Author: kono
Date: 2011-01-25 15:08:56 -0800 (Tue, 25 Jan 2011)
New Revision: 23618
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTask.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
Log:
Attribute list update timing problem fixed.
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTask.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTask.java
2011-01-25 22:29:56 UTC (rev 23617)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTask.java
2011-01-25 23:08:56 UTC (rev 23618)
@@ -23,9 +23,9 @@
}
@Override
- public void run(TaskMonitor taskMonitor) throws Exception {
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setTitle("Loading available attributes...");
+ taskMonitor.setProgress(0.0);
this.attributeVals = client.getAttributes(datasourceName);
- System.out.println("######## Attr Count: " +
this.attributeVals.size());
- taskMonitor.setProgress(1.0);
}
}
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2011-01-25 22:29:56 UTC (rev 23617)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2011-01-25 23:08:56 UTC (rev 23618)
@@ -6,7 +6,6 @@
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.CyTableManager;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.swing.GUITaskManager;
@@ -34,8 +33,8 @@
final TaskManager taskManager,
final CyApplicationManager appManager,
final CySwingApplication app) {
- super("Import Tables from Biomart...", appManager);
- setPreferredMenu("File.Import");
+ super("from Biomart...", appManager);
+ setPreferredMenu("File.Import.Table.WebService");
this.app = app;
this.taskManager = (GUITaskManager) taskManager;
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-01-25 22:29:56 UTC (rev 23617)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-01-25 23:08:56 UTC (rev 23618)
@@ -103,9 +103,9 @@
protected javax.swing.JButton importButton;
protected javax.swing.JLabel titleLabel;
protected javax.swing.JButton resetButton;
- protected CheckBoxJList attrList;
+ protected CheckBoxJList attrCheckboxList;
- protected DefaultListModel model;
+ protected DefaultListModel attrCheckboxListModel;
// Title of the panel.
protected String panelTitle;
@@ -135,9 +135,9 @@
}
private void initComponents() {
- attrList = new CheckBoxJList();
- model = new DefaultListModel();
- attrList.setModel(model);
+ attrCheckboxList = new CheckBoxJList();
+ attrCheckboxListModel = new DefaultListModel();
+ attrCheckboxList.setModel(attrCheckboxListModel);
titleLabel = new javax.swing.JLabel();
databasePanel = new javax.swing.JPanel();
@@ -275,7 +275,7 @@
.createTitledBorder(attributePanelTitle));
availableAttrScrollPane
.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
- availableAttrScrollPane.setViewportView(attrList);
+ availableAttrScrollPane.setViewportView(attrCheckboxList);
GroupLayout availableAttrPanelLayout = new GroupLayout(
availableAttrPanel);
@@ -398,9 +398,7 @@
.addContainerGap()));
} // </editor-fold>
- protected void resetButtonActionPerformed(ActionEvent evt) {
- // TODO Auto-generated method stub
- }
+ protected abstract void resetButtonActionPerformed(ActionEvent evt);
protected void importButtonActionPerformed(ActionEvent evt) {
importAttributes();
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-01-25 22:29:56 UTC (rev 23617)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-01-25 23:08:56 UTC (rev 23618)
@@ -73,7 +73,8 @@
private static final long serialVersionUID = 3574198525811249639L;
private static final Icon LOGO = new ImageIcon(
-
BiomartAttrMappingPanel.class.getResource("/images/logo_biomart2.png"));
+ BiomartAttrMappingPanel.class
+
.getResource("/images/logo_biomart2.png"));
private Map<String, String> datasourceMap;
@@ -98,7 +99,7 @@
private Window parent;
private final BiomartClient client;
-
+
private int globalTableCounter;
/**
@@ -110,8 +111,7 @@
* DOCUMENT ME!
* @throws Exception
*/
- public BiomartAttrMappingPanel(
- final BiomartClient client,
+ public BiomartAttrMappingPanel(final BiomartClient client,
final TaskManager taskManager,
final CyApplicationManager appManager,
final CyTableManager tblManager, final CyNetworkManager
netManager) {
@@ -120,10 +120,10 @@
this.client = client;
this.taskManager = (GUITaskManager) taskManager;
this.appManager = appManager;
-
+
this.globalTableCounter = 0;
}
-
+
public void setParent(final Window parent) {
this.parent = parent;
}
@@ -145,7 +145,6 @@
// Load available filters for current source.
