Author: mcreech
Date: 2011-05-19 13:35:19 -0700 (Thu, 19 May 2011)
New Revision: 25500
Removed:
csplugins/trunk/agilent/creech/HyperEdgeEditor/build.properties
csplugins/trunk/agilent/creech/HyperEdgeEditor/build.xml
csplugins/trunk/agilent/creech/HyperEdgeEditor/jarlib/
csplugins/trunk/agilent/creech/HyperEdgeEditor/lib/
csplugins/trunk/agilent/creech/HyperEdgeEditor/lsibuild.xml
Log:
v2.68
Deleted: csplugins/trunk/agilent/creech/HyperEdgeEditor/build.properties
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/build.properties
2011-05-19 18:27:47 UTC (rev 25499)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/build.properties
2011-05-19 20:35:19 UTC (rev 25500)
@@ -1,36 +0,0 @@
-# This file defines user preferences for the ANT build process for
-# this library.
-
-# Should an Internet browser present the test report after tests
-# are run? If 'yes', 'on', or 'true', present the tests.
-browse.test.report=yes
-
-# Should we copy jars created to the repository, or keep local in our
-# 'release' directory? If 'yes', 'on', or 'true', copy to repository.
-repository.release=yes
-
-# Should plugins that are dependent on a given library be updated when
-# that library changes in the repository? If 'yes', 'on', or 'true',
-# udpate plugin packages when library changes. Otherwise leave plugins
-# alone. This flag is only relevant when repository.release=yes.
-update.dependent.plugins=no
-
-# Place any local libraries (.jar files) required for compiling this
-# library:
-# local.compile.libs=
-
-# Place any local libraries (.jar files) required for executing this
-# library (do not repeat compile-time libraries):
-# local.run.libs=
-
-# Place any repository libraries (.jar files) required for compiling this
-# library:
-repository.compile.libs=lsiutils.jar;hyperedge.jar;cytoscape_editor.jar;cytoscape/cytoscape.jar;cytoscape/ding.jar;cytoscape/giny.jar;cytoscape/phoebe.jar;cytoscape/piccolo.jar
-
-# Place any repository libraries (.jar files) required for executing this
-# library (do not repeat compile-time libraries):
-repository.run.libs=
-
-# Place any repository libraries (.jar files) to be used in creating
-# the plugin:
-repository.plugin.libs=lsiutils.jar;hyperedge.jar
Deleted: csplugins/trunk/agilent/creech/HyperEdgeEditor/build.xml
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/build.xml 2011-05-19
18:27:47 UTC (rev 25499)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/build.xml 2011-05-19
20:35:19 UTC (rev 25500)
@@ -1,120 +0,0 @@
-<?xml version="1.0"?>
-<project name="HyperEdgeEditor" default="jar" basedir=".">
- <!-- TO USE THIS BUILD SCRIPT:
- 1) FILL IN the location of Cytoscape root wrt this build file in
- 'cytoscape.dir'. -->
- <!-- directory definitions -->
- <property name="root.dir" value="."/>
- <property name="src.dir" value="${root.dir}/src"/>
- <property name="doc.dir" value="${root.dir}/doc"/>
- <property name="jarlib.dir" value="${root.dir}/jarlib"/>
- <property name="build.dir" value="${root.dir}/build"/>
- <property name="build.classes.dir" value="${build.dir}/classes"/>
- <property name="apidocs.dir" location="${build.dir}/api-docs" />
-
- <property name="cytoscape.dir" value="../cytoscape-2.6"/>
- <property name="cytoscape.lib.dir" value = "${cytoscape.dir}/lib"/>
- <property name="cytoscape.plugin.dir" value =
"${cytoscape.dir}/plugins/core"/>
-
- <!-- plugin definitions -->
- <property name="plugin.name" value="${ant.project.name}" />
- <property name="plugin.loc" value = "${build.dir}/${plugin.name}.jar"/>
-
- <!-- compiler options -->
- <property name="build.compiler" value="modern"/>
-
- <!-- classpath with all lib, cytoscape, and cytoscape lib classes -->
- <path id="plugin.classpath">
- <fileset dir="${jarlib.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.lib.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.plugin.dir}">
- <include name="CytoscapeEditor.jar"/>
- </fileset>
- </path>
-
- <!-- Target to create the build directories prior to compilation -->
- <target name="prepare">
- <mkdir dir="${build.dir}"/>
- <mkdir dir="${build.classes.dir}"/>
- </target>
-
- <!-- Target to clean out all directories -->
- <target name="clean"
- description="Removes all generated jars, test, and class files.
