<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">
	<parent>
		<artifactId>gemma</artifactId>
		<groupId>gemma</groupId>
		<version>1.1.2-SNAPSHOT</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<groupId>gemma</groupId>
	<artifactId>gemma-web</artifactId>
	<packaging>war</packaging>
	<name>Gemma web</name>
	<version>1.1.2-SNAPSHOT</version>
	<description>Gemma web application</description>
	<build>
		<sourceDirectory>src/main/java</sourceDirectory>
		<testSourceDirectory>src/test/java</testSourceDirectory>
		<outputDirectory>target/classes</outputDirectory>
		<testOutputDirectory>target/test-classes</testOutputDirectory>
		<resources>
			<resource>
				<directory>src/main/resources</directory>
				<includes>
					<include>**/*</include>
				</includes>
			</resource>
			<resource>
				<directory>target/generated-sources/resources</directory>
				<includes>
					<include>**/*</include>
				</includes>
			</resource>
		</resources>
		<testResources>
			<testResource>
				<directory>src/test/resources</directory>
				<includes>
					<include>**/*.txt</include>
					<include>**/*.xml</include>
					<include>**/*.csv</include>
				</includes>
			</testResource>
			<testResource>
				<targetPath>WEB-INF</targetPath>
				<directory>target/Gemma/WEB-INF</directory>
				<includes>
					<include>**/*.xml</include>
				</includes>
			</testResource>
			<testResource>
				<targetPath>WEB-INF</targetPath>
				<directory>src/main/webapp/WEB-INF</directory>
				<includes>
					<include>**/*.xml</include>
				</includes>
			</testResource>
		</testResources>
		<directory>target</directory>
		<finalName>Gemma</finalName>
		<plugins>
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<configuration>
					<argLine>-enableassertions -Xmx2g -Djava.awt.headless=true</argLine>
					<excludes>
						<exclude>**/*Abstract*</exclude>
						<exclude>**/*IntegrationTest.java</exclude>
					</excludes>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>xdoclet-maven-plugin</artifactId>
				<executions>
					<execution>
						<id>Generate config files</id>
						<phase>generate-sources</phase>
						<goals>
							<goal>xdoclet</goal>
						</goals>
						<configuration>
							<tasks>
								<springdoclet destdir="${project.build.directory}/Gemma/WEB-INF" mergeDir="${basedir}/src/conf/xdoclet-merge" force="false" validating="false">
									<fileset includes="**/*.java" dir="${basedir}/src/main/java" />
									<springxml mergeDir="${basedir}/src/conf/xdoclet-merge" useIds="true" destDir="${project.build.directory}/Gemma/WEB-INF" destinationFile="action-servlet.xml" />
								</springdoclet>
								<webdoclet destdir="${project.build.directory}/Gemma/WEB-INF" mergeDir="${basedir}/src/conf/xdoclet-merge" force="false">
									<fileset includes="**/*.java" dir="${basedir}/src/main/java" />
									<jsptaglib taglibversion="1.0" xmlencoding="UTF-8" Jspversion="2.0" description="Custom tag library for Gemma" shortname="Gemma" mergeDir="${basedir}/src/conf/xdoclet-merge" filename="Gemma.tld" validateXML="false" destDir="${project.build.directory}/Gemma/WEB-INF" />
									<springvalidationxml />
								</webdoclet>
							</tasks>
						</configuration>
					</execution>
				</executions>
				<dependencies>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xdoclet-web-module</artifactId>
						<version>1.2.3</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xdoclet-spring-module</artifactId>
						<version>1.2.3</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xjavadoc</artifactId>
						<version>1.1</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>ant</groupId>
						<artifactId>ant</artifactId>
						<version>1.6.5</version>
					</dependency>
				</dependencies>
			</plugin>
			<plugin>
				<artifactId>maven-war-plugin</artifactId>
				<configuration>
					<excludes>
						<exclude>**/*Test*,**/Test*,**/All*Tests</exclude>
					</excludes>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-antrun-plugin</artifactId>
				<executions>
					<execution>
						<id>Generate version file</id>
						<phase>process-classes</phase>
						<goals>
							<goal>run</goal>
						</goals>
						<configuration>
							<tasks>
								<echo append="false" file="${project.build.directory}/classes/version.properties">
									gemma.version=${project.version}
