<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">
    <parent>
        <artifactId>gmql</artifactId>
        <groupId>it.polimi.genomics</groupId>
        <version>1.0-SNAPSHOT</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>
    <artifactId>GMQL-PythonAPI</artifactId>
    <packaging>jar</packaging>
    <description>Interface to the Python library</description>
    <inceptionYear>2017</inceptionYear>


    <dependencies>
        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Core</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>

        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Server</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>

        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Spark</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>./src/main/scala</sourceDirectory>
        <plugins>
            <plugin>
                <groupId>org.scala-tools</groupId>
                <artifactId>maven-scala-plugin</artifactId>

                <executions>
                    <execution>
                        <id>compile</id>
                        <goals>
                            <goal>compile</goal>
                        </goals>
                        <phase>compile</phase>
                    </execution>

                    <execution>
                        <id>test-compile</id>
                        <goals>
                            <goal>testCompile</goal>
                        </goals>
                        <phase>test-compile</phase>
                    </execution>

                    <execution>
                        <phase>process-resources</phase>
                        <goals>
                            <goal>compile</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                </configuration>
            </plugin>

            <!--<plugin>-->
            <!--<artifactId>maven-assembly-plugin</artifactId>-->
            <!--<version>2.4.1</version>-->
            <!--<configuration>-->
            <!--<descriptorRe-fs>-->
            <!--<descriptorRef>jar-with-dependencies</descriptorRef>-->
            <!--</descriptorRefs>-->
            <!--<archive>-->
            <!--<manifestEntries>-->
            <!--<Main-Class>it.polimi.genomics.spark.implementation.TestSelect</Main-Class>-->
            <!--</manifestEntries>-->
            <!--</archive>-->
            <!--</configuration>-->
            <!--<executions>-->
            <!--<execution>-->
            <!--<id>make-assembly</id>-->
            <!--<phase>package</phase>-->
            <!--<goals>-->
            <!--<goal>single</goal>-->
            <!--</goals>-->
            <!--</execution>-->
            <!--</executions>-->
            <!--</plugin>-->

            <!--<plugin>-->
                <!--<artifactId>maven-assembly-plugin</artifactId>-->
                <!--<version>2.4.1</version>-->
                <!--<configuration>-->
                    <!--<descriptorRefs>-->
                        <!--<descriptorRef>jar-with-dependencies</descriptorRef>-->
                    <!--</descriptorRefs>-->
                    <!--<archive>-->
                        <!--<manifestEntries>-->
                            <!--<Main-Class>it.polimi.genomics.pythonapi.EntryPoint</Main-Class>-->
                        <!--</manifestEntries>-->
                    <!--</archive>-->
                <!--</configuration>-->
                <!--<executions>-->
                    <!--<execution>-->
                        <!--<id>make-assembly</id>-->
                        <!--<phase>package</phase>-->
                        <!--<goals>-->
                            <!--<goal>single</goal>-->
                        <!--</goals>-->
                    <!--</execution>-->
                <!--</executions>-->
            <!--</plugin>-->

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>it.polimi.genomics.pythonapi.EntryPoint</mainClass>
                            <!--<addClasspath>true</addClasspath>-->
                            <!--<classpathPrefix>./lib/</classpathPrefix>-->
                        </manifest>
                    </archive>
                </configuration>
            </plugin>

            <!--Builds the directory ./lib in which all the dependencies are put-->
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/lib</outputDirectory>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.3</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <!--This is needed because GMQL-Repository and GMQL-Spark both use Hadoop configurations
                    therefore we need to merge the sources of Hadoop code-->
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
                    </transformers>
                    <filters>
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
                    </filters>
                    <!--<finalName>uber-${project.artifactId}-${project.version}</finalName>-->
                    <finalName>pythonAPI-0.0.8</finalName>
                </configuration>
            </plugin><commit_msg>added jar with dependencies to the deployment<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">
    <parent>
        <artifactId>gmql</artifactId>
        <groupId>it.polimi.genomics</groupId>
        <version>1.0-SNAPSHOT</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>
    <artifactId>GMQL-PythonAPI</artifactId>
    <packaging>jar</packaging>
    <description>Interface to the Python library</description>
    <inceptionYear>2017</inceptionYear>


