<commit_before><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>

    <parent>
        <groupId>org.mousephenotype.cda</groupId>
        <artifactId>parent</artifactId>
        <version>1.0.0</version>
        <relativePath>../parent/pom.xml</relativePath>
    </parent>

    <artifactId>thirdparty_loads</artifactId>
    <packaging>jar</packaging>

    <name>thirdparty_loads</name>
    <description>Code for backend part of integrating 3i with IMPC</description>

    <dependencies>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>data-model-db</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>data-model-solr</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>reports</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>loads</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.dcc.exportlibrary.xmlvalidationresourcescollection</groupId>
            <artifactId>exportlibrary.xmlvalidationresourcescollection</artifactId>
            <version>2.0.0</version>
            <exclusions>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-classic</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-core</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>log4j-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>


        <dependency>
            <groupId>org.mousephenotype.dcc.exportlibrary.xmlserialization</groupId>
            <artifactId>exportlibrary.xmlserialization</artifactId>
            <version>1.3.1</version>
            <exclusions>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-classic</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-core</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>log4j-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.springframework.batch</groupId>
            <artifactId>spring-batch-core</artifactId>
        </dependency>

        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
            <version>1.4.1</version>
        </dependency>

        <!-- For command line option parsing -->
        <dependency>
            <groupId>net.sf.jopt-simple</groupId>
            <artifactId>jopt-simple</artifactId>
        </dependency>

		<!-- MGI intermine project -->
	    <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>metadata</artifactId>
            <version>1.0.0</version>
        </dependency>

        <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>pathquery</artifactId>
            <version>1.0.0</version>
        </dependency>

         <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>webservice</artifactId>
            <version>1.0.0</version>
        </dependency>

        <!-- Jersey web services client dependencies -->
        <dependency>
            <groupId>org.glassfish.jersey.media</groupId>
            <artifactId>jersey-media-moxy</artifactId>
            <version>2.2</version>
        </dependency>

        <dependency>
            <groupId>org.glassfish.jersey.core</groupId>
            <artifactId>jersey-client</artifactId>
            <version>2.2</version>
        </dependency>

        <dependency>
            <groupId>org.glassfish.jersey.connectors</groupId>
            <artifactId>jersey-apache-connector</artifactId>
            <version>2.2</version>
        </dependency>

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

        <dependency>
            <groupId>com.h2database</groupId>
            <artifactId>h2</artifactId>
            <scope>test</scope>
        </dependency>

    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.springframework.boot</groupId>
                <artifactId>spring-boot-maven-plugin</artifactId>
                <configuration>
                    <!-- Discuss with Jeremy and Jonathan, but for now have 
                         variable I can pass it
                    -->
                    <!--mainClass>org.springframework.boot.loader.PropertiesLauncher</mainClass-->
                    <!--mainClass>org.mousephenotype.cda.loads.create.extract.dcc.ExtractDccSpecimens</mainClass-->
                    <mainClass>${myMainClass}</mainClass>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>repackage</goal>
                        </goals>
                        <configuration>
                            <classifier>exec</classifier>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>

</project><commit_msg>Modify POM to use application.properties for main class as use of variable was causing build of module to fail in jenkins<commit_after><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>

    <parent>
        <groupId>org.mousephenotype.cda</groupId>
        <artifactId>parent</artifactId>
        <version>1.0.0</version>
        <relativePath>../parent/pom.xml</relativePath>
    </parent>

    <artifactId>thirdparty_loads</artifactId>
    <packaging>jar</packaging>

    <name>thirdparty_loads</name>
    <description>Code for backend part of integrating 3i with IMPC</description>

    <dependencies>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>data-model-db</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>data-model-solr</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>reports</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.cda</groupId>
            <artifactId>loads</artifactId>
        </dependency>

        <dependency>
            <groupId>org.mousephenotype.dcc.exportlibrary.xmlvalidationresourcescollection</groupId>
            <artifactId>exportlibrary.xmlvalidationresourcescollection</artifactId>
            <version>2.0.0</version>
            <exclusions>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-classic</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-core</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>log4j-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>


        <dependency>
            <groupId>org.mousephenotype.dcc.exportlibrary.xmlserialization</groupId>
            <artifactId>exportlibrary.xmlserialization</artifactId>
            <version>1.3.1</version>
            <exclusions>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-classic</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-core</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>log4j-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.springframework.batch</groupId>
            <artifactId>spring-batch-core</artifactId>
        </dependency>

        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>commons-net</groupId>
            <artifactId>commons-net</artifactId>
            <version>1.4.1</version>
        </dependency>

        <!-- For command line option parsing -->
        <dependency>
            <groupId>net.sf.jopt-simple</groupId>
            <artifactId>jopt-simple</artifactId>
        </dependency>

		<!-- MGI intermine project -->
	    <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>metadata</artifactId>
            <version>1.0.0</version>
        </dependency>

        <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>pathquery</artifactId>
            <version>1.0.0</version>
        </dependency>

         <dependency>
            <groupId>org.intermine</groupId>
            <artifactId>webservice</artifactId>
            <version>1.0.0</version>
        </dependency>

        <!-- Jersey web services client dependencies -->
        <dependency>
            <groupId>org.glassfish.jersey.media</groupId>
            <artifactId>jersey-media-moxy</artifactId>
            <version>2.2</version>
        </dependency>

        <dependency>
            <groupId>org.glassfish.jersey.core</groupId>
            <artifactId>jersey-client</artifactId>
            <version>2.2</version>
        </dependency>

        <dependency>
            <groupId>org.glassfish.jersey.connectors</groupId>
            <artifactId>jersey-apache-connector</artifactId>
            <version>2.2</version>
        </dependency>

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

        <dependency>
            <groupId>com.h2database</groupId>
            <artifactId>h2</artifactId>
            <scope>test</scope>
        </dependency>

    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.springframework.boot</groupId>
                <artifactId>spring-boot-maven-plugin</artifactId>
                <configuration>
                    <mainClass>org.springframework.boot.loader.PropertiesLauncher</mainClass>
                    <!-- Discuss with Jeremy and Jonathan, how to use properties
                         to specify main class to run. For now locally I
                         created a variable I can pass it
                    -->
                    <!--mainClass>${myMainClass}</mainClass-->
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>repackage</goal>
                        </goals>
                        <configuration>
                            <classifier>exec</classifier>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>

</project>
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{'dir': 'git-commits-cleaned', 'id': '324262', 'n_tokens_mistral': 3759, 'n_tokens_neox': 3168, 'n_words': 406}