Author: kono
Date: 2010-02-17 16:06:45 -0800 (Wed, 17 Feb 2010)
New Revision: 19356
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
Log:
Made task monitor more informative. It displays currently processed data
sources and if it fails, display error massage to on the monitor.
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
2010-02-17 23:50:53 UTC (rev 19355)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClientPlugin.java
2010-02-18 00:06:45 UTC (rev 19356)
@@ -31,35 +31,46 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
package edu.ucsd.bioeng.idekerlab.biomartclient;
import java.awt.event.ActionEvent;
import javax.swing.AbstractAction;
+import javax.swing.JMenu;
import cytoscape.Cytoscape;
import cytoscape.data.webservice.WebServiceClientManager;
import cytoscape.plugin.CytoscapePlugin;
import edu.ucsd.bioeng.idekerlab.biomartclient.ui.BiomartMainDialog;
-
/**
- * Biomart web service client plugin.
+ * Biomart web service client plugin main class.
*/
public class BiomartClientPlugin extends CytoscapePlugin {
/**
* Creates a new BiomartClientPlugin object.
+ *
* @throws Exception
*/
public BiomartClientPlugin() throws Exception {
// Register this client to the manager.
WebServiceClientManager.registerClient(BiomartClient.getClient());
-
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("File.Import").add(new
AbstractAction("Import attributes from Biomart...") {
+ final JMenu menu =
Cytoscape.getDesktop().getCyMenus().getMenuBar()
+ .getMenu("File.Import");
+
+ if (menu != null) {
+ menu.add(new AbstractAction("Import attributes from
Biomart...") {
+ private static final long serialVersionUID =
-1303677510967797368L;
+
public void actionPerformed(ActionEvent e) {
BiomartMainDialog.showUI();
}
});
+ } else {
+ throw new IllegalStateException(
+ "Could not register BioMart Client to
Cytoscape menu.");
+ }
}
}
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
2010-02-17 23:50:53 UTC (rev 19355)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartStub.java
2010-02-18 00:06:45 UTC (rev 19356)
@@ -194,7 +194,6 @@
InputStream is = URLUtil.getBasicInputStream(targetURL);
-
final Document registry = builder.parse(is);
// Extract each datasource
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
2010-02-17 23:50:53 UTC (rev 19355)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartAttrMappingPanel.java
2010-02-18 00:06:45 UTC (rev 19356)
@@ -34,66 +34,64 @@
*/
package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
import cytoscape.Cytoscape;
-
import cytoscape.data.CyAttributes;
import cytoscape.data.CyAttributesUtils;
-
import cytoscape.data.webservice.AttributeImportQuery;
import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.WebServiceClientManager;
import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
-import cytoscape.data.webservice.WebServiceClientManager;
-
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
-
import cytoscape.task.ui.JTaskConfig;
-
import cytoscape.task.util.TaskManager;
-
import cytoscape.util.swing.AttributeImportPanel;
-
import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartClient;
import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Attribute;
import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Dataset;
import edu.ucsd.bioeng.idekerlab.biomartclient.utils.Filter;
import edu.ucsd.bioeng.idekerlab.biomartclient.utils.XMLQueryBuilder;
-
import giny.model.Node;
-import java.awt.event.ActionEvent;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-
-import java.io.IOException;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import javax.swing.DefaultListModel;
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-import javax.swing.JOptionPane;
-
-
/**
*
*/
public class BiomartAttrMappingPanel extends AttributeImportPanel implements
PropertyChangeListener {
+
+ private static final long serialVersionUID = 3574198525811249639L;
+
private static final Icon LOGO = new
ImageIcon(BiomartAttrMappingPanel.class.getResource("/images/logo_biomart2.png"));
+
private Map<String, String> datasourceMap;
private Map<String, Map<String, String[]>> attributeMap;
private Map<String, List<String>> attributeListOrder;
private Map<String, Map<String, String>> attrNameMap;
private Map<String, Map<String, String>> filterMap;
+
+ private final TaskMonitor monitor;
+
private enum SourceType {
DATABASE,
ATTRIBUTE,
@@ -102,9 +100,7 @@
private boolean cancelFlag = false;
private boolean initialized = false;
-
- private String statusMessage;
-
+
private final BiomartStub stub = (BiomartStub)
WebServiceClientManager.getClient("biomart")
.getClientStub();
@@ -119,8 +115,8 @@
databaseFilter.add("Pancreatic_Expression");
}
- public BiomartAttrMappingPanel() throws Exception {
- this(LOGO, "", "Available attributes");
+ public BiomartAttrMappingPanel(final TaskMonitor monitor) throws
Exception {
+ this(LOGO, "", "Available attributes", monitor);
}
/**
@@ -130,14 +126,22 @@
* @param title DOCUMENT ME!
* @throws Exception
*/
- public BiomartAttrMappingPanel(Icon logo, String title, String
attrPanelLabel)
+ public BiomartAttrMappingPanel(Icon logo, String title, String
attrPanelLabel, final TaskMonitor monitor)
throws Exception {
super(logo, title, attrPanelLabel);
+ this.monitor = monitor;
+
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
BiomartMainDialog.getPropertyChangeSupport().addPropertyChangeListener(this);
initDataSources();
}
+
+ /**
+ * Access data sources and build GUI.
