<commit_before><?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/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.opencb.cellbase</groupId>
    <artifactId>cellbase</artifactId>
    <version>4.0.0</version>
    <packaging>pom</packaging>

    <name>CellBase project</name>
    <description>CellBase projects integrates several biological databases into a NoSQL database plus many WS to query</description>
    <url>http://www.opencb.org/subprojects/cellbase</url>

    <modules>
        <module>cellbase-app</module>
        <module>cellbase-core</module>
        <module>cellbase-mongodb</module>
        <module>cellbase-server</module>
        <module>cellbase-grpc</module>
    </modules>

    <properties>
        <cellbase.version>4.0.0</cellbase.version>
        <biodata.version>0.7.1</biodata.version>
        <java-common-libs.version>3.2.1</java-common-libs.version>
        <jackson.version>2.6.4</jackson.version>
        <jersey.version>2.22.1</jersey.version>
        <compileSource>1.8</compileSource>
        <cellbase.war.name>cellbase</cellbase.war.name>
    </properties>

    <scm>
        <url>https://github.com/opencb/cellbase</url>
        <connection>scm:git:git://github.com/opencb/cellbase.git</connection>
        <developerConnection>scm:git:git@github.com:opencb/cellbase.git</developerConnection>
    </scm>

    <licenses>
        <license>
            <name>Apache License, Version 2</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
        </license>
    </licenses>

    <developers>
        <developer>
            <id>imedina</id>
            <name>Nacho</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>javild</id>
            <name>Javier</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>pabarcgar</id>
            <name>Pablo</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>mbleda</id>
            <name>Marta</name>
            <email><EMAIL></email>
        </developer>
    </developers>

    <mailingLists>
        <mailingList>
            <name>OpenCB Mailing List</name>
            <archive>https://groups.google.com/forum/#!forum/opencb</archive>
            <post><EMAIL></post>
        </mailingList>
    </mailingLists>

    <repositories>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
            <snapshots>
                <enabled>true</enabled>
                <updatePolicy>daily</updatePolicy>
            </snapshots>
        </repository>
    </repositories>

    <dependencyManagement>
        <dependencies>
            <!-- Intra-module dependencies -->
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-core</artifactId>
                <version>${cellbase.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-grpc</artifactId>
                <version>${cellbase.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-models</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-formats</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-tools</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-lib</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-core</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-mongodb</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>

            <!-- General dependencies -->
            <dependency>
                <groupId>org.xerial</groupId>
                <artifactId>sqlite-jdbc</artifactId>
                <version>3.8.7</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java</artifactId>
                <version>3.0.0-beta-2</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java-util</artifactId>
                <version>3.0.0-beta-2</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>1.7.13</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-simple</artifactId>
                <version>1.7.13</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-databind</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.module</groupId>
                <artifactId>jackson-module-jsonSchema</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.module</groupId>
                <artifactId>jackson-dataformat-protobuf</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.containers</groupId>
                <artifactId>jersey-container-servlet</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.core</groupId>
                <artifactId>jersey-client</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.spockframework</groupId>
                <artifactId>spock-core</artifactId>
                <version>0.7-groovy-2.0</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>cglib</groupId>
                <artifactId>cglib-nodep</artifactId>
                <version>3.1</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.objenesis</groupId>
                <artifactId>objenesis</artifactId>
                <version>2.1</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.12</version>
                <scope>test</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <build>
        <sourceDirectory>src/main/java</sourceDirectory>
        <testSourceDirectory>src/test/java</testSourceDirectory>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.2</version>
                <configuration>
                    <source>${compileSource}</source>
                    <target>${compileSource}</target>
                    <showDeprecation>true</showDeprecation>
                    <showWarnings>true</showWarnings>
                    <encoding>UTF-8</encoding>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.codehaus.gmaven</groupId>
                <artifactId>gmaven-plugin</artifactId>
                <version>1.5</version>
                <configuration>
                    <providerSelection>2.0</providerSelection>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>testCompile</goal>
                        </goals>
                    </execution>
                </executions>
                <dependencies>
                    <dependency>
                        <groupId>org.codehaus.gmaven.runtime</groupId>
                        <artifactId>gmaven-runtime-2.0</artifactId>
                        <version>1.5</version>
                    </dependency>
                    <dependency>
                        <groupId>org.codehaus.groovy</groupId>
                        <artifactId>groovy-all</artifactId>
                        <version>2.0.8</version>
                    </dependency>
                </dependencies>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-checkstyle-plugin</artifactId>
                <version>2.16</version>
                <executions>
                    <execution>
                        <id>validate</id>
                        <phase>validate</phase>
                        <configuration>
                            <configLocation>checkstyle.xml</configLocation>
                            <excludes>org/opencb/cellbase/app/cli/CliOptionsParser.java,org/opencb/cellbase/app/transform/GeneParserProto.java</excludes>
                        </configuration>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <distributionManagement>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
        </repository>
        <snapshotRepository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
        </snapshotRepository>
    </distributionManagement>

