Author: kono
Date: 2011-01-24 19:22:27 -0800 (Mon, 24 Jan 2011)
New Revision: 23594
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartQuery.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.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
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
This version imports global table. Need to map this table to locals by virtual
column.
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartQuery.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartQuery.java
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartQuery.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -5,10 +5,12 @@
private final String xmlQuery;
private final String keyColumnName;
+ private final String tableName;
- public BiomartQuery(final String xmlQuery, final String keyColumnName) {
+ public BiomartQuery(final String xmlQuery, final String keyColumnName,
final String tableName) {
this.keyColumnName = keyColumnName;
this.xmlQuery = xmlQuery;
+ this.tableName = tableName;
}
public String getKeyColumnName () {
@@ -19,5 +21,9 @@
public String getQueryString() {
return xmlQuery;
}
+
+ public String getTableName() {
+ return tableName;
+ }
}
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -12,6 +12,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.work.AbstractTask;
@@ -55,8 +56,10 @@
final Set<CyTable> newTables = new HashSet<CyTable>();
- final CyTable table = tableFactory.createTable("Test Table
name", key,
+ final CyTable globalTable =
tableFactory.createTable(query.getTableName(), key,
String.class, true);
+
+ newTables.add(globalTable);
// Read result from reader
String line = reader.readLine();
@@ -76,133 +79,102 @@
// Search column index of the key
for (int i = 0; i < colSize; i++) {
- table.createListColumn(columnNames[i], String.class);
+ globalTable.createColumn(columnNames[i], String.class);
if (columnNames[i].equals(key))
keyIdx = i;
}
+
- // byte attrDataType =
- // Cytoscape.getNodeAttributes().getType(keyAttrName);
- final List<String> nodeIdList = new ArrayList<String>();
+ String[] row;
+ String val;
- // Prepare list of nodes FROM ALL NETWORKS.
+ List<List<Object>> listOfValList;
+ List<String> ids = null;
- final Set<CyNetwork> allNetworks = manager.getNetworkSet();
+ List<Object> testList;
+ String keyVal = null;
+ int rowLength = 0;
- for (final CyNetwork network : allNetworks) {
- final List<CyNode> nodes = network.getNodeList();
- for (CyNode node : nodes) {
+ int hitCount = 0;
+ long start = System.currentTimeMillis();
+ while ((line = reader.readLine()) != null) {
+
+ row = line.split("\\t");
+
+ // Ignore invalid length entry.
+ if ((row.length <= keyIdx) || (row.length == 0))
+ continue;
+
+ recordCount++;
+ keyVal = row[keyIdx];
+//
+// System.out.println("Key ====>" + keyVal + "<==");
+
+ rowLength = row.length;
+
+ for (int j = 0; j < rowLength; j++) {
+ val = row[j];
+
+ if ((val != null) && (val.length() != 0) && (j
!= keyIdx)) {
+ listOfValList = new
ArrayList<List<Object>>();
+
+ final CyRow cyRow =
globalTable.getRow(keyVal);
+ cyRow.set(columnNames[j], val);
+// if (keyAttrName.equals("ID")) {
+// testList = attr
+//
.getListAttribute(keyVal, columnNames[j]);
+//
+// if (testList != null)
+//
listOfValList.add(testList);
+// } else {
+// ids =
getIdFromAttrValue(attrDataType, keyAttrName,
+// keyVal,
nodeIdList, attr);
+//
+// if (ids.size() == 0)
+// continue;
+//
+// for (String id : ids)
+//
listOfValList.add(attr.getListAttribute(id,
+//
columnNames[j]));
+// }
+//
+// if (listOfValList.size() == 0) {
+// List<Object> valList = new
ArrayList<Object>();
+// listOfValList.add(valList);
+// }
+//
+// int index = 0;
+// for (List<Object> valList :
listOfValList) {
+// if (valList == null)
+// valList = new
ArrayList<Object>();
+//
+// if (valList.contains(row[j]) ==
false)
+// valList.add(row[j]);
+//
+// if (keyAttrName.equals("ID")) {
+//
attr.setListAttribute(keyVal, columnNames[j],
+//
valList);
+//
attr.setAttribute(keyVal, columnNames[j] + "-TOP",
+//
valList.get(0).toString());
+// } else {
+//
attr.setListAttribute(ids.get(index),
+//
columnNames[j], valList);
+//
attr.setAttribute(ids.get(index), columnNames[j]
+// +
"-TOP", valList.get(0).toString());
+//
+// }
+// hitCount++;
+// index++;
+// }
+ }
+ System.out.println();
}
}
- // String[] row;
- // String val;
- //
- // List<List<Object>> listOfValList;
- // List<String> ids = null;
- //
- // List<Object> testList;
- // String keyVal = null;
- // int rowLength = 0;
- //
- // int hitCount = 0;
- //
- // long start = System.currentTimeMillis();
- // while ((line = reader.readLine()) != null) {
- // // Cancel the job.
