Author: kono
Date: 2008-09-24 16:11:20 -0700 (Wed, 24 Sep 2008)
New Revision: 14959
Added:
csplugins/trunk/ucsd/kono/PythonEnginePlugin/build.xml
csplugins/trunk/ucsd/kono/PythonEnginePlugin/plugin.props
Log:
Initial checkin for Python plugin code.
Added: csplugins/trunk/ucsd/kono/PythonEnginePlugin/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/PythonEnginePlugin/build.xml 2008-09-24
23:11:07 UTC (rev 14958)
+++ csplugins/trunk/ucsd/kono/PythonEnginePlugin/build.xml 2008-09-24
23:11:20 UTC (rev 14959)
@@ -0,0 +1,129 @@
+<?xml version="1.0"?>
+<!--
+
+ Python Scripting Engine for Cytoscape by Kei Ono
+
+ To build this plugin, you need to download Jython separately.
+
+-->
+
+<project name="PythonScriptingEngine" default="all" basedir=".">
+
+ <!-- Name of jython directory. -->
+ <property name="jython.version" value="jython-2.2.1" />
+
+ <!-- You need modify this to your Cytoscape -->
+ <property name="cytoscape.dir" value="../c26" />
+
+ <!-- All files generated by ant go here -->
+ <property name="build.dir" value="${basedir}/build" />
+
+ <!-- The java source directory-->
+ <property name="src.dir" value="${basedir}/src" />
+
+ <property name="project.jar" value="PythonScriptingEngine.jar" />
+
+ <!-- ============ Compilation Control Options =======================
-->
+ <property name="compile.debug" value="true" />
+ <property name="compile.deprecation" value="true" />
+ <property name="compile.optimize" value="true" />
+
+
+ <!-- ==================== Compilation Classpath ======================
-->
+ <path id="compile.classpath">
+ <fileset dir="${cytoscape.dir}">
+ <include name="cytoscape.jar" />
+ </fileset>
+ <fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${basedir}/${jython.version}">
+ <include name="jython.jar" />
+ <include name="JyConsole.jar" />
+ </fileset>
+
+ </path>
+
+ <!-- ==================== Clean Target ===============================
-->
+ <target name="clean" description="Deletes all build files and starts
fresh">
+ <delete dir="${build.dir}" />
+ <delete file="${project.jar}" />
+ </target>
+
+ <!-- ==================== Compile Target
==============================-->
+ <target name="compile" depends="prepare" description="Compiles all Java
source files">
+ <mkdir dir="${build.dir}/classes" />
+ <javac srcdir="${src.dir}" source="1.5"
destdir="${build.dir}/classes" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}">
+ <classpath refid="compile.classpath" />
+ </javac>
+ </target>
+
+ <!-- ==================== Jar Target ============================== -->
+ <target name="jar" depends="compile" description="Creates Plugin Jar:
${project.jar}">
+
+ <unjar dest="${build.dir}/classes">
+ <!--fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset-->
+ <fileset dir="${basedir}/${jython.version}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset
dir="${basedir}/JyConsole-1.4-bin/thirdpart/ArtTk">
+ <include name="*.jar" />
+ </fileset>
+ </unjar>
+
+
+ <copy toDir="${build.dir}/script">
+ <fileset dir="${basedir}/JyConsole-1.4-bin/script"
includes="**/*" />
+ </copy>
+
+ <copy toDir="${build.dir}/classes/Lib">
+ <fileset dir="${basedir}/${jython.version}/Lib"
includes="**/*" />
+ </copy>
+
+ <copy toDir="${build.dir}/classes/Tools">
+ <fileset dir="${basedir}/${jython.version}/Tools"
includes="**/*" />
+ </copy>
+
+ <copy toDir="${build.dir}/classes/util-scripts">
+ <fileset dir="${basedir}/util-scripts" includes="**/*"
/>
+ </copy>
+ <copy
todir="${build.dir}/classes/edu/ucsd/bioeng/idekerlab/pythonengine"
file="${basedir}/plugin.props" />
+
+ <copy todir="${build.dir}/classes/images">
+ <fileset dir="${basedir}/images" />
+ </copy>
+
+
+
+ <jar destfile="${project.jar}" basedir="${build.dir}/classes">
+
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="edu.ucsd.bioeng.idekerlab.pythonengine.PythonEnginePlugin" />
+ </manifest>
+
+ </jar>
+ </target>
+
+ <!-- ==================== Build and test jar
============================== -->
+ <target name="all" depends="jar" />
+
+ <!-- ==================== Prepare Target ==============================
-->
+ <target name="prepare">
+ <!-- Create build directories as needed -->
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${build.dir}/classes" />
+
+ </target>
+
+ <!-- ==================== JUnit Test Target ===========================
-->
+ <target name="test" description="Runs all JUnit tests"
depends="compile">
+ <junit printsummary="yes" fork="yes" haltonfailure="yes">
+ <formatter type="plain" usefile="false" />
+ <test name="cytoscape.test.AllTest" />
+ <classpath refid="compile.classpath" />
+ </junit>
+ </target>
+
+</project>
Added: csplugins/trunk/ucsd/kono/PythonEnginePlugin/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/PythonEnginePlugin/plugin.props 2008-09-24
23:11:07 UTC (rev 14958)
+++ csplugins/trunk/ucsd/kono/PythonEnginePlugin/plugin.props 2008-09-24
23:11:20 UTC (rev 14959)
@@ -0,0 +1,22 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=PythonScriptingEngine
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=<p>Scripting engine based on Jython 2.2.1 implementation.
This plugin uses JyConsole library by Artenum OpenSource
project.</p><p><strong><font color="red">This plugin is for technology
evaluation purpose ONLY! Totally experimental.</font></strong>
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.02
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Communication/Scripting
+
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD Bioengineering
\ No newline at end of file
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