Description

<dependency>
    <groupId>org.opencb.opencga</groupId>
    <artifactId>opencga-server</artifactId>
    <version>3.6.0</version>
</dependency>

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ Copyright 2015-2020 OpenCB
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~     http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  -->

<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xmlns="http://maven.apache.org/POM/4.0.0"
         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.opencb.opencga</groupId>
        <artifactId>opencga</artifactId>
        <version>3.6.0</version>
        <relativePath>../pom.xml</relativePath>
    </parent>

    <artifactId>opencga-server</artifactId>
    <packaging>war</packaging>
    <name>OpenCGA Server</name>

    <dependencies>
        <dependency>
            <groupId>org.opencb.opencga</groupId>
            <artifactId>opencga-catalog</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.opencga</groupId>
            <artifactId>opencga-storage-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.opencga</groupId>
            <artifactId>opencga-analysis</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.biodata</groupId>
            <artifactId>biodata-tools</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.biodata</groupId>
            <artifactId>biodata-models</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.opencga</groupId>
            <artifactId>opencga-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.commons</groupId>
            <artifactId>commons-datastore-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.commons</groupId>
            <artifactId>commons-lib</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.ga4gh</groupId>
            <artifactId>ga4gh</artifactId>
            <exclusions>
                <exclusion>
                    <groupId>org.mortbay.jetty</groupId>
                    <artifactId>jetty</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>org.mortbay.jetty</groupId>
                    <artifactId>servlet-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.opencb.opencga</groupId>
            <artifactId>opencga-catalog</artifactId>
            <scope>test</scope>
            <type>test-jar</type>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.media</groupId>
            <artifactId>jersey-media-multipart</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.core</groupId>
            <artifactId>jersey-server</artifactId>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.dataformat</groupId>
            <artifactId>jackson-dataformat-yaml</artifactId>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-annotations</artifactId>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-core</artifactId>
        </dependency>
        <dependency>
            <groupId>com.google.protobuf</groupId>
            <artifactId>protobuf-java</artifactId>
        </dependency>
        <dependency>
            <groupId>io.grpc</groupId>
            <artifactId>grpc-protobuf</artifactId>
        </dependency>
        <dependency>
            <groupId>org.eclipse.jetty</groupId>
            <artifactId>jetty-server</artifactId>
        </dependency>
        <dependency>
            <groupId>org.eclipse.jetty</groupId>
            <artifactId>jetty-webapp</artifactId>
        </dependency>
        <dependency>
            <groupId>org.eclipse.jetty</groupId>
            <artifactId>jetty-servlet</artifactId>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>log4j-core</artifactId>
        </dependency>

        <!-- Added dependencies -->

        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>io.grpc</groupId>
            <artifactId>grpc-api</artifactId>
        </dependency>
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
        </dependency>
        <dependency>
            <groupId>jakarta.ws.rs</groupId>
            <artifactId>jakarta.ws.rs-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.solr</groupId>
            <artifactId>solr-solrj</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>

        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>javax.servlet-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-collections4</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.avro</groupId>
            <artifactId>avro</artifactId>
        </dependency>
        <dependency>
            <groupId>io.grpc</groupId>
            <artifactId>grpc-stub</artifactId>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.core</groupId>
            <artifactId>jersey-client</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.containers</groupId>
            <artifactId>jersey-container-servlet-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.commons</groupId>
            <artifactId>commons-datastore-mongodb</artifactId>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
        </dependency>


        <!-- TODO Review -->
        <dependency>
            <groupId>org.glassfish.jersey.media</groupId>
            <artifactId>jersey-media-json-jackson</artifactId>
        </dependency>
        <dependency>
            <groupId>io.grpc</groupId>
            <artifactId>grpc-all</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.inject</groupId>
            <artifactId>jersey-hk2</artifactId>
        </dependency>
        <dependency>
            <groupId>org.glassfish.jersey.containers</groupId>
            <artifactId>jersey-container-servlet</artifactId>
        </dependency>
    </dependencies>

    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>
        <extensions>
            <extension>
                <groupId>kr.motd.maven</groupId>
                <artifactId>os-maven-plugin</artifactId>
                <version>1.7.1</version>
            </extension>
        </extensions>