    <profiles>
        <profile>
            <id>war-dev</id>
            <activation>
                <activeByDefault>false</activeByDefault>
            </activation>
            <properties>
                <cellbase.war.name>cellbase-dev-v4.0</cellbase.war.name>
            </properties>
        </profile>
        <profile>
            <id>mongodb</id>
            <activation>
                <activeByDefault>true</activeByDefault>
            </activation>
            <dependencyManagement>
                <dependencies>
                    <dependency>
                        <groupId>org.opencb.cellbase</groupId>
                        <artifactId>cellbase-mongodb</artifactId>
                        <version>${cellbase.version}</version>
                    </dependency>
                </dependencies>
            </dependencyManagement>
        </profile>
        <profile>
            <id>deploy</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-source-plugin</artifactId>
                        <version>2.4</version>
                        <executions>
                            <execution>
                                <id>attach-sources</id>
                                <goals>
                                    <goal>jar-no-fork</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <version>2.10.1</version>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                        <configuration>
                            <additionalparam>-Xdoclint:none</additionalparam>
                        </configuration>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>1.6</version>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>deploy</phase>
                                <goals>
                                    <goal>sign</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.sonatype.plugins</groupId>
                        <artifactId>nexus-staging-maven-plugin</artifactId>
                        <version>1.6.5</version>
                        <extensions>true</extensions>
                        <configuration>
                            <serverId>ossrh</serverId>
                            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                            <skipLocalStaging>true</skipLocalStaging>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>

</project>
<commit_msg>release/v4.0.0: upgraded biodata dependency to 0.8.3<commit_after><?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/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.opencb.cellbase</groupId>
    <artifactId>cellbase</artifactId>
    <version>4.0.0</version>
    <packaging>pom</packaging>

    <name>CellBase project</name>
    <description>CellBase projects integrates several biological databases into a NoSQL database plus many WS to query</description>
    <url>http://www.opencb.org/subprojects/cellbase</url>

    <modules>
        <module>cellbase-app</module>
        <module>cellbase-core</module>
        <module>cellbase-mongodb</module>
        <module>cellbase-server</module>
        <module>cellbase-grpc</module>
    </modules>

    <properties>
        <cellbase.version>4.0.0</cellbase.version>
        <biodata.version>0.7.3</biodata.version>
        <java-common-libs.version>3.2.1</java-common-libs.version>
        <jackson.version>2.6.4</jackson.version>
        <jersey.version>2.22.1</jersey.version>
        <compileSource>1.8</compileSource>
        <cellbase.war.name>cellbase</cellbase.war.name>
    </properties>

    <scm>
        <url>https://github.com/opencb/cellbase</url>
        <connection>scm:git:git://github.com/opencb/cellbase.git</connection>
        <developerConnection>scm:git:git@github.com:opencb/cellbase.git</developerConnection>
    </scm>

    <licenses>
        <license>
            <name>Apache License, Version 2</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
        </license>
    </licenses>

    <developers>
        <developer>
            <id>imedina</id>
            <name>Nacho</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>javild</id>
            <name>Javier</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>pabarcgar</id>
            <name>Pablo</name>
            <email><EMAIL></email>
        </developer>
        <developer>
            <id>mbleda</id>
            <name>Marta</name>
            <email><EMAIL></email>
        </developer>
    </developers>

    <mailingLists>
        <mailingList>
            <name>OpenCB Mailing List</name>
            <archive>https://groups.google.com/forum/#!forum/opencb</archive>
            <post><EMAIL></post>
        </mailingList>
    </mailingLists>

    <repositories>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
            <snapshots>
                <enabled>true</enabled>
                <updatePolicy>daily</updatePolicy>
            </snapshots>
        </repository>
    </repositories>

    <dependencyManagement>
        <dependencies>
            <!-- Intra-module dependencies -->
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-core</artifactId>
                <version>${cellbase.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.cellbase</groupId>
                <artifactId>cellbase-grpc</artifactId>
                <version>${cellbase.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-models</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-formats</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.biodata</groupId>
                <artifactId>biodata-tools</artifactId>
                <version>${biodata.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-lib</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-core</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>
            <dependency>
                <groupId>org.opencb.commons</groupId>
                <artifactId>commons-datastore-mongodb</artifactId>
                <version>${java-common-libs.version}</version>
            </dependency>