								</echo>
							</tasks>
						</configuration>
					</execution>
				</executions>
			</plugin>
		</plugins>
	</build>
	<profiles>
		<profile>
			<id>eclipse build</id>
			<activation />
			<build>
				<plugins>
					<plugin>
						<artifactId>maven-antrun-plugin</artifactId>
						<executions>
							<execution>
								<id>Copy generated WEB-INF files for eclipse</id>
								<phase>process-resources</phase>
								<goals>
									<goal>run</goal>
								</goals>
								<configuration>
									<tasks>
										<copy verbose="true" todir="${basedir}/../generated-sources/Gemma/WEB-INF">
											<fileset dir="${project.build.directory}/Gemma/WEB-INF">
												<include name="validation.xml" />
												<include name="Gemma.tld" />
												<include name="action-servlet.xml" />
											</fileset>
										</copy><commit_msg>javascript minifying when building war file (will not affect development in eclipse) bug 1230<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">
	<parent>
		<artifactId>gemma</artifactId>
		<groupId>gemma</groupId>
		<version>1.1.2-SNAPSHOT</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<groupId>gemma</groupId>
	<artifactId>gemma-web</artifactId>
	<packaging>war</packaging>
	<name>Gemma web</name>
	<version>1.1.2-SNAPSHOT</version>
	<description>Gemma web application</description>
	<build>
		<sourceDirectory>src/main/java</sourceDirectory>
		<testSourceDirectory>src/test/java</testSourceDirectory>
		<outputDirectory>target/classes</outputDirectory>
		<testOutputDirectory>target/test-classes</testOutputDirectory>
		<resources>
			<resource>
				<directory>src/main/resources</directory>
				<includes>
					<include>**/*</include>
				</includes>
			</resource>
			<resource>
				<directory>target/generated-sources/resources</directory>
				<includes>
					<include>**/*</include>
				</includes>
			</resource>
		</resources>
		<testResources>
			<testResource>
				<directory>src/test/resources</directory>
				<includes>
					<include>**/*.txt</include>
					<include>**/*.xml</include>
					<include>**/*.csv</include>
				</includes>
			</testResource>
			<testResource>
				<targetPath>WEB-INF</targetPath>
				<directory>target/Gemma/WEB-INF</directory>
				<includes>
					<include>**/*.xml</include>
				</includes>
			</testResource>
			<testResource>
				<targetPath>WEB-INF</targetPath>
				<directory>src/main/webapp/WEB-INF</directory>
				<includes>
					<include>**/*.xml</include>
				</includes>
			</testResource>
		</testResources>
		<directory>target</directory>
		<finalName>Gemma</finalName>
		<plugins>
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<configuration>
					<argLine>-enableassertions -Xmx2g -Djava.awt.headless=true</argLine>
					<excludes>
						<exclude>**/*Abstract*</exclude>
						<exclude>**/*IntegrationTest.java</exclude>
					</excludes>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>xdoclet-maven-plugin</artifactId>
				<executions>
					<execution>
						<id>Generate config files</id>
						<phase>generate-sources</phase>
						<goals>
							<goal>xdoclet</goal>
						</goals>
						<configuration>
							<tasks>
								<springdoclet destdir="${project.build.directory}/Gemma/WEB-INF"
									mergeDir="${basedir}/src/conf/xdoclet-merge" force="false" validating="false">
									<fileset includes="**/*.java" dir="${basedir}/src/main/java" />
									<springxml mergeDir="${basedir}/src/conf/xdoclet-merge" useIds="true"
										destDir="${project.build.directory}/Gemma/WEB-INF" destinationFile="action-servlet.xml" />
								</springdoclet>
								<webdoclet destdir="${project.build.directory}/Gemma/WEB-INF"
									mergeDir="${basedir}/src/conf/xdoclet-merge" force="false">
									<fileset includes="**/*.java" dir="${basedir}/src/main/java" />
									<jsptaglib taglibversion="1.0" xmlencoding="UTF-8" Jspversion="2.0"
										description="Custom tag library for Gemma" shortname="Gemma" mergeDir="${basedir}/src/conf/xdoclet-merge"
										filename="Gemma.tld" validateXML="false" destDir="${project.build.directory}/Gemma/WEB-INF" />
									<springvalidationxml />
								</webdoclet>
							</tasks>
						</configuration>
					</execution>
				</executions>
				<dependencies>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xdoclet-web-module</artifactId>