    <dependencies>
        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Core</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>

        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Server</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>

        <dependency>
            <groupId>it.polimi.genomics</groupId>
            <artifactId>GMQL-Spark</artifactId>
            <version>1.0-SNAPSHOT</version>
        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>./src/main/scala</sourceDirectory>
        <plugins>
            <plugin>
                <groupId>org.scala-tools</groupId>
                <artifactId>maven-scala-plugin</artifactId>

                <executions>
                    <execution>
                        <id>compile</id>
                        <goals>
                            <goal>compile</goal>
                        </goals>
                        <phase>compile</phase>
                    </execution>

                    <execution>
                        <id>test-compile</id>
                        <goals>
                            <goal>testCompile</goal>
                        </goals>
                        <phase>test-compile</phase>
                    </execution>

                    <execution>
                        <phase>process-resources</phase>
                        <goals>
                            <goal>compile</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                </configuration>
            </plugin>

            <!--<plugin>-->
            <!--<artifactId>maven-assembly-plugin</artifactId>-->
            <!--<version>2.4.1</version>-->
            <!--<configuration>-->
            <!--<descriptorRe-fs>-->
            <!--<descriptorRef>jar-with-dependencies</descriptorRef>-->
            <!--</descriptorRefs>-->
            <!--<archive>-->
            <!--<manifestEntries>-->
            <!--<Main-Class>it.polimi.genomics.spark.implementation.TestSelect</Main-Class>-->
            <!--</manifestEntries>-->
            <!--</archive>-->
            <!--</configuration>-->
            <!--<executions>-->
            <!--<execution>-->
            <!--<id>make-assembly</id>-->
            <!--<phase>package</phase>-->
            <!--<goals>-->
            <!--<goal>single</goal>-->
            <!--</goals>-->
            <!--</execution>-->
            <!--</executions>-->
            <!--</plugin>-->

            <!--<plugin>-->
                <!--<artifactId>maven-assembly-plugin</artifactId>-->
                <!--<version>2.4.1</version>-->
                <!--<configuration>-->
                    <!--<descriptorRefs>-->
                        <!--<descriptorRef>jar-with-dependencies</descriptorRef>-->
                    <!--</descriptorRefs>-->
                    <!--<archive>-->
                        <!--<manifestEntries>-->
                            <!--<Main-Class>it.polimi.genomics.pythonapi.EntryPoint</Main-Class>-->
                        <!--</manifestEntries>-->
                    <!--</archive>-->
                <!--</configuration>-->
                <!--<executions>-->
                    <!--<execution>-->
                        <!--<id>make-assembly</id>-->
                        <!--<phase>package</phase>-->
                        <!--<goals>-->
                            <!--<goal>single</goal>-->
                        <!--</goals>-->
                    <!--</execution>-->
                <!--</executions>-->
            <!--</plugin>-->

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>it.polimi.genomics.pythonapi.EntryPoint</mainClass>
                            <!--<addClasspath>true</addClasspath>-->
                            <!--<classpathPrefix>./lib/</classpathPrefix>-->
                        </manifest>
                    </archive>
                </configuration>
            </plugin>

            <!--Builds the directory ./lib in which all the dependencies are put-->
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/lib</outputDirectory>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>3.1.0</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <shadedArtifactAttached>true</shadedArtifactAttached>
                    <shadedClassifierName>jackofall</shadedClassifierName> <!-- Any name that makes sense -->
                    <!--This is needed because GMQL-Repository and GMQL-Spark both use Hadoop configurations
                    therefore we need to merge the sources of Hadoop code-->
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
                    </transformers>
                    <filters>
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
                    </filters>
                </configuration>
            </plugin>
{'fraction_non_alphanumeric': 0.15118530884808012, 'fraction_numerical': 0.006410684474123539, 'mean_word_length': 1.065655172413793, 'pattern_counts': {'":': 0, '<': 575, '<?xml version=': 2, '>': 575, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 6}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4402113', 'n_tokens_mistral': 3988, 'n_tokens_neox': 3463, 'n_words': 434}