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

	<description>simple uima examples</description>

	<groupId>com.croeder</groupId>
	<artifactId>uima_examples</artifactId>
	<version>1.0-SNAPSHOT</version>

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

    <distributionManagement>
        <snapshotRepository>
            <id>amc-bakeoff.ucdenver.pvt</id>
            <name>amc-bakeoff.ucdenver.pvt</name>
            <url>http://amc-bakeoff.ucdenver.pvt:8081/artifactory/libs-snapshot-local</url>
        </snapshotRepository>
    </distributionManagement>

	<dependencies>
  		<dependency>
            <groupId>org.apache.uima</groupId>
            <artifactId>uimaj-core</artifactId>
            <version>2.4.0</version>
        </dependency>
        <dependency>
            <groupId>org.uimafit</groupId>
            <artifactId>uimafit</artifactId>
            <version>1.4.0</version>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.8.2</version>
        </dependency>
 		<dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.12</version>
        </dependency>
        <dependency>
            <groupId>org.apache.uima</groupId>
            <artifactId>ConceptMapper</artifactId>
            <version>2.3.1</version>
        </dependency>
	</dependencies>


	<build>
		<plugins>
			<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
         		<version>2.12</version>
         		<configuration>
         		<argLine>-Xmx16g -d64</argLine>
   	      		</configuration>
	       </plugin>

			<!-- specify the java version -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>2.0.2</version>
				<configuration>
					<source>1.6</source>
					<target>1.6</target>
				</configuration>
			</plugin>

  			<plugin>
	            <!-- run using "mvn exec:java" -->
	            <groupId>org.codehaus.mojo</groupId>
	            <artifactId>exec-maven-plugin</artifactId>
	            <version>1.1</version>
	            <executions>
	                <execution>
	                    <goals>
	                        <goal>java</goal>
	                    </goals>
	                </execution>
	            </executions>
	            <configuration>
						<!-- mvn -e exec:java -Dinput=//net/amc-colfax/RAID1/data/medline/pubmed_batches/batch_pubmed_002740 -Dbionlp_output=output/batch_pubmed_002740  -Drdf_output=output/rdf -Dontology=CC -->

	                <mainClass>com.croeder.uima_sample.BaseUimaFitPipeline</mainClass>
	                <arguments>
	                  <argument>target/classes/dictionaries/cmDict-GO-CC.xml</argument>
					  <argument>${input}</argument> 
	                  <argument>${bionlp_output}</argument>
	                  <argument>${rdf_output}</argument>
					  <argument>0</argument>
					  <argument>-1</argument>
					  <argument>.txt</argument>
	                </arguments>
	            </configuration>
          	</plugin>


		</plugins>
	</build>
</project><commit_msg>added jcasgen<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/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>

	<description>simple uima examples</description>

	<groupId>com.croeder</groupId>
	<artifactId>uima_examples</artifactId>
	<version>1.0-SNAPSHOT</version>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <jcasgen.typesystem>descriptors/TutorialTypeSystem.xml</jcasgen.typesystem>
    </properties>


    <distributionManagement>
        <snapshotRepository>
            <id>amc-bakeoff.ucdenver.pvt</id>
            <name>amc-bakeoff.ucdenver.pvt</name>
            <url>http://amc-bakeoff.ucdenver.pvt:8081/artifactory/libs-snapshot-local</url>
        </snapshotRepository>
    </distributionManagement>

	<dependencies>
  		<dependency>
            <groupId>org.apache.uima</groupId>
            <artifactId>uimaj-core</artifactId>
            <version>2.4.0</version>
        </dependency>
        <dependency>
            <groupId>org.uimafit</groupId>
            <artifactId>uimafit</artifactId>
            <version>1.4.0</version>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.8.2</version>
        </dependency>
 		<dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.12</version>
        </dependency>
        <dependency>
            <groupId>org.apache.uima</groupId>
            <artifactId>ConceptMapper</artifactId>
            <version>2.3.1</version>
        </dependency>
	</dependencies>


	<build>
		<plugins>
			<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
         		<version>2.12</version>
         		<configuration>
         		<argLine>-Xmx16g -d64</argLine>
   	      		</configuration>
	       </plugin>

			<!-- specify the java version -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>2.0.2</version>
				<configuration>
					<source>1.6</source>
					<target>1.6</target>
				</configuration>
			</plugin>

  			<plugin>
	            <!-- run using "mvn exec:java" -->
	            <groupId>org.codehaus.mojo</groupId>
	            <artifactId>exec-maven-plugin</artifactId>
	            <version>1.1</version>
	            <executions>
	                <execution>
	                    <goals>
	                        <goal>java</goal>
	                    </goals>
	                </execution>
	            </executions>
	            <configuration>
					<!-- mvn compile exec:java -Dinput=/Users/roederc/work/data/medline/pubmed_batches/batch_pubmed_005533/ -->
	                <!--<mainClass>com.croeder.uima_sample.GetStartedQuickAE</mainClass> -->
	                <!-- <mainClass>com.croeder.uima_sample.BaseUimaFitPipeline</mainClass> -->
					<mainClass>com.croeder.uima_sample.ProteinPipeline</mainClass>
	                <arguments>
					  <argument>${input}</argument> 
	                </arguments>
	            </configuration>
          	</plugin>
			<plugin>
                    <!-- This plugin generates java files with JCasGen.
						The phase makes it run with "mvn compile".
						A plugin below adds the generated code to source to be compiled. -->
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>exec-maven-plugin</artifactId>
                    <version>1.2</version>
                    <executions>
                        <execution>
                            <id>run-jcasgen</id>
                            <phase>process-resources</phase>
                            <goals>
                                <goal>java</goal>
                            </goals>
                            <configuration>
                                <mainClass>org.uimafit.util.JCasGenPomFriendly</mainClass>
                                <arguments>
                                    <argument>file:${project.basedir}/src/main/resources/${jcasgen.typesystem}
                                    </argument>
                                    <argument>${project.build.directory}/generated-sources/jcasgen</argument>
                                </arguments>
                            </configuration>
                        </execution>
                        <!-- <execution> <id>export-descriptor-xml</id> <phase>prepare-package</phase>
                            <goals> <goal>java</goal> </goals> <configuration> <mainClass>edu.ucdenver.ccp.nlp.core.uima.build.XmlDescriptorWriter</mainClass>
                            <arguments> <argument>${project.basedir}/src/main/java</argument> <argument>${project.build.directory}/uima-descriptors</argument>
                            <argument>${project.version}</argument> </arguments> </configuration> </execution> -->
                    </executions>
            </plugin>
  			<plugin><!-- This plugin adds the jcasgen generated source code folder
                        as a project source folder -->
                    <groupId>org.codehaus.mojo</groupId>
                    <artifactId>build-helper-maven-plugin</artifactId>
                    <version>1.5</version>
                    <executions>
                        <execution>
                            <id>add-jcasgen-sources-${project.artifactId}</id>
                            <phase>process-resources</phase>
                            <goals>
                                <goal>add-source</goal>
                            </goals>
                            <configuration>
                                <sources>
                                    <source>${project.build.directory}/generated-sources/jcasgen</source>
                                </sources>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>


		</plugins>
	</build>
</project>
{'fraction_non_alphanumeric': 0.1360403998763269, 'fraction_numerical': 0.014531588168607647, 'mean_word_length': 1.6608171099533864, 'pattern_counts': {'":': 0, '<': 354, '<?xml version=': 0, '>': 354, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 7}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6279512', 'n_tokens_mistral': 3187, 'n_tokens_neox': 2718, 'n_words': 313}