            <!-- General dependencies -->
            <dependency>
                <groupId>org.xerial</groupId>
                <artifactId>sqlite-jdbc</artifactId>
                <version>3.8.7</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java</artifactId>
                <version>3.0.0-beta-2</version>
            </dependency>
            <dependency>
                <groupId>com.google.protobuf</groupId>
                <artifactId>protobuf-java-util</artifactId>
                <version>3.0.0-beta-2</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>1.7.13</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-simple</artifactId>
                <version>1.7.13</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.core</groupId>
                <artifactId>jackson-databind</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.module</groupId>
                <artifactId>jackson-module-jsonSchema</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>com.fasterxml.jackson.module</groupId>
                <artifactId>jackson-dataformat-protobuf</artifactId>
                <version>${jackson.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.containers</groupId>
                <artifactId>jersey-container-servlet</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.glassfish.jersey.core</groupId>
                <artifactId>jersey-client</artifactId>
                <version>${jersey.version}</version>
            </dependency>
            <dependency>
                <groupId>org.spockframework</groupId>
                <artifactId>spock-core</artifactId>
                <version>0.7-groovy-2.0</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>cglib</groupId>
                <artifactId>cglib-nodep</artifactId>
                <version>3.1</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.objenesis</groupId>
                <artifactId>objenesis</artifactId>
                <version>2.1</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.12</version>
                <scope>test</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <build>
        <sourceDirectory>src/main/java</sourceDirectory>
        <testSourceDirectory>src/test/java</testSourceDirectory>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.2</version>
                <configuration>
                    <source>${compileSource}</source>
                    <target>${compileSource}</target>
                    <showDeprecation>true</showDeprecation>
                    <showWarnings>true</showWarnings>
                    <encoding>UTF-8</encoding>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.codehaus.gmaven</groupId>
                <artifactId>gmaven-plugin</artifactId>
                <version>1.5</version>
                <configuration>
                    <providerSelection>2.0</providerSelection>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>testCompile</goal>
                        </goals>
                    </execution>
                </executions>
                <dependencies>
                    <dependency>
                        <groupId>org.codehaus.gmaven.runtime</groupId>
                        <artifactId>gmaven-runtime-2.0</artifactId>
                        <version>1.5</version>
                    </dependency>
                    <dependency>
                        <groupId>org.codehaus.groovy</groupId>
                        <artifactId>groovy-all</artifactId>
                        <version>2.0.8</version>
                    </dependency>
                </dependencies>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-checkstyle-plugin</artifactId>
                <version>2.16</version>
                <executions>
                    <execution>
                        <id>validate</id>
                        <phase>validate</phase>
                        <configuration>
                            <configLocation>checkstyle.xml</configLocation>
                            <excludes>org/opencb/cellbase/app/cli/CliOptionsParser.java,org/opencb/cellbase/app/transform/GeneParserProto.java</excludes>
                        </configuration>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <distributionManagement>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
        </repository>
        <snapshotRepository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
        </snapshotRepository>
    </distributionManagement>

    <profiles>
        <profile>
            <id>war-dev</id>
            <activation>
                <activeByDefault>false</activeByDefault>
            </activation>
            <properties>
                <cellbase.war.name>cellbase-dev-v4.0</cellbase.war.name>
            </properties>
        </profile>
        <profile>
            <id>mongodb</id>
            <activation>
                <activeByDefault>true</activeByDefault>
            </activation>
            <dependencyManagement>
                <dependencies>
                    <dependency>
                        <groupId>org.opencb.cellbase</groupId>
                        <artifactId>cellbase-mongodb</artifactId>
                        <version>${cellbase.version}</version>
                    </dependency>
                </dependencies>
            </dependencyManagement>
        </profile>
        <profile>
            <id>deploy</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-source-plugin</artifactId>
                        <version>2.4</version>
                        <executions>
                            <execution>
                                <id>attach-sources</id>
                                <goals>
                                    <goal>jar-no-fork</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <version>2.10.1</version>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                        <configuration>
                            <additionalparam>-Xdoclint:none</additionalparam>
                        </configuration>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>1.6</version>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>deploy</phase>
                                <goals>
                                    <goal>sign</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.sonatype.plugins</groupId>
                        <artifactId>nexus-staging-maven-plugin</artifactId>
                        <version>1.6.5</version>
                        <extensions>true</extensions>
                        <configuration>
                            <serverId>ossrh</serverId>
                            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                            <skipLocalStaging>true</skipLocalStaging>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>

</project>

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