactId>
                    </exclusion>

                    <exclusion>
                        <groupId>org.slf4j</groupId>
                        <artifactId>slf4j-log4j12</artifactId>
                    </exclusion>

                </exclusions>
                <!--<scope>runtime</scope>-->
            </dependency>

        </dependencies>
    </dependencyManagement>

    <dependencies>

        <dependency>
            <groupId>net.java.dev.fuse</groupId>
            <artifactId>fuse-core</artifactId>
        </dependency>

        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
        </dependency>

        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>

        <dependency>
            <groupId>net.sourceforge.collections</groupId>
            <artifactId>collections-generic</artifactId>
        </dependency>

        <dependency>
            <groupId>net.sf.opencsv</groupId>
            <artifactId>opencsv</artifactId>
        </dependency>

        <dependency>
            <groupId>prefuse</groupId>
            <artifactId>prefuse</artifactId>
        </dependency>

        <dependency>
            <groupId>org.profusians</groupId>
            <artifactId>profusians</artifactId>
        </dependency>

        <dependency>
            <groupId>net.minidev</groupId>
            <artifactId>json-smart</artifactId>
        </dependency>

        <dependency>
            <groupId>commons-lang</groupId>
            <artifactId>commons-lang</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.xml.ws</groupId>
            <artifactId>jaxws-api</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.activation</groupId>
            <artifactId>activation</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.xml.bind</groupId>
            <artifactId>jaxb-api</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.jws</groupId>
            <artifactId>jsr181-api</artifactId>
        </dependency>

        <dependency>
            <groupId>xml-apis</groupId>
            <artifactId>xml-apis</artifactId>
        </dependency>

        <dependency>
            <groupId>stax</groupId>
            <artifactId>stax-api</artifactId>
        </dependency>

        <dependency>
            <groupId>net.sourceforge.jexcelapi</groupId>
            <artifactId>jxl</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.xmlbeans</groupId>
            <artifactId>xmlbeans</artifactId>
            <version>3.0.0</version>
        </dependency>

        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
        </dependency>

        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.isatools</groupId>
            <artifactId>ISAtabErrorReporter</artifactId>
        </dependency>

        <dependency>
            <groupId>com.explodingpixels</groupId>
            <artifactId>scroller</artifactId>
        </dependency>

        <dependency>
            <groupId>uk.ac.ebi</groupId>
            <artifactId>jutils</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.felix</groupId>
            <artifactId>org.apache.felix.main</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.felix</groupId>
            <artifactId>org.apache.felix.framework</artifactId>
        </dependency>

        <dependency>
            <groupId>org.isatools</groupId>
            <artifactId>import_layer</artifactId>
        </dependency>


        <!-- Dependencies for GS code -->
        <dependency>
            <groupId>genomespace</groupId>
            <artifactId>cdk</artifactId>
        </dependency>

        <dependency>
            <groupId>genomespace</groupId>
            <artifactId>dm-messages</artifactId>
        </dependency>

        <dependency>
            <groupId>com.google.zxing</groupId>
            <artifactId>core</artifactId>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
        </dependency>

        <dependency>
            <groupId>genomespace</groupId>
            <artifactId>org.genomespace.jersey-apache-client</artifactId>
            <version>1.11</version>
            <scope>runtime</scope>
        </dependency>


        <dependency>
            <groupId>genomespace</groupId>
            <artifactId>identityServer-messages</artifactId>
            <version>1.0</version>
            <scope>runtime</scope>
        </dependency>

        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-bundle</artifactId>
            <version>1.11</version>
        </dependency>

        <dependency>
            <groupId>com.sun.jersey.contribs</groupId>
            <artifactId>jersey-multipart</artifactId>
            <version>1.18</version>
        </dependency>

        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-json</artifactId>
            <version>1.11</version>
            <scope>runtime</scope>
        </dependency>

        <dependency>
            <groupId>com.amazonaws</groupId>
            <artifactId>aws-java-sdk</artifactId>
            <version>1.3.0</version>
        </dependency>

        <dependency>
            <groupId>org.jets3t</groupId>
            <artifactId>com.springsource.org.jets3t</artifactId>
            <version>0.8.0</version>
        </dependency>

        <dependency>
            <groupId>org.glassfish</groupId>
            <artifactId>javax.json</artifactId>
            <version>1.0</version>
        </dependency>

    </dependencies>

    <profiles>
        <!--<profile>-->
            <!--<id>default-tools.jar</id>-->
            <!--<activation>-->
                <!--<property>-->
                    <!--<name>java.vendor</name>-->
                    <!--<value>Sun Microsystems Inc.</value>-->
                <!--</property>-->
            <!--</activation>-->
            <!--<dependencies>-->
                <!--<dependency>-->
                    <!--<groupId>com.sun</groupId>-->
                    <!--<artifactId>tools</artifactId>-->
                    <!--<version>1.4.2</version>-->
                    <!--<scope>system</scope>-->
                    <!--<systemPath>${java.home}/../lib/tools.jar</systemPath>-->
                <!--</dependency>-->
            <!--</dependencies>-->
        <!--</profile>-->

        <profile>
            <id>toxbank</id>
            <properties>
                <isacreator.alwaysShowInvestigation>true</isacreator.alwaysShowInvestigation>
            </properties>

        </profile>

        <profile>
            <id>build</id>
            <properties>
                <isacreator.version>${project.version}</isacreator.version>
                <isacreator.alwaysShowInvestigation>false</isacreator.alwaysShowInvestigation>
            </properties>

        </profile>
    </profiles>


    <distributionManagement>
        <repository>
            <id>oerc-repo</id>
            <name>OeRC Maven repository</name>
            <url>http://frog.oerc.ox.ac.uk:8080/nexus-2.1.2/content/repositories/releases</url>
        </repository>
    </distributionManagement>


</project>