Author: mes
Date: 2012-07-31 16:24:25 -0700 (Tue, 31 Jul 2012)
New Revision: 30056
Added:
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/README.txt
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/pom.xml
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/jnlp/
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/jnlp/template.vm
csplugins/trunk/ucsd/mes/genomespace/weblaunch/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/pom.xml
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/LaunchHelper.java
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/StreamGobbler.java
Modified:
csplugins/trunk/ucsd/mes/genomespace/pom.xml
Log:
added new weblaunch code
Modified: csplugins/trunk/ucsd/mes/genomespace/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/pom.xml 2012-07-31 23:04:06 UTC
(rev 30055)
+++ csplugins/trunk/ucsd/mes/genomespace/pom.xml 2012-07-31 23:24:25 UTC
(rev 30056)
@@ -13,6 +13,8 @@
<module>genomespace-plugin</module>
<module>ndb-reader</module>
<module>cytable-reader</module>
+ <module>weblaunch</module>
+ <module>weblaunch-webstart</module>
<!-- webstart actually has a different parent
(cytoscape-webstart)
so we don't include it here! It needs to be built
separately.
<module>genomespace-webstart</module>
Added: csplugins/trunk/ucsd/mes/genomespace/weblaunch/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/weblaunch/pom.xml
(rev 0)
+++ csplugins/trunk/ucsd/mes/genomespace/weblaunch/pom.xml 2012-07-31
23:24:25 UTC (rev 30056)
@@ -0,0 +1,82 @@
+<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/maven-v4_0_0.xsd";>
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <artifactId>genomespace-parent</artifactId>
+ <groupId>cytoscape</groupId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>weblaunch</artifactId>
+ <packaging>jar</packaging>
+ <name>Cytoscape Web Launch</name>
+
+
+
+ <build>
+
+ <!-- This block allows fields to be substituted into resource files,
+ such as the version number in cytoscape.props. -->
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <filtering>true</filtering>
+ </resource>
+ </resources>
+
+ <plugins>
+ <plugin>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2</version>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <archive>
+ <manifest>
+ <mainClass>cytoscape.weblaunch.LaunchHelper</mainClass>
+ </manifest>
+ </archive>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots
-->
+ <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>
+ </repositories>
+
+</project>
+
Added:
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/LaunchHelper.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/LaunchHelper.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/LaunchHelper.java
2012-07-31 23:24:25 UTC (rev 30056)
@@ -0,0 +1,226 @@
+package cytoscape.weblaunch;
+
+import java.awt.Desktop;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URL;
+import java.net.URISyntaxException;
+import java.net.MalformedURLException;
+import javax.swing.JEditorPane;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.JFileChooser;
+import java.nio.channels.*;
+import java.io.FileOutputStream;
+
+public class LaunchHelper {
+ private static String version = "Cytoscape_v2.8.3";
+ private static String installerURL =
"http://www.cytoscape.org/download.html";;
+
+ private static final String MAC = "mac os x";
+ private static final String WINDOWS = "windows";
+
+ public static void main(String[] args) {
+
+ String os = System.getProperty("os.name").toLowerCase();
+
+ String exe = getExecutable(os);
+ String path = getBestGuessPath(os);
+
+ if ( !executableExists(path,exe) ) {
+ File file = getDirectory();
+ if ( file != null )
+ path = file.getAbsolutePath();
+ }
+
+ while ( !executableExists(path,exe) ) {
+ int res = JOptionPane.showConfirmDialog(null, "We can't
find the Cytoscape executable in the specified location.\nWould you like to try
another location?", "Select Cytoscape Installation Directory",
JOptionPane.YES_NO_OPTION);
+
+ if ( res == JOptionPane.YES_OPTION ) {
+ JFileChooser fc = new JFileChooser();
+
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ fc.setDialogTitle("Select Cytoscape
Installation Directory");
+
+ int returnVal = fc.showOpenDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION)
+ path =
fc.getSelectedFile().getAbsolutePath();
+ } else {
+ return;
+ }
+ }
+
+ String[] command =
createCommand(getFile(path,exe),downloadPlugins());
+
+ try {
+ Runtime rt = Runtime.getRuntime();
+ Process p = rt.exec(command);
+ StreamGobbler errorGobbler = new
StreamGobbler(p.getErrorStream(), "ERROR");
+ StreamGobbler outputGobbler = new
StreamGobbler(p.getInputStream(), "OUTPUT");