        <plugins>
            <plugin>
                <artifactId>maven-war-plugin</artifactId>
                <configuration>
                    <warName>${opencga.war.name}</warName>
                    <!--
                      Exclude JCL and LOG4J since all logging should go through SLF4J.
                      Note that we're excluding log4j-<version>.jar but keeping
                      log4j-over-slf4j-<version>.jar
                    -->
                    <!--<packagingExcludes>-->
                    <!--WEB-INF/lib/commons-logging-*.jar,-->
                    <!--%regex[WEB-INF/lib/log4j-(?!over-slf4j).*.jar]-->
                    <!--</packagingExcludes>-->
                    <webResources>
                        <resource>
                            <directory>src/main/webapp/WEB-INF/</directory>
                            <filtering>true</filtering>
                            <targetPath>WEB-INF</targetPath>
                        </resource>
                        <!--                       <resource>-->
                        <!--                           <directory>../opencga-core/src/main/resources/</directory>-->
                        <!--                           <targetPath>WEB-INF/classes</targetPath>-->
                        <!--                           <includes>-->
                        <!--                               <include>log4j.properties</include>-->
                        <!--                           </includes>-->
                        <!--                       </resource>-->
                    </webResources>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <executions>
                    <execution>
                        <id>make-a-jar</id>
                        <phase>compile</phase>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-install-plugin</artifactId>
                <version>3.1.1</version>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <goals>
                            <goal>install-file</goal>
                        </goals>
                        <configuration>
                            <packaging>jar</packaging>
                            <groupId>${project.groupId}</groupId>
                            <artifactId>${project.artifactId}</artifactId>
                            <version>${project.version}</version>
                            <file>
                                ${project.build.directory}/${project.artifactId}-${project.version}.jar
                            </file>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.xolstice.maven.plugins</groupId>
                <artifactId>protobuf-maven-plugin</artifactId>
                <version>0.5.0</version>
                <configuration>
                    <!--
                      The version of protoc must match protobuf-java. If you don't depend on
                      protobuf-java directly, you will be transitively depending on the
                      protobuf-java version that grpc depends on.
                    -->
                    <protocArtifact>com.google.protobuf:protoc:${protobuf.version}:exe:${os.detected.classifier}
                    </protocArtifact>
                    <pluginId>grpc-java</pluginId>
                    <pluginArtifact>io.grpc:protoc-gen-grpc-java:${grpc.version}:exe:${os.detected.classifier}
                    </pluginArtifact>
                    <!--<protoSourceRoot>src/main/resources/protobuf</protoSourceRoot>-->
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>compile</goal>
                            <goal>compile-custom</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.sonatype.plugins</groupId>
                <artifactId>nexus-staging-maven-plugin</artifactId>
                <version>1.6.2</version>
                <extensions>true</extensions>
                <configuration>
                    <serverId>ossrh</serverId>
                    <skipNexusStagingDeployMojo>true</skipNexusStagingDeployMojo>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>3.6.0</version>
                <executions>
                    <execution>
                        <id>analyze</id>
                        <goals>
                            <goal>analyze-only</goal>
                        </goals>
                        <configuration>
                            <failOnWarning>true</failOnWarning>
                            <ignoredNonTestScopedDependencies>
                                <ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
                            </ignoredNonTestScopedDependencies>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
    <profiles>
        <profile>
            <id>storage-hadoop</id>
            <activation>
                <property>
                    <name>!skipStorageHadoop</name>
                </property>
            </activation>
            <dependencies>
                <dependency>
                    <groupId>org.opencb.opencga</groupId>
                    <artifactId>opencga-storage-hadoop-core</artifactId>
                    <version>${project.parent.version}</version>
                </dependency>
                <dependency>
                    <groupId>org.opencb.opencga</groupId>
                    <artifactId>${opencga-hadoop-lib.artifactId}</artifactId>
                    <version>${project.parent.version}</version>
                    <optional>true</optional>
                </dependency>
            </dependencies>
        </profile>

        <profile>
            <id>CodeGen</id>
            <activation>
                <property>
                    <name>!skipCodeGen</name>
                </property>
            </activation>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.codehaus.mojo</groupId>
                        <artifactId>exec-maven-plugin</artifactId>
                        <version>3.0.0</version>
                        <executions>
                            <execution>
                                <id>CLIWriter</id>
                                <phase>package</phase>
                                <goals>
                                    <goal>java</goal>
                                </goals>
                            </execution>
                        </executions>
                        <configuration>
                            <mainClass>org.opencb.opencga.server.generator.ClientsGeneratorMain</mainClass>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>


</project>