Author: mes Date: 2010-11-15 15:30:05 -0800 (Mon, 15 Nov 2010) New Revision: 22861
Added: csplugins/trunk/ucsd/mes/genomespace-plugin/ csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml csplugins/trunk/ucsd/mes/genomespace-plugin/src/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/genomespace/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/genomespace/plugin.props csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/genomespace/ csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/genomespace/UploadFileToGenomeSpaceTest.java Log: initial checking Added: csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml =================================================================== --- csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml 2010-11-15 23:30:05 UTC (rev 22861) @@ -0,0 +1,187 @@ +<?xml version="1.0" encoding="UTF-8"?> +<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</groupId> + <artifactId>genomespace-plugin</artifactId> + <version>1.0-SNAPSHOT</version> + <packaging>jar</packaging> + <name>sample-plugin</name> + + <build> + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-compiler-plugin</artifactId> + <configuration> + <source>1.6</source> + <target>1.6</target> + <optimize>true</optimize> + <showWarnings>true</showWarnings> + <showDeprecation>true</showDeprecation> + </configuration> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-jar-plugin</artifactId> + <configuration> + <archive> + <manifestEntries> + <Cytoscape-Plugin>cytoscape.genomespace.GenomeSpacePlugin</Cytoscape-Plugin> + </manifestEntries> + </archive> + </configuration> + </plugin> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>2.2-beta-5</version> + <configuration> + <descriptorRefs> + <descriptorRef>jar-with-dependencies</descriptorRef> + </descriptorRefs> + </configuration> + <executions> + <execution> + <id>make-assembly</id> + <phase>package</phase> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>cytoscape</groupId> + <artifactId>application</artifactId> + <version>2.8.0-beta3</version> + <scope>provided</scope> + </dependency> + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>3.8.1</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>commons-codec</groupId> + <artifactId>commons-codec</artifactId> + <version>1.4</version> + </dependency> + <dependency> + <groupId>commons-httpclient</groupId> + <artifactId>commons-httpclient</artifactId> + <version>3.1</version> + </dependency> + <dependency> + <groupId>commons-io</groupId> + <artifactId>commons-io</artifactId> + <version>1.4</version> + </dependency> + <dependency> + <groupId>commons-lang</groupId> + <artifactId>commons-lang</artifactId> + <version>2.5</version> + </dependency> + <dependency> + <groupId>commons-logging</groupId> + <artifactId>commons-logging</artifactId> + <version>1.1.1</version> + </dependency> + <dependency> + <groupId>commons-logging</groupId> + <artifactId>commons-logging</artifactId> + <version>1.1.1</version> + </dependency> + <dependency> + <groupId>log4j</groupId> + <artifactId>log4j</artifactId> + <version>1.2.16</version> + </dependency> + <dependency> + <groupId>net.java.dev.jets3t</groupId> + <artifactId>jets3t</artifactId> + <version>0.7.4</version> + </dependency> + <dependency> + <groupId>org.codehaus.jettison</groupId> + <artifactId>jettison</artifactId> + <version>1.2</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-core</artifactId> + <version>1.2</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-client</artifactId> + <version>1.2</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-json</artifactId> + <version>1.3</version> + </dependency> + <dependency> + <groupId>javax.ws.rs</groupId> + <artifactId>jsr311-api</artifactId> + <version>1.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>genomespace-cdk</artifactId> + <version>1.0-beta1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>gs-common-util</artifactId> + <version>1.0-beta1</version> + </dependency> + </dependencies> + + <repositories> + <repository> + <id>java.net</id> + <name>Java.net</name> + <url>http://download.java.net/maven/2/</url> + </repository> + <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>cytoscape_thirdparty</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Third Party</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> + </repository> + </repositories> + +</project> Added: csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java 2010-11-15 23:30:05 UTC (rev 22861) @@ -0,0 +1,23 @@ +package cytoscape.genomespace; + +import cytoscape.Cytoscape; +import cytoscape.plugin.CytoscapePlugin; + + +/** + * This class is used to instantiate your plugin. Put whatever initialization code + * you need into the no argument constructor (the only one that will be called). + * The actual functionality of your plugin can be in this class, but should + * probably be separated into separted classes that get instantiated here. + */ +public class GenomeSpacePlugin extends CytoscapePlugin { + + public GenomeSpacePlugin() { + // Properly initializes things. + super(); + + // This