+ errorGobbler.start();
+ outputGobbler.start();
+ int exitVal = p.waitFor();
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(null,
+ "Cannot launch
"+exe+" in\n" + path,
+ "Cannot Launch
Executable",
+
JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ private static String[] createCommand(File f, String[] plugins) {
+ String[] command = new String[ (plugins.length * 2) + 1];
+ int i = 0;
+ command[i] = f.getAbsolutePath();
+ for ( String p : plugins ) {
+ command[++i] = "-p";
+ command[++i] = p;
+ }
+ return command;
+ }
+
+ private static String[] downloadPlugins() {
+
+ String[] urls = new String[] {
+
"http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=496";, //
GenomeSpace libs
+
"http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=495";, //
GenomeSpace
+
"http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=494";, //
CyTable reader
+
"http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=493"; // NDB
Reader
+ };
+
+ String[] filePaths = new String[urls.length];
+ for (int i = 0; i < urls.length; i++) {
+ filePaths[i] = downloadURL(urls[i]).getAbsolutePath();
+ }
+ return filePaths;
+ }
+
+ private static File downloadURL(String u) {
+ File f = null;
+ FileOutputStream fos = null;
+ try {
+ URL url = new URL(u);
+ f = File.createTempFile("plugin",".jar");
+ ReadableByteChannel rbc =
Channels.newChannel(url.openStream());
+ fos = new FileOutputStream(f);
+ fos.getChannel().transferFrom(rbc, 0, 1 << 24);
+ fos.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ } finally {
+ if ( fos != null ) {
+ try { fos.close(); } catch (IOException ioe) { }
+ fos = null;
+ }
+ }
+ return f;
+ }
+
+ private static boolean executableExists(String path, String exe) {
+ File file = getFile(path,exe);
+ return file.exists();
+ }
+
+ private static File getFile(String path, String exe) {
+ return new File(path + System.getProperty("file.separator") +
exe);
+ }
+
+ private static String getExecutable(String os) {
+ String exe;
+ if (os.startsWith(WINDOWS))
+ exe = "cytoscape.bat";
+ else
+ exe = "cytoscape.sh";
+
+ return exe;
+ }
+
+ private static String getBestGuessPath(String os) {
+ String path;
+ if (os.equals(MAC))
+ path = "/Applications";
+ else
+ path = System.getProperty("user.home");
+ path += "/" + version;
+ return path;
+ }
+
+ private static void openURL(String urlString) {
+ URL url = null;
+
+ try {
+
+ url = new URL(urlString);
+
+ if (!Desktop.isDesktopSupported()) {
+ JOptionPane.showMessageDialog(null,
+ "Java Desktop
is not supported",
+ "Cannot
Launch Link",
+
JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ Desktop desktop = Desktop.getDesktop();
+ if (!desktop.isSupported(Desktop.Action.BROWSE)) {
+ JOptionPane.showMessageDialog(null,
+ "Java Desktop
doesn't support the browse action",
+ "Cannot
Launch Link",
+
JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ if (url == null) {
+ JOptionPane.showMessageDialog(null,
+ "InvalidURL:
Failed to launch the link to installer:\n"+installerURL,
+ "Cannot
Launch Link",
+
JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ URI uri = new URI(url.toString());
+ desktop.browse(uri);
+ } catch (URISyntaxException e) {
+ JOptionPane.showMessageDialog(null,
+ "URISyntaxException:
Failed to launch the link to installer:\n"+url,
+ "Cannot Launch Link",
+
JOptionPane.ERROR_MESSAGE);
+ } catch (MalformedURLException e) {
+ JOptionPane.showMessageDialog(null,
+
"MalformedURLException: Failed to launch the link to installer:\n"+url,
+ "Cannot Launch Link",
+
JOptionPane.ERROR_MESSAGE);
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(null,
+ "IOException: Failed
to launch the link to installer:\n"+url,
+ "Cannot Launch Link",
+
JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ private static File getDirectory() {
+ int res = JOptionPane.showConfirmDialog(null, "Is Cytoscape
installed on this computer?", "Select Cytoscape Installation Directory",
JOptionPane.YES_NO_OPTION);
+
+ if ( res == JOptionPane.YES_OPTION ) {
+ JOptionPane.showMessageDialog(null, "Please choose the
directory where\nCytoscape is installed on your system.", "Select Cytoscape
Installation Directory", JOptionPane.INFORMATION_MESSAGE);
+ JFileChooser fc = new JFileChooser();
+ fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ fc.setDialogTitle("Select Cytoscape Installation
Directory");
+
+ int returnVal = fc.showOpenDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION)
+ return fc.getSelectedFile();
+ else
+ return null;
+ } else {
+ JOptionPane.showMessageDialog(null, "Please download
and install Cytoscape.\nWe'll open a browser to the download page.", "Select
