Author: mcreech
Date: 2011-05-19 14:02:15 -0700 (Thu, 19 May 2011)
New Revision: 25505
Added:
csplugins/trunk/agilent/creech/HyperEdgeEditor/pom.xml
csplugins/trunk/agilent/creech/HyperEdgeEditor/readme.txt
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/just-classes.xml
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/java/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/plugin.props
Modified:
csplugins/trunk/agilent/creech/HyperEdgeEditor/release-notes.html
csplugins/trunk/agilent/creech/HyperEdgeEditor/version-history.html
Log:
v2.68
Added: csplugins/trunk/agilent/creech/HyperEdgeEditor/pom.xml
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/pom.xml
(rev 0)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/pom.xml 2011-05-19
21:02:15 UTC (rev 25505)
@@ -0,0 +1,211 @@
+<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/xsd/maven-4.0.0.xsd";>
+ <modelVersion>4.0.0</modelVersion>
+
+
+ <groupId>cytoscape.hyperedge</groupId>
+ <artifactId>HyperEdgeEditor</artifactId>
+<!-- We'd like to just pass in a 'version' parameter, but passing in something
like '-Dversion=2.63' throws
+ a NPE in maven, so we instead use 'my-version': -->
+<!-- <version>2.6x-SNAPSHOT</version> -->
+ <version>${my-version}</version>
+ <packaging>jar</packaging>
+
+ <name>HyperEdgeEditor</name>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <!-- The default is to build the SNAPSHOT if no repo-type param is
present: -->
+ <repo-type>snapshot</repo-type>
+ <repo-name>Ramblas Snaphots</repo-name>
+
<repo-url>http://ramblas.scs.agilent.com:8081/nexus/content/repositories/snapshots</repo-url>
+ <repo-unique>false</repo-unique>
+ </properties>
+
+ <profiles>
+ <profile>
+ <id>release</id>
+ <activation>
+ <property>
+ <name>repo-type</name>
+ <value>release</value>
+ </property>
+ </activation>
+ <properties>
+ <repo-name>Ramblas Releases</repo-name>
+
<repo-url>http://ramblas.scs.agilent.com:8081/nexus/content/repositories/releases</repo-url>
+ <repo-unique>true</repo-unique>
+ </properties>
+ </profile>
+ </profiles>
+
+ <build>
+ <plugins>
+ <plugin>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.8.1</version>
+ </plugin>
+ <plugin>
+ <!-- running maven javadoc:javadoc will produce javadocs in
target/apidocs -->
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.7</version>
+ <!-- bind to the install phase: -->
+ <executions>
+ <execution>
+ <phase>install</phase>
+ <goals>
+ <goal>javadoc</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <encoding>UTF-8</encoding>
+ <locale>en</locale>
+ <javadocVersion>1.6</javadocVersion>
+
<reportOutputDirectory>${project.build.directory}</reportOutputDirectory>
+ <destDir>apidocs</destDir>
+ <links>
+ <link>http://download.oracle.com/javase/1.6.0/docs/api/</link>
+ </links>
+ <footer>HyperEdgeEditor ${project.version} API</footer>
+ <header>HyperEdgeEditor ${project.version} API</header>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2.1</version>
+ <executions>
+ <!-- Associate this assembly with the package lifecycle stage (e.g.,
'mvn package'): -->
+ <execution>
+ <id>my-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <!-- use predefined descriptor: -->
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <!-- Also assemble a jar using our custom descriptor to gather just
classes: -->
+ <descriptors>
+ <descriptor>src/main/assembly/just-classes.xml</descriptor>
+ </descriptors>
+ <!-- Manifest additions: -->
+ <archive>
+ <manifestEntries>
+
<Cytoscape-Plugin>cytoscape.hyperedge.editor.HyperEdgeEditorPlugin</Cytoscape-Plugin>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ <repository>
+ <id>ramblas_releases</id>
+ <name>Ramblas Releases</name>
+
<url>http://ramblas.scs.agilent.com:8081/nexus/content/repositories/releases</url>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ </repository>
+ <repository>
+ <id>ramblas_snapshots</id>
+ <name>Ramblas Snapshots</name>
+
<url>http://ramblas.scs.agilent.com:8081/nexus/content/repositories/snapshots</url>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>cytoscape</artifactId>
+ <version>2.8.1</version>
+ <!-- At runtime, we don't need to include Cytoscape since it is already
there: -->
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>editor</artifactId>
+ <version>2.8.1</version>
+ <classifier>jar-with-dependencies</classifier>
+ <!-- At runtime, we don't need to include the Editor plugin since it is
already there: -->
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>com.agilent.labs.lsiutils</groupId>
+ <artifactId>LSIUtils</artifactId>
+ <version>0.1x-SNAPSHOT</version>
+ </dependency>
+ <!-- This is a dependency from LSIUtils, but we include here to stop
including
+ all the skinlf code in the plugin jar created, which we don't use -->
+ <dependency>
+ <groupId>com.l2prod.gui.plaf.skin</groupId>
+ <artifactId>skinlf</artifactId>
+ <version>5.8.2006</version>
+ <scope>provided</scope>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.hyperedge</groupId>
+ <artifactId>HyperEdge</artifactId>
+ <version>2.6x-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.2</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <distributionManagement>
+ <repository>
+ <id>ramblas_deployment</id>
+ <name>${repo-name}</name>
+ <url>${repo-url}</url>
+ <!-- keep replacing the snapshot-don't save unique versions of each
snapshot released -->
+ <uniqueVersion>${repo-unique}</uniqueVersion>
+ </repository>
+ </distributionManagement>
+</project>
\ No newline at end of file
Property changes on: csplugins/trunk/agilent/creech/HyperEdgeEditor/pom.xml
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added: csplugins/trunk/agilent/creech/HyperEdgeEditor/readme.txt
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/readme.txt
(rev 0)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/readme.txt 2011-05-19
21:02:15 UTC (rev 25505)
@@ -0,0 +1,30 @@
+How To Build
+------------
+
+Use Maven to build this project.