						<version>1.2.3</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xdoclet-spring-module</artifactId>
						<version>1.2.3</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>xdoclet</groupId>
						<artifactId>xjavadoc</artifactId>
						<version>1.1</version>
						<scope>provided</scope>
					</dependency>
					<dependency>
						<groupId>ant</groupId>
						<artifactId>ant</artifactId>
						<version>1.6.5</version>
					</dependency>
				</dependencies>
			</plugin>
			<plugin>
				<artifactId>maven-war-plugin</artifactId>
				<configuration>
					<excludes>
						<exclude>**/*Test*,**/Test*,**/All*Tests</exclude>
					</excludes>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-antrun-plugin</artifactId>
				<executions>
					<execution>
						<id>Generate version file</id>
						<phase>process-classes</phase>
						<goals>
							<goal>run</goal>
						</goals>
						<configuration>
							<tasks>
								<echo append="false" file="${project.build.directory}/classes/version.properties">
									gemma.version=${project.version}
								</echo>
							</tasks>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>net.sf.alchim</groupId>
				<artifactId>yuicompressor-maven-plugin</artifactId>
				<executions>
					<execution>
						<goals>
							<!-- 	<goal>jslint</goal> -->
							<goal>compress</goal>
						</goals>
					</execution>
				</executions>
				<configuration>
					<force>true</force>
					<jswarn>false</jswarn>
					<nosuffix>true</nosuffix>
					<linebreakpos>5000</linebreakpos>
					<preserveAllSemiColons>true</preserveAllSemiColons>
					<nomunge>false</nomunge>
					<excludes>
						<exclude>**/*.vm</exclude>
						<exclude>**/*.css</exclude>
						<exclude>**/*.xml</exclude>
						<exclude>**/*.html</exclude>
						<exclude>**/*.properties</exclude>
						<exclude>**/ext-all.js</exclude>
						<exclude>**/ext-all-debug.js</exclude>
					</excludes>
					<!-- Currently aggregations do not work. But we can still minify the code
					<aggregations>
						<aggregation>
							<removeIncluded>true</removeIncluded>
								<insertNewLine>true</insertNewLine>
							<output>${project.build.directory}/${project.build.finalName}/scripts/gemma-all.js</output>
							<includes>
								<include>**/*.js</include>
							</includes>
							<excludes>
								<exclude>lib/*.js</exclude>
								<exclude>app/*.js</exclude>
								<exclude>app/test/*.js</exclude>
								<exclude>prototype.js</exclude>
								<exclude>scriptaculous/*.js</exclude>
								<exclude>scriptaculous-all.js</exclude>
								<exclude>ext/*.js</exclude>
								<exclude>ext/adapter/**/*.js</exclude>
								<exclude>ext/adapter/**/*.js</exclude>
								<exclude>flotr-0.1.0alpha/**/*.js</exclude>
							</excludes>
						</aggregation>
						<aggregation>
							<removeIncluded>true</removeIncluded>
							<insertNewLine>true</insertNewLine>
							<output>
								${project.build.directory}/${project.build.finalName}/scripts/scriptaculous-all.js
							</output>
							<includes>
								<include>**/scriptaculous/*.js</include>
							</includes>
						</aggregation>
					</aggregations> -->
				</configuration>
			</plugin>
		</plugins>
	</build>
	<profiles>
		<profile>
			<id>eclipse build</id>
			<activation />
			<build>
				<plugins>
					<plugin>
						<artifactId>maven-antrun-plugin</artifactId>
						<executions>
							<execution>
								<id>Copy generated WEB-INF files for eclipse</id>
								<phase>process-resources</phase>
								<goals>
									<goal>run</goal>
								</goals>
								<configuration>
									<tasks>
										<copy verbose="true" todir="${basedir}/../generated-sources/Gemma/WEB-INF">
											<fileset dir="${project.build.directory}/Gemma/WEB-INF">
												<include name="validation.xml" />
												<include name="Gemma.tld" />
												<include name="action-servlet.xml" />
											</fileset>
										</copy>
{'fraction_non_alphanumeric': 0.17387755102040817, 'fraction_numerical': 0.006753246753246753, 'mean_word_length': 2.9380479251899474, 'pattern_counts': {'":': 0, '<': 573, '<?xml version=': 0, '>': 573, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 23}, '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': '3577014', 'n_tokens_mistral': 6391, 'n_tokens_neox': 4392, 'n_words': 541}