- // if (cancelImport) {
- // cancelImport = false;
- // return null;
- // }
- //
- // row = line.split("\\t");
- //
- // // Ignore invalid length entry.
- // if ((row.length <= keyIdx) || (row.length == 0))
- // continue;
- //
- // recordCount++;
- // keyVal = row[keyIdx];
- //
- // // System.out.println("Key ====>" + keyVal + "<==");
- // // for(String s: entry)
- // // System.out.println("ENT ======>" + s + "<===");
- // rowLength = row.length;
- //
- // for (int j = 0; j < rowLength; j++) {
- // val = row[j];
- //
- // if ((val != null) && (val.length() != 0) && (j != keyIdx)) {
- // listOfValList = new ArrayList<List<Object>>();
- //
- // if (keyAttrName.equals("ID")) {
- // testList = attr
- // .getListAttribute(keyVal, columnNames[j]);
- //
- // if (testList != null)
- // listOfValList.add(testList);
- // } else {
- // ids = getIdFromAttrValue(attrDataType, keyAttrName,
- // keyVal, nodeIdList, attr);
- //
- // if (ids.size() == 0)
- // continue;
- //
- // for (String id : ids)
- // listOfValList.add(attr.getListAttribute(id,
- // columnNames[j]));
- // }
- //
- // if (listOfValList.size() == 0) {
- // List<Object> valList = new ArrayList<Object>();
- // listOfValList.add(valList);
- // }
- //
- // int index = 0;
- // for (List<Object> valList : listOfValList) {
- // if (valList == null)
- // valList = new ArrayList<Object>();
- //
- // if (valList.contains(row[j]) == false)
- // valList.add(row[j]);
- //
- // if (keyAttrName.equals("ID")) {
- // attr.setListAttribute(keyVal, columnNames[j],
- // valList);
- // attr.setAttribute(keyVal, columnNames[j] + "-TOP",
- // valList.get(0).toString());
- // } else {
- // attr.setListAttribute(ids.get(index),
- // columnNames[j], valList);
- // attr.setAttribute(ids.get(index), columnNames[j]
- // + "-TOP", valList.get(0).toString());
- //
- // }
- // hitCount++;
- // index++;
- // }
- // }
- // }
- // }
- //
- // // System.out.println("Time =====> " +
- // // (System.currentTimeMillis()-start));
- //
- // reader.close();
- // reader = null;
- //
- // report.add("Number of Records (Rows) from BioMart = " +
recordCount
- // + "\n");
- // report.add("Number of Terms Mapped = " + hitCount + "\n");
- // report.add("The following node attributes are created:" +
"\n");
- // for (String s : columnNames) {
- // report.add(s + ", " + s + "-TOP");
- // }
- // report.add("\nAttributes name ends with \'TOP\' contains
first entry of the list");
- // return report;
-
+ reader.close();
+ reader = null;
return newTables;
}
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -2,6 +2,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.io.webservice.biomart.BiomartClient;
+import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
import org.cytoscape.io.webservice.biomart.ui.BiomartMainDialog;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.session.CyApplicationManager;
@@ -19,23 +20,18 @@
private BiomartMainDialog dialog;
private final BiomartClient client;
- private final GUITaskManager taskManager;
- private final CyApplicationManager appManager;
- private final CyTableManager tblManager;
private final CySwingApplication app;
+ private final BiomartAttrMappingPanel panel;
