Author: kono
Date: 2012-07-05 15:18:01 -0700 (Thu, 05 Jul 2012)
New Revision: 29775
Removed:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
Log:
fixed #967 Datasource can be selected before initialization to avoid very long
initialization time.
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
2012-07-05 20:53:55 UTC (rev 29774)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
2012-07-05 22:18:01 UTC (rev 29775)
@@ -6,12 +6,15 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.TreeSet;
import javax.xml.parsers.ParserConfigurationException;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.util.ListMultipleSelection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
@@ -24,7 +27,7 @@
private final BiomartRestClient client;
private Map<String, Map<String, String>> reg;
-
+ private final Map<String, String> name2DatasourceMap;
private LoadRepositoryResult result;
@@ -41,15 +44,42 @@
private Map<String, String> datasourceMap;
private List<String> dsList;
+
+ @Tunable(description="Please slect services you want to use")
+ public ListMultipleSelection<String> services;
public LoadRepositoryTask(final BiomartRestClient client) {
this.client = client;
+ this.name2DatasourceMap = new HashMap<String, String>();
+ try {
+ initServiceList();
+ } catch (Exception e) {
+ throw new IllegalStateException("Could not obtain
registry", e);
+ }
}
+
+ private final void initServiceList() throws IOException,
ParserConfigurationException, SAXException {
+ reg = client.getRegistry();
+
+ for (String databaseName : reg.keySet()) {
+ final Map<String, String> detail =
reg.get(databaseName);
+ if (detail.get("visible").equals("1")
+ &&
(databaseFilter.contains(databaseName) == false)) {
+ String dispName = detail.get("displayName");
+ name2DatasourceMap.put(dispName, databaseName);
+ }
+ }
+ final TreeSet<String> sortedSet = new
TreeSet<String>(name2DatasourceMap.keySet());
+ services = new ListMultipleSelection<String>(new
ArrayList<String>(sortedSet));
+ }
+
@Override
public void run(TaskMonitor taskMonitor) throws IOException,
ParserConfigurationException, SAXException {
+ final List<String> selected = services.getSelectedValues();
+
taskMonitor.setTitle("Loading list of available BioMart
Services. Please wait...");
taskMonitor.setStatusMessage("Loading list of available
Marts...");
@@ -58,9 +88,8 @@
logger.debug("Loading Repository...");
- reg = client.getRegistry();
taskMonitor.setProgress(0.1);
- final int registryCount = reg.size();
+ final int registryCount = selected.size();
float increment = 0.9f / registryCount;
float percentCompleted = 0.1f;
@@ -75,19 +104,22 @@
if (detail.get("visible").equals("1")
&&
(databaseFilter.contains(databaseName) == false)) {
String dispName = detail.get("displayName");
- try {
- datasources =
client.getAvailableDatasets(databaseName);
- } catch (IOException e) {
- // If timeout/connection error is
found, skip the source.
- percentCompleted += increment;
- continue;
- }
+ if (selected.contains(dispName)) {
+ try {
+ datasources =
client.getAvailableDatasets(databaseName);
+ } catch (IOException e) {
+ // If timeout/connection error
is found, skip the
+ // source.