action represents the actual behavior of the plugin. + UploadFileToGenomeSpace action = new UploadFileToGenomeSpace(); + Cytoscape.getDesktop().getCyMenus().addAction(action); + } +} Added: csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java 2010-11-15 23:30:05 UTC (rev 22861) @@ -0,0 +1,99 @@ +package cytoscape.genomespace; + +import cytoscape.Cytoscape; +import cytoscape.util.CytoscapeAction; +import cytoscape.util.FileUtil; +import cytoscape.logger.CyLogger; +import java.awt.event.ActionEvent; +import javax.swing.JOptionPane; + +import java.io.File; +import java.awt.FileDialog; +import java.util.List; + +import org.genomespace.client.GsFile; +import org.genomespace.client.GsSession; +import org.genomespace.client.User; + +/** + * A simple action. Change the names as appropriate and + * then fill in your expected behavior in the actionPerformed() + * method. + */ +public class UploadFileToGenomeSpace extends CytoscapeAction { + + private static final long serialVersionUID = 9988760123456789L; + private static final CyLogger logger = CyLogger.getLogger(UploadFileToGenomeSpace.class); + + public UploadFileToGenomeSpace() { + // Give your action a name here + super("Upload File"); + + // Set the menu you'd like here. Plugins don't need + // to live in the Plugins menu, so choose whatever + // is appropriate! + setPreferredMenu("Plugins.GenomeSpace"); + } + + public void actionPerformed(ActionEvent e) { + + try { + File f = FileUtil.getFile("",FileDialog.LOAD); + if ( f == null ) + return; + + // login to GenomeSpace + GsSession client = new GsSession(); + String username = "test"; + String password = "password"; + User user = client.login(username, password); + System.out.println("Logged in to GenomeSpace: " + client.isLoggedIn() + " as " + user.getUsername()); + + + + + GsFile gsf = new GsFile(f); + client.uploadFile(gsf); + + // list the files present for this user + List<GsFile> myFiles = client.list(); + System.out.println("Files on GenomeSpace for " + user.getUsername()); + for (GsFile aFile: myFiles){ + System.out.println("\t" + aFile.getFilename()); + } + + // Download the file back from GenomeSpace + myFiles = client.list(); + if (myFiles.size() > 0){ + System.out.println("Downloading " + myFiles.get(0).getFilename()); + GsFile localCopy = client.downloadFile(myFiles.get(0)); + System.out.println("\t saved to: " + localCopy.getFile().getAbsolutePath()); + } + + + // Delete a file from GenomeSpace + myFiles = client.list(); + if (myFiles.size() > 0){ + System.out.println("Deleting " + myFiles.get(0).getFilename()); + client.delete(myFiles.get(0)); + } + myFiles = client.list(); + System.out.println("After deletion, files on GenomeSpace for " + user.getUsername()); + for (GsFile aFile: myFiles){ + System.out.println("\t" + aFile.getFilename()); + } + + + // register a new user account + // (note this will fail for a duplicate username since there can only be one account for each name) + String newUsername = "test_cdk_" + System.currentTimeMillis(); + GsSession newClient = new GsSession(); + + User newUser = newClient.registerUser(newUsername, "password", "[email protected]"); + System.out.println("Logged in to GenomeSpace: " + newClient.isLoggedIn() +" as " + newUser.getUsername()); + } catch (Exception ex) { + logger.error("GenomeSpace failed",ex); + } + } + +} Added: csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/genomespace/plugin.props =================================================================== --- csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/genomespace/plugin.props (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/resources/cytoscape/genomespace/plugin.props 2010-11-15 23:30:05 UTC (rev 22861) @@ -0,0 +1,26 @@ +# 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=GenomeSpacePlugin + +# Description used to give users information about the plugin such as what it does. +# Html tags are encouraged for formatting purposes. +pluginDescription=GenomeSpace Plugin + +# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03 +pluginVersion=0.1 + +# Compatible Cytoscape version +cytoscapeVersion=2.8 + +# Category, use one of the categories listed on the website or create your own +pluginCategory=Other + +# 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=Mike Smoot:UCSD + Added: csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/genomespace/UploadFileToGenomeSpaceTest.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/genomespace/UploadFileToGenomeSpaceTest.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace-plugin/src/test/java/cytoscape/genomespace/UploadFileToGenomeSpaceTest.java 2010-11-15 23:30:05 UTC (rev 22861) @@ -0,0 +1,17 @@ +package cytoscape.genomespace; + +import junit.framework.Test; +import junit.framework.TestCase; + +/** + * Unit test for MyAction. + */ +public class UploadFileToGenomeSpaceTest extends TestCase { + + /** + * Rigourous Test :-) + */ + public void testMyAction() { + assertTrue( true ); + } +} -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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