Author: rodche
Date: 2010-02-02 07:37:17 -0800 (Tue, 02 Feb 2010)
New Revision: 19114
Removed:
csplugins/trunk/toronto/rodche/BioPAX/build.xml
Modified:
csplugins/trunk/toronto/rodche/BioPAX/
Log:
MOVED PERMANENTLY to the 'coreplugins' code base!
Property changes on: csplugins/trunk/toronto/rodche/BioPAX
___________________________________________________________________
Name: svn:ignore
- .settings
build
+ .settings
build
.externalToolBuilders
Deleted: csplugins/trunk/toronto/rodche/BioPAX/build.xml
===================================================================
--- csplugins/trunk/toronto/rodche/BioPAX/build.xml 2010-02-02 15:28:52 UTC
(rev 19113)
+++ csplugins/trunk/toronto/rodche/BioPAX/build.xml 2010-02-02 15:37:17 UTC
(rev 19114)
@@ -1,267 +0,0 @@
-<?xml version="1.0"?>
-<!-- build.xml - Build file for Cytoscape BioPAX Plug In -->
-<project default="all" name="Cytoscape Core BioPAX PlugIn">
-
- <!-- project name -->
- <property name="project_name" value="biopax"/>
- <!-- environment -->
- <property environment="env"/>
- <!-- tools dir -->
- <property name="pathway.tools.root" value="${env.PATHWAY_TOOLS_ROOT}"/>
- <!-- version numbers -->
- <property name="biopax_version" value="0_7"/>
- <!-- define check style task -->
- <taskdef resource="checkstyletask.properties"/>
- <!-- source code dir -->
- <property name="src.dir" value="src"/>
- <property name="test.src.dir" value="test"/>
- <!-- scripts/bin dir -->
- <property name="bin.dir" value="bin"/>
- <!-- config dir -->
- <property name="config.dir" value="config"/>
- <!-- build dir -->
- <property name="build.dir" value="build"/>
- <property name="build.classes" value="${build.dir}/classes"/>
- <property name="build.test.classes" value="${build.dir}/test-classes"/>
- <!-- jars dir -->
- <property name="jars.dir" value="${build.dir}/jars"/>
- <!-- resources dir -->
- <property name="resources.dir" value="resources"/>
- <!-- styles dir -->
- <property name="style.dir" value="style"/>
- <!-- release dir -->
- <property name="release.dir" value="${build.dir}/release"/>
- <!-- versioned release dir -->
- <property name="version_release.dir"
- value="${release.dir}/biopax_${biopax_version}"/>
- <!-- zip release dir -->
- <property name="zip.dir" value="${build.dir}/zip_release"/>
- <!-- global "magic" property for <javac> -->
- <property name="build.compiler" value="modern"/>
- <!-- junit dir -->
- <property name="junit.dir" value="${build.dir}/junit"/>
- <!-- temp dir -->
- <property name="temp.dir" value="temp"/>
- <!-- LayoutUtil.java file -->
- <property name="layout.util.file"
value="${src.dir}/cytoscape/coreplugins/biopax/util/LayoutUtil.java"/>
- <!-- jar file -->
- <property name="jar_file" value="${project_name}.jar"/>
- <!-- obfuscation file -->
- <property name="obfuscationlog" value="${project_name}_obflog.xml.gz"/>
-
- <!-- cytoscape dir -->
- <property name="cytoscape.dir" value="../../cytoscape"/>
-
- <!-- runtime classpath -->
- <path id="runtime.classpath">
- <fileset dir="${cytoscape.dir}/lib">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.dir}">
- <include name="cytoscape.jar"/>
- </fileset>
- </path>
-
- <!-- classpath without reference to yfiles -->
- <path id="classpath.without.yfiles">
- <pathelement path="${build.classes}"/>
- <!-- not required, because these jars are unpacked to ${build.classes}
(see target:prepare)
- <fileset dir="${basedir}/lib">
- <include name="*.jar"/>
- </fileset>
- -->
- <path refid="runtime.classpath"/>
- </path>
-
- <path id="test.classpath">
- <pathelement path="${build.test.classes}"/>
- <path refid="classpath.without.yfiles"/>
- </path>
-
- <!-- classpath with reference to yfiles -->