+
+Most of the Maven goals take a my-version parameter as in:
+
+ -Dmy-version=<version>
+
+<version> is the version string to use for this release. For a SNAPSHOT
release, it may be something like '2.6x-SNAPSHOT' and for a specific release,
it may be something like '2.68'. For example, -Dmy-version=2.68 or
-Dmy-version-2.6x-SNAPSHOT.
+
+A few of the important Maven goals are:
+ package--compiles, runs tests and stores jar of code in the 'target'
directory (uses my-version param). This includes
+ two important jars:
+ target/HyperEdgeEditor-<version>-just-classes.jar -- just the
classes that make up the HyperEdgeEditor
+ target/HyperEdgeEditor-<version>-jar-with-dependencies.jar --
everything needed to run the HyperEdgeEditor
+
as a plugin of Cytoscape.
+ install--same as package, but also generates javadocs (in target/apidocs)
and places the
+ jar in your local repository (uses my-version param).
+ deploy [-Drepo-type=release]--
+ same as install but includes placing the jars in the ramblas snapshot
or release repository.
+ If the optional -Drepo-type=release is present, the jar will be placed
in the
+ release repository.
+ Example usage:
+ mvn deploy -Dmy-version=2.6x-SNAPSHOT
+ mvn deploy -Dmy-version=2.68 -Drepo-type=release
+
+Building JavaDocs
+
+ mvn javadoc:javadoc -Dmy-version=2.68--builds javadoc documentation placed
in the target/apidocs directory
Property changes on: csplugins/trunk/agilent/creech/HyperEdgeEditor/readme.txt
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified: csplugins/trunk/agilent/creech/HyperEdgeEditor/release-notes.html
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/release-notes.html
2011-05-19 20:56:51 UTC (rev 25504)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/release-notes.html
2011-05-19 21:02:15 UTC (rev 25505)
@@ -1,16 +1,33 @@
<HTML>
<HEAD>
-<TITLE>HyperEdgeEditor Release Notes (version 2.66)</TITLE>
+<TITLE>HyperEdgeEditor Release Notes (version 2.68)</TITLE>
</HEAD>
<BODY>
-<H1>HyperEdgeEditor Release Notes (version 2.65)</H1>
+<H1>HyperEdgeEditor Release Notes (version 2.68)</H1>
<OL>
-<LI>No source code changes--just changes to packaging so HEE will show up
under the Cytoscape 2.6.3 plugin manager.</LI>
+<LI>Various changes to update HyperEdgeEditor to work under Cytoscape 2.8.
This included:
+<OL type=a>
+<LI>Updating deprecated references to old Cytoscape visual style API.</LI>
+<LI>Updating the HyperEdge Sample Networks menu item to work correctly under
Cytoscape 2.8.</LI>
+<LI>Complete change to Maven 3 build environment.</LI>
</OL>
+<LI>Added Cytoscape legal headers to all java files.</LI>
+</OL>
<H1>Prior Notes</H1>
+<H2>HyperEdgeEditor Release Notes (version 2.67)</H2>
+<OL>
+<LI>Developer Note: Changed build.xml to take cytoscape.dir parameter.</LI>
+<LI>Updated to use new Cytoscape 2.7.0 libraries and changed packaging so HEE
will show up under the Cytoscape 2.7.0 plugin manager.</LI>
+</OL>
+
+<H2>HyperEdgeEditor Release Notes (version 2.66)</H2>
+<OL>
+<LI>No source code changes--just changes to packaging so HEE will show up
under the Cytoscape 2.6.3 plugin manager.</LI>
+</OL>
+
<H2>HyperEdgeEditor Release Notes (version 2.65)</H2>
<OL>
<li>Fixed bug where itemDropped() would allow dropping of a palette entry
@@ -327,7 +344,7 @@
<HR>
-<SMALL><EM>This page was last updated: 07/08/09</EM></SMALL>
+<SMALL><EM>This page was last updated: 05/18/11</EM></SMALL>
</BODY>
-</HTML>
\ No newline at end of file
+</HTML>
Added:
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/just-classes.xml
===================================================================
---
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/just-classes.xml
(rev 0)
+++
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/just-classes.xml
2011-05-19 21:02:15 UTC (rev 25505)
@@ -0,0 +1,25 @@
+<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
http://maven.apache.org/xsd/assembly-1.1.2.xsd";>
+ <!-- This assembly builds a jar of just the class files for use as
middleware for a higher
+ level application. -->
+ <id>just-classes</id>
+ <formats>
+ <format>jar</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <fileSets>
+ <fileSet>
+ <!-- Don't add any extra directories to the ones under ${basedir}/bin in
the fileset.