+
private final LoadRepositoryTask loadTask;
- public ShowBiomartDialogTask(final BiomartClient client,
- final TaskManager taskManager,
- final CyApplicationManager appManager,
- final CyTableManager tblManager, final
CySwingApplication app, final LoadRepositoryTask loadTask) {
+ public ShowBiomartDialogTask(final BiomartAttrMappingPanel panel, final
BiomartClient client,
+ final CySwingApplication app, final LoadRepositoryTask
loadTask) {
+ this.panel = panel;
this.app = app;
this.client = client;
- this.taskManager = (GUITaskManager) taskManager;
- this.appManager = appManager;
- this.tblManager = tblManager;
this.loadTask = loadTask;
}
@@ -43,7 +39,7 @@
public void run(TaskMonitor taskMonitor) throws Exception {
if(dialog == null) {
final LoadRepositoryResult result =
loadTask.getResult();
- dialog = new BiomartMainDialog(client, taskManager,
appManager, tblManager, app, result);
+ dialog = new BiomartMainDialog(panel, client, result);
dialog.setLocationRelativeTo(app.getJFrame());
dialog.setVisible(true);
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 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -5,6 +5,7 @@
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.CyTableManager;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.work.TaskManager;
@@ -22,9 +23,6 @@
private static final Logger logger =
LoggerFactory.getLogger(ShowBiomartGUIAction.class);
- private final BiomartClient client;
- private final CyApplicationManager appManager;
- private final CyTableManager tblManager;
private final GUITaskManager taskManager;
private final CySwingApplication app;
@@ -32,21 +30,18 @@
private final LoadRepositoryTask firstTask;
- public ShowBiomartGUIAction(final BiomartClient client,
+ public ShowBiomartGUIAction(final BiomartAttrMappingPanel panel, final
BiomartClient client,
final TaskManager taskManager,
final CyApplicationManager appManager,
- final CyTableManager tblManager, final
CySwingApplication app) {
+ final CySwingApplication app) {
super("Import Tables from Biomart...", appManager);
setPreferredMenu("File.Import");
- this.tblManager = tblManager;
- this.appManager = appManager;
this.app = app;
- this.client = client;
this.taskManager = (GUITaskManager) taskManager;
this.firstTask = new LoadRepositoryTask(client.getRestClient());
- this.showDialogTask = new ShowBiomartDialogTask(client,
taskManager, appManager, tblManager, app, firstTask);
+ this.showDialogTask = new ShowBiomartDialogTask(panel, client,
app, firstTask);
}
@Override
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 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -36,6 +36,8 @@
import java.awt.Color;
import java.awt.event.ActionEvent;
+import java.util.Map;
+import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -46,6 +48,12 @@
import javax.swing.JPanel;
import javax.swing.LayoutStyle;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedEvent;
@@ -64,6 +72,8 @@
ColumnCreatedListener, ColumnDeletedListener {
private static final long serialVersionUID = 8665197023334496167L;
+
+ protected static final String TABLE_PREFIX = "BioMart Table ";
/**
* Will be caught by parent object (usually a dialog.)