+ percentCompleted += increment;
+ continue;
+ }
- for (String key : datasources.keySet()) {
- final String dataSource = dispName + "
- " + datasources.get(key);
- dsList.add(dataSource);
- datasourceMap.put(dataSource, key);
- taskMonitor.setStatusMessage("Loading
Data Source: " + dataSource);
+ for (String key : datasources.keySet())
{
+ final String dataSource =
dispName + " - " + datasources.get(key);
+ dsList.add(dataSource);
+ datasourceMap.put(dataSource,
key);
+
taskMonitor.setStatusMessage("Loading Data Source: " + dataSource);
+ }
}
}
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2012-07-05 20:53:55 UTC (rev 29774)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2012-07-05 22:18:01 UTC (rev 29775)
@@ -1,42 +1,30 @@
package org.cytoscape.io.webservice.biomart.task;
-import org.cytoscape.io.webservice.biomart.BiomartClient;
+import javax.swing.JDialog;
+
import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
-import org.cytoscape.io.webservice.biomart.ui.BiomartMainDialog;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ShowBiomartDialogTask extends AbstractTask {
-
+
private static final Logger logger =
LoggerFactory.getLogger(ShowBiomartDialogTask.class);
-
- private BiomartMainDialog dialog;
-
- private final BiomartClient client;
-
+
private final BiomartAttrMappingPanel panel;
-
private final LoadRepositoryTask loadTask;
-
- public ShowBiomartDialogTask(final BiomartAttrMappingPanel panel, final
BiomartClient client, final LoadRepositoryTask loadTask) {
-
+
+ public ShowBiomartDialogTask(final BiomartAttrMappingPanel panel, final
LoadRepositoryTask loadTask) {
this.panel = panel;
- this.client = client;
this.loadTask = loadTask;
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
- if(dialog == null) {
- final LoadRepositoryResult result =
loadTask.getResult();
- panel.initDataSources(result);
- logger.info("BioMart Client initialized.");
- }
+ final LoadRepositoryResult result = loadTask.getResult();
+ panel.initDataSources(result);
+ logger.info("BioMart Client initialized.");
+ ((JDialog)panel.getRootPane().getParent()).toFront();
}
-
- public BiomartMainDialog getDialog() {
- return dialog;
- }
}
Deleted:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2012-07-05 20:53:55 UTC (rev 29774)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2012-07-05 22:18:01 UTC (rev 29775)
@@ -1,76 +0,0 @@
-package org.cytoscape.io.webservice.biomart.task;
-
-import java.awt.event.ActionEvent;
-
-import javax.swing.JOptionPane;
-
-import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.application.swing.AbstractCyAction;
-import org.cytoscape.application.swing.CySwingApplication;
-import org.cytoscape.io.webservice.biomart.BiomartClient;
-import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.swing.DialogTaskManager;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- *
- * TODO: Add cancel function
- */
-public class ShowBiomartGUIAction extends AbstractCyAction {
-
- private static final long serialVersionUID = -1329132199540543764L;
-
- private static final Logger logger =
LoggerFactory.getLogger(ShowBiomartGUIAction.class);
-
- private final DialogTaskManager taskManager;
- private final CySwingApplication app;
-
- private ShowBiomartDialogTask showDialogTask;
- private final CyApplicationManager appManager;
-
- private final LoadRepositoryTask firstTask;
-
- public ShowBiomartGUIAction(final BiomartAttrMappingPanel panel, final
BiomartClient client,
- final TaskManager taskManager,
- final CyApplicationManager appManager,
- final CySwingApplication app) {
- super("Biomart...");
- setPreferredMenu("File.Import.Table.Public Databases");
-
- this.appManager = appManager;
- this.app = app;
- this.taskManager = (DialogTaskManager) taskManager;
-
- this.firstTask = new LoadRepositoryTask(client.getRestClient());
- this.showDialogTask = new ShowBiomartDialogTask(panel, client,
firstTask);
- }
-
- @Override
- public void actionPerformed(ActionEvent ae) {
- // State check: BioMart client needs at least a network to
create query string.
- final CyNetwork net = appManager.getCurrentNetwork();
- if(net == null) {
- JOptionPane.showMessageDialog(app.getJFrame(), "BioMart
Client needs at least one network to create query. Please import a network
first.",
- "No Network Found",
JOptionPane.INFORMATION_MESSAGE);
- return;
- }
-
- // Lazy instantiation. This process depends on network
connection.
