Author: ruschein
Date: 2011-06-20 16:10:14 -0700 (Mon, 20 Jun 2011)
New Revision: 25823
Added:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadOntologyAndAnnotationFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableNetworkFromGenomeSpace.java
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/LoadAttrsFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadSessionFromGenomeSpace.java
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
Log:
Added more GS import support and clean up some minor issues.
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
2011-06-20 22:52:18 UTC (rev 25822)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/GenomeSpacePlugin.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -32,10 +32,15 @@
LoadNetworkFromGenomeSpace loadNetworkAction = new
LoadNetworkFromGenomeSpace();
Cytoscape.getDesktop().getCyMenus().addAction(loadNetworkAction);
+ LoadTableNetworkFromGenomeSpace loadTableNetworkAction =
+ new LoadTableNetworkFromGenomeSpace();
+
Cytoscape.getDesktop().getCyMenus().addAction(loadTableNetworkAction);
+
LoadAttrsFromGenomeSpace loadAttrsAction = new
LoadAttrsFromGenomeSpace();
Cytoscape.getDesktop().getCyMenus().addAction(loadAttrsAction);
- LoadTableAttrsFromGenomeSpace loadTableAttrsAction = new
LoadTableAttrsFromGenomeSpace();
+ LoadTableAttrsFromGenomeSpace loadTableAttrsAction =
+ new LoadTableAttrsFromGenomeSpace();
Cytoscape.getDesktop().getCyMenus().addAction(loadTableAttrsAction);
LoadSessionFromGenomeSpace loadSessionAction = new
LoadSessionFromGenomeSpace();
@@ -46,5 +51,9 @@
SaveNetworkToGenomeSpace saveNetworkAction = new
SaveNetworkToGenomeSpace();
Cytoscape.getDesktop().getCyMenus().addAction(saveNetworkAction);
+
+ LoadOntologyAndAnnotationFromGenomeSpace
loadOntologyAndAnnotationFromGenomeSpace =
+ new LoadOntologyAndAnnotationFromGenomeSpace();
+
Cytoscape.getDesktop().getCyMenus().addAction(loadOntologyAndAnnotationFromGenomeSpace);
}
}
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadAttrsFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadAttrsFromGenomeSpace.java
2011-06-20 22:52:18 UTC (rev 25822)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadAttrsFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -26,7 +26,7 @@
private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
public LoadAttrsFromGenomeSpace() {
- super("Load Attributes",
+ super("Load Attributes...",
new
ImageIcon(LoadAttrsFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
// Set the menu you'd like here. Plugins don't need
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
2011-06-20 22:52:18 UTC (rev 25822)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadNetworkFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -29,7 +29,7 @@
private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
public LoadNetworkFromGenomeSpace() {
- super("Load Network",
+ super("Load Network...",
new
ImageIcon(LoadNetworkFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
// Set the menu you'd like here. Plugins don't need
Copied:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadOntologyAndAnnotationFromGenomeSpace.java
(from rev 25819,
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java)
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadOntologyAndAnnotationFromGenomeSpace.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadOntologyAndAnnotationFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -0,0 +1,88 @@
+package cytoscape.genomespace;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.List;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import org.genomespace.client.DataManagerClient;
+import org.genomespace.client.GsSession;
+import org.genomespace.client.User;
+import org.genomespace.client.ui.GSFileBrowserDialog;
+import org.genomespace.datamanager.core.GSFileMetadata;
+
+
+public class LoadOntologyAndAnnotationFromGenomeSpace extends CytoscapeAction {
+ private static final long serialVersionUID = 7571788473486759L;
+ private static final CyLogger logger =
CyLogger.getLogger(LoadOntologyAndAnnotationFromGenomeSpace.class);
+
+ public LoadOntologyAndAnnotationFromGenomeSpace() {
+ super("Load Ontology and Annotations...",
+ new
ImageIcon(LoadAttrsFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
+
+ // Set the menu you'd like here. Plugins don't need
+ // to live in the Plugins menu, so choose whatever
+ // is appropriate!