@@ -105,18 +115,23 @@
// Attribute panel border title
protected String attributePanelTitle;
+
+ protected final CyTableManager tblManager;
+ private final CyNetworkManager netManager;
- protected AttributeImportPanel() {
- this(null, DEF_TITLE, ATTR_PANEL_TITLE);
- }
- protected AttributeImportPanel(Icon logo, String title,
+ protected AttributeImportPanel(final CyTableManager tblManager, final
CyNetworkManager netManager,
+ Icon logo, String title,
String attrPanelTitle) {
this.logo = logo;
this.panelTitle = title;
this.attributePanelTitle = attrPanelTitle;
+ this.tblManager = tblManager;
+ this.netManager = netManager;
initComponents();
+
+ setAttributeComboBox();
}
private void initComponents() {
@@ -406,21 +421,40 @@
abstract protected void databaseComboBoxActionPerformed(
java.awt.event.ActionEvent evt);
+
protected abstract void importAttributes();
+
+
+ private void setAttributeComboBox() {
+ final Set<CyNetwork> networks = this.netManager.getNetworkSet();
+
+ for(CyNetwork network: networks) {
+ final Map<String, CyTable> tables =
this.tblManager.getTableMap(CyNode.class, network);
+ final CyTable nodeTable =
tables.get(CyNetwork.DEFAULT_ATTRS);
+ final Map<String, Class<?>> columns =
nodeTable.getColumnTypeMap();
+ for (String name : columns.keySet())
+ attributeComboBox.addItem(name);
+ }
+ }
protected void addAttribute(final String attributeName) {
if (attributeName == null)
return;
+ final Object currentSelection =
attributeComboBox.getSelectedItem();
+
final SortedSet<String> attrNameSet = new TreeSet<String>();
attrNameSet.add(attributeName);
- for (int i = 0; i < model.getSize(); i++)
- attrNameSet.add(model.get(i).toString());
+ for (int i = 0; i < attributeComboBox.getItemCount(); i++)
+
attrNameSet.add(attributeComboBox.getItemAt(i).toString());
attributeComboBox.removeAllItems();
for (String name : attrNameSet)
attributeComboBox.addItem(name);
+
+ if(currentSelection != null)
+
attributeComboBox.setSelectedItem(currentSelection.toString());
}
protected void removeAttribute(final String attributeName) {
@@ -432,15 +466,13 @@
@Override
public void handleEvent(ColumnCreatedEvent e) {
- final String attrName = e.getColumnName();
-
+ final String attrName = e.getColumnName();
addAttribute(attrName);
}
@Override
public void handleEvent(ColumnDeletedEvent e) {
final String attrName = e.getColumnName();
-
removeAttribute(attrName);
}
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 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -57,6 +57,7 @@
import org.cytoscape.io.webservice.biomart.task.ImportFilterTask;
import org.cytoscape.io.webservice.biomart.task.LoadRepositoryResult;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
@@ -93,11 +94,12 @@
private final GUITaskManager taskManager;
private final CyApplicationManager appManager;
- private final CyTableManager tblManager;
- private final Window parent;
+ private Window parent;
private final BiomartClient client;
+
+ private int globalTableCounter;
/**
* Creates a new BiomartNameMappingPanel object.
@@ -108,20 +110,22 @@
* DOCUMENT ME!
* @throws Exception
*/
- public BiomartAttrMappingPanel(final LoadRepositoryResult res, final
BiomartClient client,
+ public BiomartAttrMappingPanel(
+ final BiomartClient client,
final TaskManager taskManager,
final CyApplicationManager appManager,
- final CyTableManager tblManager, final Window parent) {
- super(LOGO, "Biomart", "Import Settings");
+ final CyTableManager tblManager, final CyNetworkManager
netManager) {
+ super(tblManager, netManager, LOGO, "Biomart", "Import
Settings");
this.client = client;
this.taskManager = (GUITaskManager) taskManager;
this.appManager = appManager;
- this.tblManager = tblManager;
+
+ this.globalTableCounter = 0;
+ }
+
+ public void setParent(final Window parent) {
this.parent = parent;
-
- // Access the MartService and get the available services.
- initDataSources(res);
}
/**
@@ -129,7 +133,7 @@
*
* @throws Exception
*/
- private void initDataSources(LoadRepositoryResult res) {
+ public void initDataSources(LoadRepositoryResult res) {
attributeMap = new HashMap<String, Map<String, String[]>>();
attributeListOrder = new HashMap<String, List<String>>();
filterMap = new HashMap<String, Map<String, String>>();
@@ -141,6 +145,7 @@
// Load available filters for current source.
// loadFilter();
}
+
public void setMartServiceList(LoadRepositoryResult res) {
this.datasourceMap = res.getDatasourceMap();
@@ -241,8 +246,7 @@
// 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());
@@ -320,10 +324,9 @@
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("Target attr name found: " + keyAttrName);
+ System.out.println("Selected attr name: " + keyAttrName);
Dataset dataset;
Attribute[] attrs;
@@ -387,7 +390,8 @@
final String query = XMLQueryBuilder.getQueryString(dataset,
attrs,
filters);
- return new BiomartQuery(query, keyAttrName);
+ final String tableName = TABLE_PREFIX + (++globalTableCounter);
+ return new BiomartQuery(query, keyAttrName, tableName);
}
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
2011-01-25 03:22:27 UTC (rev 23594)
@@ -42,12 +42,8 @@
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
-import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.io.webservice.biomart.BiomartClient;
import org.cytoscape.io.webservice.biomart.task.LoadRepositoryResult;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.session.CyApplicationManager;
-import org.cytoscape.work.TaskManager;
/**
* BioMart client main GUI.
