Author: mes
Date: 2012-05-01 11:58:55 -0700 (Tue, 01 May 2012)
New Revision: 29059
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/NetworkTypeSelectionDialog.java
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveNetworkToGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveSessionToGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace/genomespace-webstart/README.txt
Log:
updates to export networks to genomespace
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-05-01 18:52:17 UTC (rev 29058)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/GSUtils.java
2012-05-01 18:58:55 UTC (rev 29059)
@@ -163,5 +163,19 @@
final int lastDotPos = fileName.lastIndexOf('.');
return lastDotPos == -1 ? fileName : fileName.substring(0,
lastDotPos);
}
+
+ // Returns the directory component of "path"
+ public static String dirName(final String path) {
+ final int lastSlashPos = path.lastIndexOf('/');
+ return path.substring(0, lastSlashPos + 1);
+ }
+
+
+ // Returns the basename component of "path"
+ public static String baseName(final String path) {
+ final int lastSlashPos = path.lastIndexOf('/');
+ return lastSlashPos == -1 ? path : path.substring(lastSlashPos + 1);
+ }
+
}
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/NetworkTypeSelectionDialog.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/NetworkTypeSelectionDialog.java
2012-05-01 18:52:17 UTC (rev 29058)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/NetworkTypeSelectionDialog.java
2012-05-01 18:58:55 UTC (rev 29059)
@@ -18,7 +18,7 @@
final class NetworkTypeSelectionDialog extends JDialog {
private String networkType;
private final JRadioButton sifRadioButton;
- private final JRadioButton nnfRadioButton;
+// private final JRadioButton nnfRadioButton;
private final JRadioButton xgmmlRadioButton;
private final JRadioButton gmlRadioButton;
private final JButton okButton;
@@ -39,9 +39,9 @@
sifRadioButton = new JRadioButton("SIF", true);
group.add(sifRadioButton);
radioButtonPane.add(sifRadioButton);
- nnfRadioButton = new JRadioButton("NNF");
- group.add(nnfRadioButton);
- radioButtonPane.add(nnfRadioButton);
+// nnfRadioButton = new JRadioButton("NNF");
+// group.add(nnfRadioButton);
+// radioButtonPane.add(nnfRadioButton);
xgmmlRadioButton = new JRadioButton("XGMML");
group.add(xgmmlRadioButton);
radioButtonPane.add(xgmmlRadioButton);
@@ -58,8 +58,8 @@
public void actionPerformed(ActionEvent
actionEvent) {
if
(NetworkTypeSelectionDialog.this.sifRadioButton.isSelected())
NetworkTypeSelectionDialog.this.networkType = "SIF";
- else if
(NetworkTypeSelectionDialog.this.nnfRadioButton.isSelected())
-
NetworkTypeSelectionDialog.this.networkType = "NNF";
+// else if
(NetworkTypeSelectionDialog.this.nnfRadioButton.isSelected())
+//
NetworkTypeSelectionDialog.this.networkType = "NNF";
else if
(NetworkTypeSelectionDialog.this.xgmmlRadioButton.isSelected())
NetworkTypeSelectionDialog.this.networkType = "XGMML";
else if
(NetworkTypeSelectionDialog.this.gmlRadioButton.isSelected())
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveNetworkToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveNetworkToGenomeSpace.java
2012-05-01 18:52:17 UTC (rev 29058)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveNetworkToGenomeSpace.java
2012-05-01 18:58:55 UTC (rev 29059)
@@ -1,8 +1,9 @@
package cytoscape.genomespace;
+import cytoscape.CyNetwork;
+import cytoscape.view.CyNetworkView;
import cytoscape.Cytoscape;
-import cytoscape.data.writers.CytoscapeSessionWriter;
import cytoscape.logger.CyLogger;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
@@ -11,14 +12,25 @@
import cytoscape.util.CytoscapeAction;
import cytoscape.util.FileUtil;
+import cytoscape.data.readers.GMLParser;
+import cytoscape.data.readers.GMLWriter;
+import cytoscape.data.writers.InteractionWriter;
+import cytoscape.data.writers.XGMMLWriter;
+
import java.awt.FileDialog;
import java.awt.event.ActionEvent;
import java.io.File;
+import java.io.FileWriter;
+import java.io.OutputStreamWriter;
+import java.io.FileOutputStream;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
+import java.util.Vector;
import javax.swing.ImageIcon;
import javax.swing.JOptionPane;
+import java.net.URISyntaxException;
import org.genomespace.datamanager.core.GSFileMetadata;
import org.genomespace.client.DataManagerClient;
@@ -70,24 +82,14 @@
// Make sure the file name ends with the network type
extension:
if (!saveFileName.toLowerCase().endsWith("." +
networkType))
saveFileName += "." + networkType;
-/*
- // Create Task
- final File tempFile = File.createTempFile("temp",
"cysession");
- final Task task = new
SaveSessionTask(tempFile.getPath(), saveFileName,
-
dataManagerClient);
- // Configure JTask Dialog Pop-Up Box
- JTaskConfig jTaskConfig = new JTaskConfig();
+ final File localNetworkFile = saveNetworkLocally(
networkType );
- jTaskConfig.displayCancelButton(false);
- jTaskConfig.setOwner(Cytoscape.getDesktop());
- jTaskConfig.displayCloseButton(true);
- jTaskConfig.displayStatus(true);
- jTaskConfig.setAutoDispose(true);
+ GSFileMetadata uploadedFileMetadata =
dataManagerClient.uploadFile(localNetworkFile,
+
GSUtils.dirName(saveFileName),
+
GSUtils.baseName(saveFileName));
+ localNetworkFile.delete();
- // Execute Task in New Thread; pop open JTask Dialog
Box.