+ setPreferredMenu("File.Import.GenomeSpace");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ File tempFile = null;
+ try {
+ final GsSession client = GSUtils.getSession();
+ final DataManagerClient dataManagerClient =
client.getDataManagerClient();
+
+ // Select the GenomeSpace file:
+ final List<String> acceptableExtensions = new
ArrayList<String>();
+ final GSFileBrowserDialog browserDialog =
+ new GSFileBrowserDialog(Cytoscape.getDesktop(),
dataManagerClient,
+ acceptableExtensions,
+
GSFileBrowserDialog.DialogType.FILE_SELECTION_DIALOG);
+ final GSFileMetadata fileMetadata =
browserDialog.getSelectedFileMetadata();
+ if (fileMetadata == null)
+ return;
+
+ // Download the GenomeSpace file:
+ tempFile = File.createTempFile("temp", "ont");
+ dataManagerClient.downloadFile(fileMetadata, tempFile,
true);
+
+ final ImportTextTableDialog dialog =
+ new
ImportTextTableDialog(Cytoscape.getDesktop(), tempFile,
+
fileMetadata.getName(),
+
ImportTextTableDialog.ONTOLOGY_AND_ANNOTATION_IMPORT);
+ dialog.pack();
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setVisible(true);
+ } catch (Exception ex) {
+ logger.error("GenomeSpace failed", ex);
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ ex.getMessage(),
"GenomeSpace Error",
+
JOptionPane.ERROR_MESSAGE);
+ } finally {
+ if (tempFile != null)
+ tempFile.delete();
+ }
+ }
+
+ private static String getExtension(final String fileName) {
+ final int lastDotPos = fileName.lastIndexOf('.');
+ return (lastDotPos == -1 ? fileName :
fileName.substring(lastDotPos)).toLowerCase();
+ }
+
+ private static String getNetworkTitle(final String fileName) {
+ final int lastDotPos = fileName.lastIndexOf('.');
+ return lastDotPos == -1 ? fileName : fileName.substring(0,
lastDotPos);
+ }
+}
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadSessionFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadSessionFromGenomeSpace.java
2011-06-20 22:52:18 UTC (rev 25822)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadSessionFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -36,7 +36,7 @@
static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
public LoadSessionFromGenomeSpace() {
- super("Load Session",
+ super("Load Session...",
new
ImageIcon(LoadSessionFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
// Set the menu you'd like here. Plugins don't need
Modified:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
2011-06-20 22:52:18 UTC (rev 25822)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -25,11 +25,11 @@
public class LoadTableAttrsFromGenomeSpace extends CytoscapeAction {
- private static final long serialVersionUID = 7577788473487659L;
- private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
+ private static final long serialVersionUID = 7572758437487659L;
+ private static final CyLogger logger =
CyLogger.getLogger(LoadTableAttrsFromGenomeSpace.class);
public LoadTableAttrsFromGenomeSpace() {
- super("Load Attributes from Table",
+ super("Load Attributes from Table...",
new
ImageIcon(LoadAttrsFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
// Set the menu you'd like here. Plugins don't need
Copied:
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableNetworkFromGenomeSpace.java
(from rev 25819,
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableAttrsFromGenomeSpace.java)
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableNetworkFromGenomeSpace.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace-plugin/src/main/java/cytoscape/genomespace/LoadTableNetworkFromGenomeSpace.java
2011-06-20 23:10:14 UTC (rev 25823)
@@ -0,0 +1,88 @@
+package cytoscape.genomespace;
+
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.readers.CyAttributesReader;
+import cytoscape.logger.CyLogger;
+import cytoscape.util.CytoscapeAction;
+
+import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
+
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.List;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import org.genomespace.client.DataManagerClient;
+import org.genomespace.client.GsSession;
+import org.genomespace.client.User;
+import org.genomespace.client.ui.GSFileBrowserDialog;
+import org.genomespace.datamanager.core.GSFileMetadata;
+
+
+public class LoadTableNetworkFromGenomeSpace extends CytoscapeAction {
+ private static final long serialVersionUID = 7577788473487659L;
+ private static final CyLogger logger =
CyLogger.getLogger(LoadTableNetworkFromGenomeSpace.class);
+
+ public LoadTableNetworkFromGenomeSpace() {
+ super("Load Network from Table...",
+ new
ImageIcon(LoadAttrsFromGenomeSpace.class.getResource("/images/genomespace_icon.gif")));
+
+ // Set the menu you'd like here. Plugins don't need
+ // to live in the Plugins menu, so choose whatever
+ // is appropriate!
+ setPreferredMenu("File.Import.GenomeSpace");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ File tempFile = null;
+ try {
+ final GsSession client = GSUtils.getSession();
+ final DataManagerClient dataManagerClient =
client.getDataManagerClient();
+
+ // Select the GenomeSpace file:
+ final List<String> acceptableExtensions = new
ArrayList<String>();
+ final GSFileBrowserDialog browserDialog =
+ new GSFileBrowserDialog(Cytoscape.getDesktop(),
dataManagerClient,
+ acceptableExtensions,
+
GSFileBrowserDialog.DialogType.FILE_SELECTION_DIALOG);
+ final GSFileMetadata fileMetadata =
browserDialog.getSelectedFileMetadata();
+ if (fileMetadata == null)
+ return;
+
+ // Download the GenomeSpace file:
+ tempFile = File.createTempFile("temp", "network");
+ dataManagerClient.downloadFile(fileMetadata, tempFile,
true);
+
+ final ImportTextTableDialog dialog =
+ new
ImportTextTableDialog(Cytoscape.getDesktop(), tempFile,
+
fileMetadata.getName(),
+
ImportTextTableDialog.NETWORK_IMPORT);
+ dialog.pack();
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setVisible(true);
+ } catch (Exception ex) {
+ logger.error("GenomeSpace failed", ex);
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ ex.getMessage(),
"GenomeSpace Error",
+
JOptionPane.ERROR_MESSAGE);
+ } finally {
+ if (tempFile != null)
+ tempFile.delete();
+ }
+ }
+
+ private static String getExtension(final String fileName) {
+ final int lastDotPos = fileName.lastIndexOf('.');
+ return (lastDotPos == -1 ? fileName :
fileName.substring(lastDotPos)).toLowerCase();
+ }
+
+ private static String getNetworkTitle(final String fileName) {
+ final int lastDotPos = fileName.lastIndexOf('.');
+ return lastDotPos == -1 ? fileName : fileName.substring(0,
lastDotPos);
+ }
+}
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