Leaves API docs.">
- <!-- would be better to delete build.dir excluding the api-docs
directory,
- but can't get that to work: -->
- <delete dir="${build.classes.dir}" />
- <delete dir="${plugin.loc}" />
- <delete dir="${test.dir}" />
- </target>
-
- <target name="clean-docs" description="Remove all generated java API
docs.">
- <delete dir="${apidocs.dir}" />
- </target>
-
- <!-- Target to create the javadoc information -->
- <target name="doc"
- depends="clean-docs">
- <mkdir dir="${apidocs.dir}"/>
- <javadoc destdir="${apidocs.dir}"
- classpathref="plugin.classpath"
- Windowtitle="${plugin.name} API Docs"
- header="${plugin.name}"
- Private="yes">
- <fileset dir="${src.dir}" defaultexcludes="yes">
- <include name="**/*.java" />
- </fileset>
- <doctitle>${plugin.name} API Docs</doctitle>
- </javadoc>
- </target>
-
-
- <!-- Target to compile all Plug In Code -->
- <target name="compile"
- depends="prepare"
- description="compile all HyperEdgeEditor code.">
- <javac debug="Yes"
- srcdir="${src.dir}"
- destdir="${build.classes.dir}"
- deprecation="true"
- classpathref="plugin.classpath"/>
- <echo message="Finished compile." />
- </target>
-
- <!-- Copy needed files into ${build.classes.dir} for jaring and
testing. -->
- <target name="add-data-files">
- <copy todir="${build.classes.dir}" preservelastmodified="true">
- <fileset dir="${src.dir}"
includes="cytoscape/hyperedge/editor/images/*.png" />
- </copy>
- <copy todir="${build.classes.dir}/cytoscape/hyperedge/editor"
preservelastmodified="true" file="plugin.props" />
- </target>
-
- <!-- Create PlugIn Jar File -->
- <target name="jar"
- depends="clean,compile,add-data-files"
- description="Compile code and create ${plugin.name} jar.">
- <unjar dest="${build.classes.dir}">
- <fileset dir="${jarlib.dir}">
- <include name="*.jar"/>
- </fileset>
- </unjar>
- <jar destfile="${plugin.loc}">
- <manifest>
- <attribute name="Cytoscape-Plugin"
-
value="cytoscape.hyperedge.editor.HyperEdgeEditorPlugin"/>
- </manifest>
- <fileset dir="${build.classes.dir}"/>
- </jar>
- <echo message="${plugin.loc} is now complete." />
- </target>
-
- <target name="all"
- depends="clean,jar,doc"/>
-</project>
Deleted: csplugins/trunk/agilent/creech/HyperEdgeEditor/lsibuild.xml
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/lsibuild.xml 2011-05-19
18:27:47 UTC (rev 25499)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/lsibuild.xml 2011-05-19
20:35:19 UTC (rev 25500)
@@ -1,157 +0,0 @@
-<?xml version="1.0"?>
-<!-- Prepare to load build-common-properties file: -->
-<!-- We would like to load build-common-properties.xml from one, non-hardcoded
- location, but we can't figure out how: -->
-<!DOCTYPE project [
- <!ENTITY common-properties SYSTEM
"../repository/ant/build-common-properties.xml">
-<!ENTITY common-tasks SYSTEM "../repository/ant/build-common-tasks.xml">
- ]>
-<!--This ANT file handles all the building tasks for the HyperEdgeEditor
package.
- External libraries needed for compilation and testing are loaded
- from some combination of a library repository and project-local libraries.
- This is controlled by the contents of the build.properties file.
