Author: mes
Date: 2010-11-15 17:42:53 -0800 (Mon, 15 Nov 2010)
New Revision: 22862
Added:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/assembly/
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/assembly/src.xml
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml
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
Log:
added a bunch of new actions
Modified: csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml 2010-11-15 23:30:05 UTC
(rev 22861)
+++ csplugins/trunk/ucsd/mes/genomespace-plugin/pom.xml 2010-11-16 01:42:53 UTC
(rev 22862)
@@ -6,7 +6,7 @@
<artifactId>genomespace-plugin</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
- <name>sample-plugin</name>
+ <name>GenomeSpace Plugin</name>
<build>
<plugins>
@@ -22,24 +22,18 @@
</configuration>
</plugin>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jar-plugin</artifactId>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2-beta-5</version>
<configuration>
<archive>
<manifestEntries>
<Cytoscape-Plugin>cytoscape.genomespace.GenomeSpacePlugin</Cytoscape-Plugin>
</manifestEntries>
</archive>
+ <descriptors>
+ <descriptor>src/main/assembly/src.xml</descriptor>
+ </descriptors>
</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>
@@ -109,7 +103,7 @@
<dependency>
<groupId>org.codehaus.jettison</groupId>
<artifactId>jettison</artifactId>
- <version>1.2</version>
+ <version>1.1</version>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
Added: csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/assembly/src.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/assembly/src.xml
(rev 0)
+++ csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/assembly/src.xml
2010-11-16 01:42:53 UTC (rev 22862)
@@ -0,0 +1,18 @@
+<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0
http://maven.apache.org/xsd/assembly-1.1.0.xsd";>
+ <id>jar-with-dependencies</id>
+ <formats>
+ <format>jar</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <dependencySets>
+ <dependencySet>
+ <outputDirectory>/</outputDirectory>
+ <useProjectArtifact>true</useProjectArtifact>
+ <unpack>true</unpack>
+ <scope>runtime</scope>
+ <useTransitiveDependencies>false</useTransitiveDependencies>
+ </dependencySet>
+ </dependencySets>
+</assembly>
Added:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DeleteFileInGenomeSpace.java
2010-11-16 01:42:53 UTC (rev 22862)
@@ -0,0 +1,61 @@
+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 DeleteFileInGenomeSpace extends CytoscapeAction {
+
+ private static final long serialVersionUID = 4234432889999989L;
+ private static final CyLogger logger =
CyLogger.getLogger(DeleteFileInGenomeSpace.class);
+
+ public DeleteFileInGenomeSpace() {
+ // Give your action a name here
+ super("Delete 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 {
+
+ // login to GenomeSpace
+ GsSession client = new GsSession();
+ String username = "test";
+ String password = "password";
+ User user = client.login(username, password);
+ logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+
+ // list the files present for this user
+ List<GsFile> myFiles = client.list();
+ if (myFiles.size() > 0){
+ logger.info("Deleting " + myFiles.get(0).getFilename());
+ client.delete(myFiles.get(0));
+ }
+
+ } catch (Exception ex) {
+ logger.error("GenomeSpace failed",ex);
+ }
+ }
+
+}
Added:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/DownloadFileFromGenomeSpace.java
2010-11-16 01:42:53 UTC (rev 22862)
@@ -0,0 +1,64 @@
+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 DownloadFileFromGenomeSpace extends CytoscapeAction {
+
+ private static final long serialVersionUID = 7777788473487659L;
+ private static final CyLogger logger =
CyLogger.getLogger(DownloadFileFromGenomeSpace.class);
+
+ public DownloadFileFromGenomeSpace() {
+ // Give your action a name here
+ super("Download 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 {
+
+ // login to GenomeSpace
+ GsSession client = new GsSession();
+ String username = "test";
+ String password = "password";
+ User user = client.login(username, password);
+ logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+
+ // list the files present for this user
+ List<GsFile> myFiles = client.list();
+
+ // Download the file back from GenomeSpace
+ myFiles = client.list();
+ if (myFiles.size() > 0){
+ logger.info("Downloading " +
myFiles.get(0).getFilename());
+ GsFile localCopy = client.downloadFile(myFiles.get(0));
+ logger.info("\t saved to: " +
localCopy.getFile().getAbsolutePath());
+ }
+
+ } catch (Exception ex) {
+ logger.error("GenomeSpace failed",ex);
+ }
+ }
+}
Modified:
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
2010-11-15 23:30:05 UTC (rev 22861)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
2010-11-16 01:42:53 UTC (rev 22862)
@@ -17,7 +17,17 @@
super();
// This action represents the actual behavior of the plugin.
- UploadFileToGenomeSpace action = new UploadFileToGenomeSpace();
- Cytoscape.getDesktop().getCyMenus().addAction(action);
+ UploadFileToGenomeSpace uploadAction = new
UploadFileToGenomeSpace();
+ Cytoscape.getDesktop().getCyMenus().addAction(uploadAction);
+
+ DeleteFileInGenomeSpace deleteAction = new
DeleteFileInGenomeSpace();
+ Cytoscape.getDesktop().getCyMenus().addAction(deleteAction);
+
+ DownloadFileFromGenomeSpace downloadAction = new
DownloadFileFromGenomeSpace();
+ Cytoscape.getDesktop().getCyMenus().addAction(downloadAction);
+
+ ListFilesInGenomeSpace listAction = new
ListFilesInGenomeSpace();
+ Cytoscape.getDesktop().getCyMenus().addAction(listAction);
+
}
}
Added:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/ListFilesInGenomeSpace.java
2010-11-16 01:42:53 UTC (rev 22862)
@@ -0,0 +1,79 @@
+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 javax.swing.JList;
+import javax.swing.JScrollPane;
+import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+
+import java.io.File;
+import java.awt.FileDialog;
+import java.awt.Dimension;
+import java.util.List;
+import java.util.Vector;
+
+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 ListFilesInGenomeSpace extends CytoscapeAction {
+
+ private static final long serialVersionUID = 1234487711999989L;
+ private static final CyLogger logger =
CyLogger.getLogger(ListFilesInGenomeSpace.class);
+
+ public ListFilesInGenomeSpace() {
+ // Give your action a name here
+ super("List Available Files");
+
+ // 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 {
+
+ // login to GenomeSpace
+ GsSession client = new GsSession();
+ String username = "test";
+ String password = "password";
+ User user = client.login(username, password);
+ logger.info("Logged in to GenomeSpace: " + client.isLoggedIn()
+ " as " + user.getUsername());
+
+ // list the files present for this user
+ List<GsFile> myFiles = client.list();
+ logger.info("Files on GenomeSpace for " + user.getUsername());
+ Vector<String> fileNames = new Vector<String>();
+ for (GsFile aFile: myFiles) {
+ fileNames.add(aFile.getFilename());
+ }
+
+ displayFiles(fileNames);
+
+ } catch (Exception ex) {
+ logger.error("GenomeSpace failed",ex);
+ }
+ }
+
+ private void displayFiles(Vector<String> fileNames) {
+ JList jl = new JList( fileNames );
+ jl.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ JScrollPane scrollPane = new JScrollPane(jl);
+ scrollPane.setPreferredSize(new Dimension(250, 80));
+ JPanel jp = new JPanel();
+ jp.add(scrollPane);
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),jp);
+ }
+}
Modified:
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
2010-11-15 23:30:05 UTC (rev 22861)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/UploadFileToGenomeSpace.java
2010-11-16 01:42:53 UTC (rev 22862)
@@ -42,55 +42,15 @@
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());
+ logger.info("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);
}
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