- if (showDialogTask.getDialog() == null) {
- initDialog();
- } else {
-
showDialogTask.getDialog().setLocationRelativeTo(app.getJFrame());
- showDialogTask.getDialog().setVisible(true);
- }
- }
-
-
- private void initDialog() {
- taskManager.setExecutionContext(app.getJFrame());
- taskManager.execute(new TaskIterator(firstTask,
showDialogTask));
- }
-}
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2012-07-05 20:53:55 UTC (rev 29774)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2012-07-05 22:18:01 UTC (rev 29775)
@@ -100,6 +100,7 @@
protected JButton importButton;
protected JLabel titleLabel;
protected JButton resetButton;
+ protected JButton refreshButton;
protected CheckBoxJList attrCheckboxList;
protected DefaultListModel attrCheckboxListModel;
@@ -148,6 +149,7 @@
importButton = new JButton();
cancelButton = new JButton();
resetButton = new JButton();
+ refreshButton= new JButton();
setBackground(new java.awt.Color(255, 255, 255));
titleLabel.setBackground(new java.awt.Color(255, 255, 255));
@@ -262,13 +264,21 @@
});
cancelButton.setBackground(Color.white);
- resetButton.setText("Reset");
+ resetButton.setText("Clear");
resetButton.addActionListener(new
java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent
evt) {
resetButtonActionPerformed(evt);
}
});
resetButton.setBackground(Color.white);
+
+ refreshButton.setText("Refresh");
+ refreshButton.addActionListener(new
java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent
evt) {
+ refreshButtonActionPerformed(evt);
+ }
+ });
+ refreshButton.setBackground(Color.white);
GroupLayout layout = new GroupLayout(this);
this.setLayout(layout);
@@ -287,7 +297,7 @@
.addComponent(titleLabel)
.addGroup(
layout.createSequentialGroup()
-
.addComponent(resetButton)
+
.addComponent(resetButton).addPreferredGap(LayoutStyle.ComponentPlacement.RELATED).addComponent(refreshButton)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, 343,
Short.MAX_VALUE).addComponent(cancelButton)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
@@ -308,10 +318,11 @@
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addGroup(
layout.createParallelGroup(GroupLayout.Alignment.BASELINE).addComponent(importButton)
-
.addComponent(cancelButton).addComponent(resetButton)).addContainerGap()));
+
.addComponent(cancelButton).addComponent(resetButton).addComponent(refreshButton)).addContainerGap()));
} // </editor-fold>
protected abstract void resetButtonActionPerformed(ActionEvent evt);
+ protected abstract void refreshButtonActionPerformed(ActionEvent evt);
protected void importButtonActionPerformed(ActionEvent evt) {
importAttributes();
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2012-07-05 20:53:55 UTC (rev 29774)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2012-07-05 22:18:01 UTC (rev 29775)
@@ -44,6 +44,7 @@
import javax.swing.DefaultListModel;
import javax.swing.Icon;
import javax.swing.ImageIcon;
+import javax.swing.JComboBox;
import javax.swing.event.AncestorEvent;
import javax.swing.event.AncestorListener;
@@ -130,7 +131,7 @@
private void initPanel() {
LoadRepositoryTask firstTask = new
LoadRepositoryTask(client.getRestClient());
- ShowBiomartDialogTask showDialogTask = new
ShowBiomartDialogTask(this, client, firstTask);
+ ShowBiomartDialogTask showDialogTask = new
ShowBiomartDialogTask(this, firstTask);
taskManager.setExecutionContext(null);
taskManager.execute(new TaskIterator(firstTask,
showDialogTask));
@@ -148,16 +149,21 @@
}
public void setMartServiceList(LoadRepositoryResult res) {
+ databaseComboBox.removeAllItems();
+
this.datasourceMap = res.getDatasourceMap();
final List<String> dsList = res.getSortedDataSourceList();
for (String ds : dsList)
- this.databaseComboBox.addItem(ds);
+ this.databaseComboBox.addItem(ds);
}
public void loadFilter() {
+ Object selected = databaseComboBox.getSelectedItem();
+ if(selected == null)
+ return;
+
attributeTypeComboBox.removeAllItems();
-
- final String selectedDB =
databaseComboBox.getSelectedItem().toString();
+ final String selectedDB = selected.toString();
final String selectedDBName = datasourceMap.get(selectedDB);
fetchData(selectedDBName, SourceType.FILTER);
@@ -172,8 +178,12 @@
loadFilter();
}
- private void updateAttributeList() {
- final String selectedDB =
databaseComboBox.getSelectedItem().toString();
+ private void updateAttributeList() {
+ Object selected = databaseComboBox.getSelectedItem();
+ if(selected == null)
+ return;
+
+ final String selectedDB = selected.toString();
final String selectedDBName = datasourceMap.get(selectedDB);
List<String> order = attributeListOrder.get(selectedDBName);
@@ -415,4 +425,9 @@
}
+ @Override
+ protected void refreshButtonActionPerformed(ActionEvent evt) {
+ initPanel();
+ }
+
}
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