- This allows for use of older versions of libraries for some packages while
- others use newer versions of libraries.
- All building takes place in a scratch 'build' directory which includes:
- api-docs-location of generated javadoc documents
- classes-location of compiled class files
- ctrees-used for testing
- release-the jar file for this library
- test-data and reports for the junit test cases run.
--->
-<project name="HyperEdgeEditor" default="jar" basedir=".">
- <echo message="${basedir}" />
-
- <property name="lib.name" value="HyperEdgeEditor" />
- <property name="test.subdir"
value="cytoscape/hyperedge/editor/unittest" />
- <!-- Actually load the common properties: -->
- &common-properties;
- <!-- Actually load the common tasks: -->
- &common-tasks;
-
- <property name="plugin.name" value="${ant.project.name}" />
- <property name="plugin.loc"
value="${build.release.dir}/${plugin.name}.jar" />
-
- <target name="test" depends="compile" description="compile code and run
all tests and create a test report.">
- <echo message="test.classes.root.dir =
${test.classes.root.dir}" />
-
- <path id="test.classpath">
- <path refid="run.classpath" />
- <pathelement location="${build.classes.dir}" />
- </path>
- <junit printsummary="false" errorProperty="test.failed"
failureProperty="test.failed">
- <!-- junit requires a different classpath then standard
compile: -->
- <classpath refid="test.classpath" />
- <formatter type="brief" usefile="false" />
- <formatter type="xml" />
- <batchtest todir="${test.data.dir}">
- <fileset dir="${test.classes.root.dir}"
includes="**/${test.subdir}/*Test.class" />
- </batchtest>
- </junit>
- <!-- create the nice HTML, browsable report of test results: -->
- <junitreport todir="${test.data.dir}">
- <fileset dir="${test.data.dir}">
- <include name="TEST-*.xml" />
- </fileset>
- <report format="frames" todir="${test.reports.dir}" />
- </junitreport>
- <antcall target="display-test-report" />
- <fail message="Test failed. Check report in
${test.reports.dir}/index.html." if="test.failed" />
- <echo message="Tests passed. Check report in
${test.reports.dir}/index.html." />
- </target>
-
- <!-- Copy needed files into ${build.classes.dir} for jaring and
testing. -->
- <target name="add-data-files">
- <copy todir="${build.classes.dir}" preservelastmodified="true">
- <fileset dir="${src.dir}"
includes="cytoscape/hyperedge/editor/images/*.png" />
- </copy>
- <copy todir="${build.classes.dir}/cytoscape/hyperedge/editor"
preservelastmodified="true" file="plugin.props" />
- </target>
-
- <!-- we must do a 'clean' because we don't want to jar up any
- classes that are now gone from a compile: -->
- <target name="jar" depends="clean,compile,add-data-files"
description="Compile code, create library jar, copy to repository, update
dependent plugins (based on build.properties).">
-
- <convertpath resultId="plugin.include.jars"
localPath="${local.plugin.libs}" repoPath="${repository.plugin.libs}"
localLibHome="${repository.local.dir}" repoLibHome="${repository.dir}" />
- <property name="pi-to-print" refid="plugin.include.jars" />
- <echo message="plugin.include.jars = ${pi-to-print}" />
- <taskdef name="pathtofileset"
classname="net.sf.antcontrib.property.PathToFileSet" />
- <!-- return a fileset of all the repository based items in our
- plugin.inlude.jars: -->
- <pathtofileset name="repository.fileset"
pathrefid="plugin.include.jars" dir="${repository.dir}"
ignorenonrelative="true" />
- <!-- return a fileset of all the local based items in our
- plugin.include.jars: -->
- <pathtofileset name="local.fileset"
pathrefid="plugin.include.jars" dir="${repository.local.dir}"
ignorenonrelative="true" />
- <unjar dest="${build.classes.dir}">
- <fileset refid="repository.fileset" />