+ So, 'com' will be the top level directory. -->
+ <outputDirectory>/</outputDirectory>
+ <!-- Where to start building this file set; stuff in the bin directory
-->
+ <directory>${basedir}/bin</directory>
+ <excludes>
+ <exclude>cytoscape/hyperedge/editor/unittest/**</exclude>
+ <exclude>**/plugin.props</exclude>
+ <exclude>**/package.html</exclude>
+ </excludes>
+ </fileSet>
+ </fileSets>
+</assembly>
Property changes on:
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/assembly/just-classes.xml
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Added:
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/plugin.props
===================================================================
---
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/plugin.props
(rev 0)
+++
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/plugin.props
2011-05-19 21:02:15 UTC (rev 25505)
@@ -0,0 +1,40 @@
+# This props file would be filled out and included in the plugin jar
+# file. This props file will be used to put information into the
+# Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=HyperEdgeEditor
+
+# Description used to give users information about the plugin such as
+# what it does. Html tags are encouraged for formatting purposes.
+
+pluginDescription=Add, remove, and modify HyperEdges in a Cytoscape Network.
+
+# Plugin version number, this must be two numbers separated by a
+# decimal. Ex. 0.2, 14.03
+
+pluginVersion=2.68
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.8
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Functional Enrichment
+
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin,
+# Ex. http://my-lab-site.org
+
+# projectURL=
+
+# 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=Allan Kuchinsky and Aditya Vailaya:Agilent
Labs;Michael Creech:Blue Oak Software
+
+# Date this plugin/plugin version was released
+releaseDate=May 18, 2011
\ No newline at end of file
Property changes on:
csplugins/trunk/agilent/creech/HyperEdgeEditor/src/main/resources/cytoscape/hyperedge/editor/plugin.props
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified: csplugins/trunk/agilent/creech/HyperEdgeEditor/version-history.html
===================================================================
--- csplugins/trunk/agilent/creech/HyperEdgeEditor/version-history.html
2011-05-19 20:56:51 UTC (rev 25504)
+++ csplugins/trunk/agilent/creech/HyperEdgeEditor/version-history.html
2011-05-19 21:02:15 UTC (rev 25505)
@@ -5,7 +5,31 @@
<H1>HyperEdgeEditor Version History</H1>
<UL>
-
+<LI><STRONG>HyperEdgeEditor, Version 2.68 (05/18/11)</STRONG>
+<OL>
+<LI>Various changes to update HyperEdgeEditor to work under Cytoscape 2.8.
This included:
+<OL type=a>
+<LI>Updating deprecated references to old Cytoscape visual style API.</LI>
+<LI>Updating the HyperEdge Sample Networks menu item to work correctly under
Cytoscape 2.8.</LI>
+<LI>Complete change to Maven 3 build environment.</LI>
+</OL>
+<LI>Added Cytoscape legal headers to all java files.</LI>
+</OL>
+<LI><STRONG>HyperEdgeEditor, Version 2.67 (05/13/11)</STRONG>
+<OL>
+<LI>Various changes to update HyperEdgeEditor to work under Cytoscape 2.8.
This included:
+<OL type=a>
+<LI>Updating deprecated references to old Cytoscape visual style API.</LI>
+<LI>Updating the HyperEdge Sample Networks menu item to work correctly under
Cytoscape 2.8.</LI>
+<LI>Complete change to Maven 3 build environment.</LI>
+</OL>
+<LI>Added Cytoscape legal headers to all java files.</LI>
+</OL>
+<LI><STRONG>HyperEdgeEditor, Version 2.67 (03/19/10)</STRONG>
+<OL>
+<LI>Developer Note: Changed build.xml to take cytoscape.dir parameter.</LI>
+<LI>Changed packaging so HEE will show up under the Cytoscape 2.7.0 plugin
manager.</LI>
+</OL>
<LI><STRONG>HyperEdgeEditor, Version 2.66 (07/08/09)</STRONG>
<OL>
<LI>No source code changes--just changes to packaging so HEE will show up
under the Cytoscape 2.6.3 plugin manager.</LI>
@@ -231,4 +255,4 @@
</UL>
<HR>
-<SMALL><EM>This page was last updated: 04/08/09</EM></SMALL>
\ No newline at end of file
+<SMALL><EM>This page was last updated: 05/18/11</EM></SMALL>
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