Cytoscape Installation Directory", JOptionPane.INFORMATION_MESSAGE);
+ openURL(installerURL);
+ return null;
+ }
+ }
+}
Added:
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/StreamGobbler.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/StreamGobbler.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/weblaunch/src/main/java/cytoscape/weblaunch/StreamGobbler.java
2012-07-31 23:24:25 UTC (rev 30056)
@@ -0,0 +1,29 @@
+package cytoscape.weblaunch;
+
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.IOException;
+
+public class StreamGobbler extends Thread {
+ InputStream is;
+ String type;
+
+ StreamGobbler(InputStream is, String type) {
+ this.is = is;
+ this.type = type;
+ }
+
+ public void run() {
+ try {
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
+ String line = null;
+ while ((line = br.readLine()) != null){
+ System.out.println(type + ">" + line);
+ }
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ }
+ }
+}
Added: csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/README.txt
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/README.txt
(rev 0)
+++ csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/README.txt
2012-07-31 23:24:25 UTC (rev 30056)
@@ -0,0 +1,17 @@
+
+This project generates a JNLP file and associated jars suitable for running
+Cytoscape as a webstart. To generate things run:
+
+ mvn webstart:jnlp-inline -Dwebstart.url=http://example.com
+
+Note that the "-Dwebstart.url=http://example.com"; argument is manadatory to
+provide the jnlp file with a codebase.
+
+
+If this is your first time using Webstart you must create a keystore:
+
+ keytool -genkey -alias cytoscape -keypass secret
+ enter "secret" for the password.
+
+The actual keystore file created is assumed to be in: ${user.home}/.keystore
+
Added: csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/pom.xml
(rev 0)
+++ csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/pom.xml
2012-07-31 23:24:25 UTC (rev 30056)
@@ -0,0 +1,94 @@
+<!-- Test project which creates and signs a jar artifact -->
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <artifactId>genomespace-parent</artifactId>
+ <groupId>cytoscape</groupId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
+
+ <groupId>cytoscape</groupId>
+ <artifactId>weblaunch-webstart</artifactId>
+ <packaging>pom</packaging>
+ <name>Cytoscape Web Launch Webstart</name>
+
+ <!-- This is the url used to define the codebase of the jnlp file. -->
+ <url>${webstart.url}</url>
+
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots
-->
+ <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>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo.webstart</groupId>
+ <artifactId>webstart-maven-plugin</artifactId>
+ <version>1.0-beta-1</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>jnlp-inline</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <excludeTransitive>true</excludeTransitive>
+
<resourcesDirectory>${project.basedir}/src/main/resources</resourcesDirectory>
+ <libPath>lib</libPath>
+ <jnlp>
+
<inputTemplateResourcePath>${project.basedir}/src/main/jnlp</inputTemplateResourcePath>
+ <inputTemplate>template.vm</inputTemplate>
+ <outputFile>cytoscape.jnlp</outputFile>
+ <mainClass>cytoscape.weblaunch.LaunchHelper</mainClass>
+ </jnlp>
+ <!--
+ If this is your first time using Webstart you must create a
keystore:
+ keytool -genkey -alias cytoscape -keypass secret
+ enter "secret" for the password.
+ The actual keystore file created is assumed to be in:
${user.home}/.keystore
+ -->
+ <sign>
+ <keypass>secret</keypass>
+ <storepass>secret</storepass>
+ <alias>cytoscape</alias>
+ <verify>true</verify>
+ </sign>
+ <verbose>true</verbose>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>weblaunch</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
+ </dependencies>
+
+</project>
Added:
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/jnlp/template.vm
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/jnlp/template.vm
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/weblaunch-webstart/src/main/jnlp/template.vm
2012-07-31 23:24:25 UTC (rev 30056)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="utf-8"?>
+<jnlp codebase="$project.Url" href="$outputFile">
+ <information>
+ <title>Cytoscape</title>
+ <vendor>Cytoscape Consortium</vendor>
+ <homepage href="http://cytoscape.org"/>
+ <offline-allowed/>
+ </information>
+ <security>
+ <all-permissions/>
+ </security>
+ <resources>
+ <j2se version="$j2seVersion"/>
+ $dependencies
+ </resources>
+ <application-desc main-class="$mainClass">
+ </application-desc>
+</jnlp>
+
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