+ *
+ * @throws Exception
+ */
private void initDataSources() throws Exception {
datasourceMap = new HashMap<String, String>();
attributeMap = new HashMap<String, Map<String, String[]>>();
@@ -145,7 +149,8 @@
filterMap = new HashMap<String, Map<String, String>>();
attrNameMap = new HashMap<String, Map<String, String>>();
- loadDBList();
+ monitor.setPercentCompleted(0);
+ loadMartServiceList();
loadFilter();
}
@@ -153,20 +158,35 @@
return initialized;
}
- private void loadDBList() throws Exception {
- final Map<String, Map<String, String>> reg = stub.getRegistry();
+ private void loadMartServiceList() {
+ Map<String, Map<String, String>> reg = null;
+ monitor.setStatus("Accessing Mart service registry...");
+ try {
+ reg = stub.getRegistry();
+ } catch (IOException e1) {
+ monitor.setException(e1, "Could not retreve list of
Mart Services from registry.");
+ } catch (ParserConfigurationException e1) {
+ monitor.setException(e1, "Could not parse list of Mart
Services.");
+ } catch (SAXException e1) {
+ monitor.setException(e1, "Could not parse list of Mart
Services.");
+ }
+ monitor.setPercentCompleted(10);
+
+ final int registryCount = reg.size();
+ int increment = 90/registryCount;
+ int percentCompleted = 10;
Map<String, String> datasources;
List<String> dsList = new ArrayList<String>();
-
for (String databaseName : reg.keySet()) {
+
Map<String, String> detail = reg.get(databaseName);
// Add the datasource if its visible
if (detail.get("visible").equals("1")
&& (databaseFilter.contains(databaseName) == false)
&& (cancelFlag == false)) {
String dispName = detail.get("displayName");
-
+ monitor.setStatus("Connecting to " + dispName);
try {
datasources =
stub.getAvailableDatasets(databaseName);
} catch (IOException e) {
@@ -182,6 +202,9 @@
return;
}
+
+ percentCompleted += increment;
+ monitor.setPercentCompleted(percentCompleted);
}
Collections.sort(dsList);
Modified:
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
===================================================================
---
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
2010-02-17 23:50:53 UTC (rev 19355)
+++
coreplugins/trunk/BioMartClient/src/edu/ucsd/bioeng/idekerlab/biomartclient/ui/BiomartMainDialog.java
2010-02-18 00:06:45 UTC (rev 19356)
@@ -34,45 +34,36 @@
*/
package edu.ucsd.bioeng.idekerlab.biomartclient.ui;
-import cytoscape.Cytoscape;
-
-import cytoscape.data.webservice.WebServiceClientManager;
-
-import cytoscape.layout.Tunable;
-
-import cytoscape.task.Task;
-import cytoscape.task.TaskMonitor;
-
-import cytoscape.task.ui.JTaskConfig;
-
-import cytoscape.task.util.TaskManager;
-
-import cytoscape.util.ModuleProperties;
-import cytoscape.util.SwingWorker;
-
import java.awt.Color;
-import java.awt.GridLayout;
-
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
-
import java.util.List;
-import javax.swing.BoxLayout;
import javax.swing.JDialog;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
-import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
-import javax.swing.SpringLayout;
import javax.swing.event.SwingPropertyChangeSupport;
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.layout.Tunable;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.SwingWorker;
+
/**
- *
+ * BioMart client main GUI.
*/
public class BiomartMainDialog extends JDialog implements
PropertyChangeListener {
+
+ private static final long serialVersionUID = 8693726765795163080L;
+
+ // Actual dialog. This is a singleton.
private static BiomartMainDialog mainDialog = null;
protected static Object pcsO = new Object();
protected static PropertyChangeSupport pcs = new
SwingPropertyChangeSupport(pcsO);
@@ -91,7 +82,7 @@
private static BiomartAttrMappingPanel panel;
/**
- * DOCUMENT ME!
+ * Build and display Dialog
*/
public static void showUI() {
if ((mainDialog == null) || (initialized == false)) {
@@ -108,18 +99,17 @@
// Execute Task in New Thread; pop open JTask Dialog
Box.
TaskManager.executeTask(task, jTaskConfig);
- } else {
+ } else
mainDialog.setVisible(true);
- }
}
- private BiomartMainDialog() throws Exception {
+ private BiomartMainDialog(final TaskMonitor monitor) throws Exception {
super(Cytoscape.getDesktop(), false);
- setTitle("Biomart Web Service Client");
+ setTitle("BioMart Web Service Client");
// Create a tabbed pane
- JTabbedPane tabs = new JTabbedPane();
- List<Tunable> tunables =
WebServiceClientManager.getClient("biomart").getProps()
+ final JTabbedPane tabs = new JTabbedPane();
+ final List<Tunable> tunables =
WebServiceClientManager.getClient("biomart").getProps()
.getTunables();
final JPanel tPanel = new JPanel();
@@ -163,9 +153,9 @@
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 1.0;
tPanel.add(jLabel4, gridBagConstraints);
- //
+
- panel = new BiomartAttrMappingPanel();
+ panel = new BiomartAttrMappingPanel(monitor);
panel.addPropertyChangeListener(this);
tabs.addTab("Query", panel);
tabs.addTab("Property", tPanel);
@@ -177,9 +167,9 @@
static class SetupUITask implements Task {
private TaskMonitor taskMonitor;
- SwingWorker worker;
public SetupUITask() {
+ super();
}
/**
@@ -188,8 +178,7 @@
* @return DOCUMENT ME!
*/
public String getTitle() {
- // TODO Auto-generated method stub
- return "Accessing Biomart Web Service...";
+ return "Checking accessible BioMart Services...";
}
/**
@@ -204,11 +193,11 @@
* DOCUMENT ME!
*/
public void run() {
- taskMonitor.setStatus("Initializing Biomart Web Service
Client.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setStatus("Checking available Mart
services.\n\nThis process may take a while.\nPlease wait...");
taskMonitor.setPercentCompleted(-1);
try {
- mainDialog = new BiomartMainDialog();
+ mainDialog = new BiomartMainDialog(taskMonitor);
} catch (InterruptedException ie) {
//System.out.println("============== GOT
interaption");
} catch (Exception e) {
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