- <path id="classpath.with.yfiles">
- <path refid="classpath.without.yfiles"/>
- <fileset dir="${pathway.tools.root}/lib/">
- <include name="*.jar"/>
- </fileset>
- </path>
-
- <!-- target that sets has.yfiles property -->
- <target name="check.yfiles">
- <condition property="has.yfiles">
- <and>
- <available file="${pathway.tools.root}/lib/y.jar"/>
- <available file="${pathway.tools.root}/lib/yguard.jar"/>
- </and>
- </condition>
- </target>
-
- <!-- target that sets the classpath based on value of check.yfiles
property -->
- <target depends="check.yfiles" name="set.classpath">
- <condition property="classpath" value="classpath.with.yfiles"
else="classpath.without.yfiles">
- <istrue value="${has.yfiles}"/>
- </condition>
- <echo message="classpath = ${classpath}"/>
- </target>
-
- <!-- target to determine os -->
- <target name="check.os">
- <condition property="exe.file" value="cmd" else="/bin/sh">
- <os family="windows"/>
- </condition>
- <condition property="exe.file.arg" value="/c" else="-c">
- <os family="windows"/>
- </condition>
- <echo message="exec = ${exe.file} ${exe.file.arg}"/>
- </target>
-
- <!-- target to generate LayoutUtil.java -->
- <target depends="check.os" description="Generates custom layout file"
name="gen.layout.file">
- <condition property="gen.yfiles" value="1" else="0">
- <available file="${pathway.tools.root}/lib/y.jar"/>
- </condition>
- <exec executable="${exe.file}">
- <arg value="${exe.file.arg}" />
- <arg value="python ${bin.dir}/genLayoutUtil.py
${gen.yfiles} ${layout.util.file}"/>
- </exec>
- <echo message="using gen.yfiles = ${gen.yfiles}, layout.util.file =
${layout.util.file}"/>
- </target>
-
- <!-- target to create the build directories prior to compilation -->
- <target name="prepare">
- <mkdir dir="${build.dir}"/>
- <mkdir dir="${build.dir}/docs"/>
- <mkdir dir="${build.classes}"/>
- <mkdir dir="${build.test.classes}"/>
- <mkdir dir="${jars.dir}"/>
-
- <!-- Explicitly Include Classes from These JARs: -->
- <unjar dest="${build.classes}">
- <fileset dir="${basedir}/lib" includes="*.jar"/>
- </unjar>
-
- <echo>"basedir ${basedir}"</echo>
- </target>
-
- <!-- target to clean out all directories -->
- <target description="Removes all generated files." name="clean">
- <delete dir="${build.dir}"/>
- <delete dir="${jars.dir}"/>
- <delete dir="${junit.dir}"/>
- <delete dir="${temp.dir}"/>
- <delete>
- <fileset dir="." includes="*.log"/>
- </delete>
- <delete file="${layout.util.file}"/>
- <delete file="${obfuscationlog}"/>
- </target>
-
- <!-- target to unzip yFiles library into build - required for
obfuscation -->
- <target depends="check.yfiles" if="has.yfiles" name="unzip.yfiles">
- <unzip src="${pathway.tools.root}/lib/y.jar" dest="${build.classes}"/>
- </target>
-
- <!-- target to compile all code -->
- <target
depends="check.yfiles,prepare,gen.layout.file,set.classpath,unzip.yfiles"
- description="Compiles all source code." name="compile">
- <javac debug="true" debuglevel="source,lines,var"
- destdir="${build.classes}" nowarn="on" srcdir="${src.dir}"
deprecation="true"
- classpathref="${classpath}" target="1.5">
- </javac>
-
- <javac debug="true" debuglevel="source,lines,var"
- destdir="${build.test.classes}" nowarn="on"
srcdir="${test.src.dir}" deprecation="true"
- classpathref="${classpath}" target="1.5">
- </javac>
-
- <!-- copy all resources -->
- <copy todir="${build.classes}">
- <fileset dir="${resources.dir}">
- <exclude name="**/*.java"/>
- </fileset>
- </copy>
- </target>
-
- <!-- target to run cytoscape with biopax plugin -->
- <target depends="check.yfiles,set.classpath,jar" description="Runs
Cytoscape with BioPAX Data."