- <fileset refid="local.fileset" />
- </unjar>
-
- <jar destfile="${plugin.loc}">
- <manifest>
- <attribute name="Cytoscape-Plugin"
-
value="cytoscape.hyperedge.editor.HyperEdgeEditorPlugin"/>
- </manifest>
- <fileset dir="${build.classes.dir}">
- <!-- skip items from the test directory: -->
- <exclude name="${test.subdir}/" />
- </fileset>
- </jar>
- <echo message="${plugin.loc} is now complete." />
- <antcall target="release-plugin-to-cytoscape" />
- <!-- <antcall target="release-plugin-to-genespring" /> -->
- </target>
-
- <target name="release-plugin-to-cytoscape" depends="check-cytohome"
if="release-to-repository" description="copy plugin jar to cytoscape, when
desired (based on repository.release property).">
- <copy file="${plugin.loc}"
todir="${cytoscape.plugins.dir}/extras" preservelastmodified="true" />
- </target>
-
- <target name="release-plugin-to-genespring" if="release-to-repository"
description="copy plugin jar to GeneSpring GX and GT data directories, when
desired (based on repository.release property).">
- <!-- TODO: FIX: We are having lower-level packages know about
higher level ones! -->
- <property
file="${repository.ant.dir}/build-package-locations.properties" />
- <!-- we can't have these as "depends" for this target because
they will be
- executed before the test for 'release-to-repository' -->
- <antcall target="release-plugin-to-gx" />
- <antcall target="release-plugin-to-gt" />
- <antcall target="copy-plugin-to-gxnb-data" />
- <antcall target="copy-plugin-to-gtnb-data" />
- </target>
-
- <!-- copy plugin jar to GXNetworkBuilder plugins directory when
necessary -->
- <target name="copy-plugin-to-gxnb-data" if="gxnbhome.dir">
- <copy file="${plugin.loc}"
todir="${gxnbhome.dir}/data/GXInstall/Programs/GXNBPlugin/CytoscapePlugin/plugins"
preservelastmodified="true" />
- </target>
-
- <!-- copy plugin jar to GXNetworkBuilder plugins directory when
necessary -->
- <target name="copy-plugin-to-gtnb-data" if="gtnbhome.dir">
- <copy file="${plugin.loc}"
todir="${gtnbhome.dir}/data/GTInstall/Programs/GTNBPlugin/CytoscapePlugin/plugins"
preservelastmodified="true" />
- </target>
-
- <!-- copy plugin jar to GeneSpring GX plugins directory when necessary
-->
- <target name="release-plugin-to-gx" if="genespring.gx.plugins.dir">
- <copy file="${plugin.loc}"
todir="${genespring.gx.plugins.dir}/GXNBPlugin/CytoscapePlugin/plugins"
preservelastmodified="true" />
- </target>
-
- <!-- copy plugin jar to GeneSpring GT plugins directory when necessary
-->
- <target name="release-plugin-to-gt" if="genespring.gt.plugins.dir">
- <copy file="${plugin.loc}"
todir="${genespring.gt.plugins.dir}/GTNBPlugin/CytoscapePlugin/plugins"
preservelastmodified="true" />
- </target>
-
- <!-- ensure Cytoscape plugins directory is available -->
- <target name="check-cytohome">
- <available property="cytohome-ok"
file="${cytoscape.plugins.dir}/" />
- <fail unless="cytohome-ok" message="cytoscape.plugins.dir is
not defined!" />
- </target>
-
- <target name="doc" depends="compile,clean-docs" description="JavaDoc
${ant.project.name}.">
- <javadoc destdir="${apidocs.dir}" source="1.5"
breakiterator="true" Windowtitle="${ant.project.name} API Docs"
header="${ant.project.name}" classpathref="compile.classpath">
- <fileset dir="${src.dir}" defaultexcludes="yes">
- <exclude name="${test.subdir}/**" />
- <include name="**/*.java" />
- </fileset>
- <doctitle>${ant.project.name} API Docs</doctitle>
- </javadoc>
- </target>
-
- <target name="all" depends="clean,jar,doc,test" description="Do it
all--clean, compile code, create library jar, copy to repository, update
dependent plugins (based on build.properties), create java docs, run tests." />
-</project>
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