<commit_before><?xml version="1.0" encoding="UTF-8"?>
<project name="WikiPathwaysSearch" default="war">
	<property name="build.dir" value="bin" />
	<property name="src.dir" value="src" />
	<property name="proj.name" value="WikiPathwaysSearch" />
	<property name="web.deploy.dir" value="www" />
	<property name="war.file" value="wikipathways-search.war" />
	<property name="tmp.war.dir" value="war-tmp"/>
	
	<target name="clean">
		<delete dir="${build.dir}" />
		<delete dir="${tmp.war.dir}" />
	</target>

	<fileset id="lib.files" dir="lib">
		<include name="**/*.jar" />
	</fileset>

	<fileset id="batik.lib.files" dir="../../lib">
		<include name="batik/**/*.jar" />
		<include name="resources.jar" />
	</fileset>
			
	<fileset id="client.lib.files" dir="../../">
		<include name="lib/axis-1_4/**/*.jar" />
		<include name="pathvisio.jar" />
		<include name="wikipathways-client.jar" />
		<include name="lib/resources.jar" />
		<include name="lib/jdom.jar" />
	</fileset>

	<path id="class.path">
		<pathelement location="${build.dir}" />
		<fileset refid="lib.files" />
		<fileset refid="client.lib.files" />
		<fileset refid="batik.lib.files" />
	</path>

	<target name="gwt-compile" depends="compile">
		<exec executable="./${proj.name}-compile" failonerror="true" />
	</target>

	<target name="compile">
		<mkdir dir="${build.dir}" />
		<javac destdir="${build.dir}" srcdir="${src.dir}">
			<classpath refid="class.path" />
		</javac>
	</target>

	<target name="war" depends="gwt-compile">
		<copy flatten="true" todir="${tmp.war.dir}">
			<fileset refid="lib.files"/>
			<fileset refid="client.lib.files"/>
			<fileset refid="batik.lib.files"/>
		</copy>
		<war destfile="${war.file}" webxml="WEB-INF/web.xml">
			<lib dir="${tmp.war.dir}"/>
			<classes dir="bin" />
			<fileset dir="www/org.pathvisio.wikipathways.WikiPathwaysSearch" />
		</war>
	</target>
</project>
<commit_msg>adapted wikipathways-search to new bridgedb libraries<commit_after><?xml version="1.0" encoding="UTF-8"?>
<project name="WikiPathwaysSearch" default="war">
	<property name="build.dir" value="bin" />
	<property name="src.dir" value="src" />
	<property name="proj.name" value="WikiPathwaysSearch" />
	<property name="web.deploy.dir" value="www" />
	<property name="war.file" value="wikipathways-search.war" />
	<property name="tmp.war.dir" value="war-tmp"/>
	
	<target name="clean">
		<delete dir="${build.dir}" />
		<delete dir="${tmp.war.dir}" />
	</target>

	<fileset id="lib.files" dir="lib">
		<include name="**/*.jar" />
	</fileset>

	<fileset id="batik.lib.files" dir="../../lib">
		<include name="batik/**/*.jar" />
		<include name="resources.jar" />
	</fileset>
			
	<fileset id="client.lib.files" dir="../../">
		<include name="lib/axis-1_4/**/*.jar" />
		<include name="pathvisio.jar" />
		<include name="wikipathways-client.jar" />
		<include name="lib/resources.jar" />
		<include name="lib/jdom.jar" />
		<include name="lib/bridgedb.jar" />
		<include name="lib/bridgedb-bio.jar" />
	</fileset>

	<path id="class.path">
		<pathelement location="${build.dir}" />
		<fileset refid="lib.files" />
		<fileset refid="client.lib.files" />
		<fileset refid="batik.lib.files" />
	</path>

	<target name="gwt-compile" depends="compile">
		<exec executable="./${proj.name}-compile" failonerror="true" />
	</target>

	<target name="compile">
		<mkdir dir="${build.dir}" />
		<javac destdir="${build.dir}" srcdir="${src.dir}">
			<classpath refid="class.path" />
		</javac>
	</target>

	<target name="war" depends="gwt-compile">
		<copy flatten="true" todir="${tmp.war.dir}">
			<fileset refid="lib.files"/>
			<fileset refid="client.lib.files"/>
			<fileset refid="batik.lib.files"/>
		</copy>
		<war destfile="${war.file}" webxml="WEB-INF/web.xml">
			<lib dir="${tmp.war.dir}"/>
			<classes dir="bin" />
			<fileset dir="www/org.pathvisio.wikipathways.WikiPathwaysSearch" />
		</war>
	</target>
</project>

{'fraction_non_alphanumeric': 0.23807080554130322, 'fraction_numerical': 0.002565418163160595, 'mean_word_length': 4.212566844919786, 'pattern_counts': {'":': 0, '<': 113, '<?xml version=': 2, '>': 113, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, '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': '4536381', 'n_tokens_mistral': 1563, 'n_tokens_neox': 1453, 'n_words': 235}