- name="run">
- <copy file="${jars.dir}/${jar_file}" todir="${cytoscape.dir}/plugins"
overwrite="true" />
- <java classname="cytoscape.CyMain" classpathref="runtime.classpath"
- fork="true" maxmemory="1000M">
- <arg line="-p ${cytoscape.dir}/plugins"/>
- </java>
- </target>
-
- <!-- target to create plugin jar -->
- <target depends="compile" description="Creates PlugIn JAR" name="jar">
-
- <!-- start clean -->
- <delete dir="${jars.dir}"/>
- <mkdir dir="${jars.dir}"/>
-
- <!-- create jar -->
- <copy todir="${build.classes}/cytoscape/coreplugins/biopax"
file="${resources.dir}/plugin.props"/>
- <jar destfile="${jars.dir}/${jar_file}">
- <fileset dir="${build.classes}"/>
- <manifest>
- <attribute name="Cytoscape-Plugin"
value="cytoscape.coreplugins.biopax.BiopaxPlugin"/>
- </manifest>
- </jar>
- </target>
-
- <!-- target to run checkstyle on all source code -->
- <!-- uses the sun coding conventions configuration -->
- <target description="Checks Sun Coding Conventions" name="check">
- <checkstyle config="${config.dir}/sun_checks.xml">
- <fileset dir="${src.dir}/org">
- <include name="**/*.java"/>
- </fileset>
- </checkstyle>
- </target>
-
- <!-- target to run all junit tests -->
- <target depends="compile" description="Runs all JUnit Tests" name="test">
- <delete dir="${junit.dir}"/>
- <mkdir dir="${junit.dir}"/>
- <mkdir dir="${junit.dir}/reports"/>
- <junit printsummary="yes" fork="yes" haltonfailure="yes"
dir="${basedir}">
- <formatter type="plain" usefile="false"/>
- <test name="cytoscape.coreplugins.biopax.AllTest"/>
- <classpath refid="test.classpath"/>
- </junit>
- </target>
-
- <!-- obfuscate -->
- <target depends="check.yfiles,jar" name="obfuscate" if="has.yfiles">
- <taskdef name="obfuscate"
- classname="com.yworks.yguard.ObfuscatorTask"
- classpathref="${classpath}"/>
- <!-- the following can be adjusted to your needs -->
- <obfuscate logfile="${obfuscationlog}"
- replaceclassnamestrings="true">
- <property name="error-checking"
- value="pedantic"/>
- <property name="obfuscation-prefix"
- value="y.obf"/>
- <inoutpair in="${jars.dir}/${jar_file}"
out="${jars.dir}/${jar_file}"/>
- <expose>
- <class classes="protected" methods="protected"
fields="protected">
- <patternset>
- <include name="cytoscape.coreplugins.biopax.*"/>
- <include name="cytoscape.coreplugins.biopax.action.*"/>
- <include name="cytoscape.coreplugins.biopax.util.*"/>
- <include name="cytoscape.coreplugins.biopax.view.*"/>
- </patternset>
- </class>
- </expose>
- </obfuscate>
- </target>
-
- <!-- builds and tests everything -->
- <!--
- <target depends="jar,obfuscate,test" description="Builds and tests
everything" name="all"/>
- -->
- <target depends="jar,obfuscate" description="Builds and tests
everything" name="all">
- </target>
-
-</project>
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