- TaskManager.executeTask(task, jTaskConfig);
-*/
} catch (final Exception ex) {
logger.error("GenomeSpace failed", ex);
JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
@@ -95,4 +97,33 @@
JOptionPane.ERROR_MESSAGE);
}
}
+
+ private File saveNetworkLocally(String type) throws IOException,
URISyntaxException {
+ final File tempFile = File.createTempFile("tempNetwork", type);
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ CyNetworkView view = Cytoscape.getCurrentNetworkView();
+
+ OutputStreamWriter fileWriter = null;
+ if ( type.equalsIgnoreCase("xgmml") ) {
+ fileWriter = new OutputStreamWriter(new
FileOutputStream(tempFile), "UTF-8");
+ final XGMMLWriter writer = new XGMMLWriter(network,
view);
+ writer.write(fileWriter);
+ } else if ( type.equalsIgnoreCase("sif") ) {
+ fileWriter = new FileWriter(tempFile);
+ InteractionWriter.writeInteractions(network,
fileWriter, null);
+ } else if ( type.equalsIgnoreCase("gml") ) {
+ List list = new Vector();
+ fileWriter = new FileWriter(tempFile);
+ GMLWriter gmlWriter = new GMLWriter();
+ gmlWriter.writeGML(network, view, list);
+ GMLParser.printList(list, fileWriter);
+ } else {
+ throw new UnsupportedOperationException("Can't write "
+ type + " format files to GenomeSpace.");
+ }
+
+ if ( fileWriter != null )
+ fileWriter.close();
+
+ return tempFile;
+ }
}
Modified:
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveSessionToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveSessionToGenomeSpace.java
2012-05-01 18:52:17 UTC (rev 29058)
+++
csplugins/trunk/ucsd/mes/genomespace/genomespace-plugin/src/main/java/cytoscape/genomespace/SaveSessionToGenomeSpace.java
2012-05-01 18:58:55 UTC (rev 29059)
@@ -140,8 +140,7 @@
taskMonitor.setPercentCompleted(20);
final File localFile = new File(localFileName);
uploadedFileMetadata =
- dataManagerClient.uploadFile(localFile,
dirName(uploadPath),
-
baseName(uploadPath));
+ dataManagerClient.uploadFile(localFile,
GSUtils.dirName(uploadPath), GSUtils.baseName(uploadPath));
localFile.delete();
} catch (Exception e) {
taskMonitor.setException(e, "Could not write session to
the file: "
@@ -184,17 +183,4 @@
public String getTitle() {
return "Saving Cytoscape Session";
}
-
- // Returns the directory component of "path"
- private String dirName(final String path) {
- final int lastSlashPos = path.lastIndexOf('/');
- return path.substring(0, lastSlashPos + 1);
- }
-
-
- // Returns the basename component of "path"
- private String baseName(final String path) {
- final int lastSlashPos = path.lastIndexOf('/');
- return lastSlashPos == -1 ? path : path.substring(lastSlashPos
+ 1);
- }
}
Modified: csplugins/trunk/ucsd/mes/genomespace/genomespace-webstart/README.txt
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/genomespace-webstart/README.txt
2012-05-01 18:52:17 UTC (rev 29058)
+++ csplugins/trunk/ucsd/mes/genomespace/genomespace-webstart/README.txt
2012-05-01 18:58:55 UTC (rev 29059)
@@ -10,7 +10,7 @@
The actual command:
- mvn webstart:jnlp-inline
-Dwebstart.url=http://chianti.ucsd.edu/genomespace
+ mvn clean webstart:jnlp-inline
-Dwebstart.url=http://chianti.ucsd.edu/genomespace
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