// loadFilter();
}
-
public void setMartServiceList(LoadRepositoryResult res) {
this.datasourceMap = res.getDatasourceMap();
@@ -177,32 +176,38 @@
final String selectedDBName = datasourceMap.get(selectedDB);
List<String> order = attributeListOrder.get(selectedDBName);
- model = new DefaultListModel();
- attrList.setModel(model);
+ attrCheckboxListModel = new DefaultListModel();
+ attrCheckboxList = new CheckBoxJList();
if (order != null) {
// List<String> sortedList = new
// ArrayList<String>(singleAttrMap.keySet());
// Collections.sort(sortedList);
for (String dispAttrName : order)
- model.addElement(dispAttrName);
+ attrCheckboxListModel.addElement(dispAttrName);
+ attrCheckboxList.setModel(attrCheckboxListModel);
+
availableAttrScrollPane.setViewportView(attrCheckboxList);
+ availableAttrScrollPane.repaint();
} else {
fetchData(selectedDBName, SourceType.ATTRIBUTE);
}
+
}
private void fetchData(final String datasourceName, final SourceType
type) {
-
+
taskManager.setParent(parent);
-
+
if (type.equals(SourceType.ATTRIBUTE)) {
- final ImportAttributeListTask firstTask = new
ImportAttributeListTask(datasourceName, client.getRestClient());
+ final ImportAttributeListTask firstTask = new
ImportAttributeListTask(
+ datasourceName, client.getRestClient());
final SetAttributeTask setAttrTask = new
SetAttributeTask(firstTask);
final BioMartTaskFactory tf = new
BioMartTaskFactory(firstTask);
tf.getTaskIterator().insertTasksAfter(firstTask,
setAttrTask);
taskManager.execute(tf);
} else if (type.equals(SourceType.FILTER)) {
- final ImportFilterTask firstTask = new
ImportFilterTask(datasourceName, client.getRestClient());
+ final ImportFilterTask firstTask = new ImportFilterTask(
+ datasourceName, client.getRestClient());
final SetFilterTask setFilterTask = new
SetFilterTask(firstTask);
final BioMartTaskFactory tf = new
BioMartTaskFactory(firstTask);
tf.getTaskIterator().insertTasksAfter(firstTask,
setFilterTask);
@@ -246,7 +251,8 @@
// Use Attributes for mapping
final CyTable defTable = tblManager.getTableMap(CyNode.class,
curNetwork).get(CyNetwork.DEFAULT_ATTRS);
- final Class<?> attrDataType =
defTable.getColumnTypeMap().get(keyAttrName);
+ final Class<?> attrDataType = defTable.getColumnTypeMap().get(
+ keyAttrName);
for (CyNode node : nodes) {
final CyRow row = defTable.getRow(node.getSUID());
@@ -324,7 +330,8 @@
final Map<String, String> attrMap =
this.attrNameMap.get(datasource);
final Map<String, String> fMap = filterMap.get(datasource);
- final String keyAttrName =
attributeComboBox.getSelectedItem().toString();
+ final String keyAttrName = attributeComboBox.getSelectedItem()
+ .toString();
System.out.println("Selected attr name: " + keyAttrName);
@@ -336,7 +343,7 @@
dataset = new Dataset(datasource);
// System.out.println("Target Dataset = " + dataset.getName());
- final Object[] selectedAttr = attrList.getSelectedValues();
+ final Object[] selectedAttr =
attrCheckboxList.getSelectedValues();
attrs = new Attribute[selectedAttr.length + 1];
// This is the mapping key
@@ -393,15 +400,12 @@
final String tableName = TABLE_PREFIX + (++globalTableCounter);
return new BiomartQuery(query, keyAttrName, tableName);
}
-
-
-
-
- ////////// Local tasks
+
+ // //////// Local tasks
private final class SetAttributeTask extends AbstractTask {
-
+
private final ImportAttributeListTask firstTask;
-
+
public SetAttributeTask(ImportAttributeListTask firstTask) {
this.firstTask = firstTask;
}
@@ -409,16 +413,15 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
final List<String> order = new ArrayList<String>();
- final String selectedDB =
databaseComboBox.getSelectedItem().toString();
+ final String selectedDB =
databaseComboBox.getSelectedItem()
+ .toString();
final String selectedDBName =
datasourceMap.get(selectedDB);
-
- System.out.println("Calling attribute update task
done.");
- Map<String, String[]> attributeVals = firstTask
+ final Map<String, String[]> attributeVals = firstTask
.getAttributeValues();
- Map<String, String> names = new HashMap<String,
String>();
+
+ final Map<String, String> names = new HashMap<String,
String>();
attributeMap.put(selectedDBName, attributeVals);
- model.removeAllElements();
String[] entry;
String dispNameWithCategory;
@@ -442,34 +445,35 @@
attrNameMap.put(selectedDBName, names);
Collections.sort(order);
- for (String attrName : order) {
- model.addElement(attrName);
- }
+ attrCheckboxListModel.removeAllElements();
+ for (String attrName : order)
+ attrCheckboxListModel.addElement(attrName);
- System.out.println("!!!!!!!!! attribute update task
2.");
attributeListOrder.put(selectedDBName, order);
- // attrList.repaint();
- System.out.println("!!!!!!!!! attribute update task
done.");
+ attrCheckboxList.setModel(attrCheckboxListModel);
+
availableAttrScrollPane.setViewportView(attrCheckboxList);
+ availableAttrScrollPane.repaint();
}
-
+
}
-
+
private final class SetFilterTask extends AbstractTask {
-
+
private final ImportFilterTask firstTask;
-
+
public SetFilterTask(final ImportFilterTask firstTask) {
this.firstTask = firstTask;
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
-
+
Map<String, String> returnValMap;
- final String selectedDB =
databaseComboBox.getSelectedItem().toString();
+ final String selectedDB =
databaseComboBox.getSelectedItem()
+ .toString();
final String selectedDBName =
datasourceMap.get(selectedDB);
-
+
returnValMap = firstTask.getFilters();
filterMap.put(selectedDBName, returnValMap);
@@ -480,10 +484,7 @@
for (String filter : filterNames)
attributeTypeComboBox.addItem(filter);
}
-
+
}
-
-
-
}
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