@@ -55,9 +51,7 @@
public final class BiomartMainDialog extends JDialog {
private static final long serialVersionUID = 2382157952635589843L;
-
- private final BiomartAttrMappingPanel panel;
-
+
/**
* Basic GUI to access BioMart services.
*
@@ -66,9 +60,7 @@
* @param appManager
* @param tblManager
*/
- public BiomartMainDialog(final BiomartClient client, final TaskManager
taskManager,
- final CyApplicationManager appManager,
- final CyTableManager tblManager, final
CySwingApplication app, final LoadRepositoryResult result) {
+ public BiomartMainDialog(final BiomartAttrMappingPanel panel, final
BiomartClient client, final LoadRepositoryResult result) {
super();
setTitle("BioMart Web Service Client");
@@ -88,8 +80,9 @@
tunablePanel.add(tPanel);
- panel = new BiomartAttrMappingPanel(result, client,
taskManager, appManager, tblManager, this);
client.setGUI(panel);
+ panel.initDataSources(result);
+ panel.setParent(this);
tabs.addTab("Query", panel);
Modified:
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 03:22:27 UTC (rev 23594)
@@ -23,7 +23,11 @@
<osgi:reference id="cyTableFactoryServiceRef"
interface="org.cytoscape.model.CyTableFactory" />
- <osgi:service id="showBiomartGUIActionService" ref="showDialogAction"
+ <osgi:service id="showBiomartGUIActionService"
ref="showBiomartGUIAction"
interface="org.cytoscape.application.swing.CyAction" />
+
+
+ <!-- This is necessary to listening to Column events. -->
+ <osgi:service id="biomartAttrMappingPanelService"
ref="biomartAttrMappingPanel" auto-export="interfaces" />
</beans>
Modified:
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-25 01:09:33 UTC (rev 23593)
+++
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-25 03:22:27 UTC (rev 23594)
@@ -17,27 +17,39 @@
<import resource="bundle-context-osgi.xml" />
<context:annotation-config />
-
+
<!-- REST version of BioMart web service client -->
- <bean id="biomartRestClient"
class="org.cytoscape.io.webservice.biomart.rest.BiomartRestClient">
+ <bean id="biomartRestClient"
+
class="org.cytoscape.io.webservice.biomart.rest.BiomartRestClient">
<constructor-arg
value="http://www.biomart.org/biomart/martservice"; />
</bean>
-
+
<!-- Wrapper for the REST client -->
<bean id="biomartClient"
class="org.cytoscape.io.webservice.biomart.BiomartClient">
<constructor-arg index="0" value="BioMart Client" />
- <constructor-arg index="1" value="REST version of BioMart Web
Service Client." />
+ <constructor-arg index="1"
+ value="REST version of BioMart Web Service Client." />
<constructor-arg ref="biomartRestClient" />
<constructor-arg ref="cyTableFactoryServiceRef" />
<constructor-arg ref="cyNetworkManagerServiceRef" />
</bean>
-
+
+ <bean id="biomartAttrMappingPanel"
+
class="org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel">
+ <constructor-arg ref="biomartClient" />
+ <constructor-arg ref="taskManagerServiceRef" />
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cyTableManagerServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ </bean>
+
<!-- Task to create menu item -->
- <bean id="showDialogAction"
class="org.cytoscape.io.webservice.biomart.task.ShowBiomartGUIAction">
+ <bean id="showBiomartGUIAction"
+
class="org.cytoscape.io.webservice.biomart.task.ShowBiomartGUIAction">
+ <constructor-arg ref="biomartAttrMappingPanel" />
<constructor-arg ref="biomartClient" />
<constructor-arg ref="taskManagerServiceRef" />
<constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cyTableManagerServiceRef" />
<constructor-arg ref="cySwingApplicationServiceRef" />
</bean>
</beans>
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