Author: kono
Date: 2011-01-25 16:45:16 -0800 (Tue, 25 Jan 2011)
New Revision: 23621
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.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/resources/META-INF/spring/bundle-context.xml
Log:
Result message added. Some minor bugs are fixed.
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -39,6 +39,7 @@
import javax.naming.ConfigurationException;
+import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.io.webservice.TableImportWebServiceClient;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
import org.cytoscape.io.webservice.biomart.task.ImportTableTask;
@@ -67,6 +68,8 @@
private final CyNetworkManager networkManager;
private final CyApplicationManager applicationManager;
+
+ private final CySwingApplication app;
/**
* Creates a new Biomart Client object.
@@ -78,7 +81,7 @@
final BiomartRestClient restClient,
final CyTableFactory tableFactory,
final CyNetworkManager networkManager,
- final CyApplicationManager applicationManager) {
+ final CyApplicationManager applicationManager, final
CySwingApplication app) {
super(restClient.getBaseURL(), displayName, description);
this.tableFactory = tableFactory;
@@ -86,6 +89,7 @@
this.networkManager = networkManager;
this.applicationManager = applicationManager;
+ this.app = app;
// TODO: set optional parameters (Tunables?)
}
@@ -115,9 +119,8 @@
final BiomartQuery query = this.gui.getTableImportQuery();
- importTask = new ImportTableTask(restClient, query,
tableFactory, networkManager, applicationManager);
+ importTask = new ImportTableTask(restClient, query,
tableFactory, networkManager, applicationManager, app.getJFrame());
-
return new TaskIterator(importTask);
}
}
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -1,13 +1,15 @@
package org.cytoscape.io.webservice.biomart.task;
+import java.awt.Window;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
+import javax.swing.JOptionPane;
+
import org.cytoscape.io.webservice.biomart.BiomartQuery;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
import org.cytoscape.model.CyNetworkManager;
@@ -22,34 +24,35 @@
/**
* Task to import actual data tables from BioMart service.
- *
+ *
*/
public class ImportTableTask extends AbstractTask {
private final BiomartRestClient client;
private final BiomartQuery query;
-
+
private final CyTableFactory tableFactory;
private Set<CyTable> tables;
-
+
private final CyNetworkManager networkManager;
private final CyApplicationManager applicationManager;
-
-
+ private final Window parent;
+
public ImportTableTask(final BiomartRestClient client,
- final BiomartQuery query, final CyTableFactory
tableFactory,
+ final BiomartQuery query, final CyTableFactory
tableFactory,
final CyNetworkManager networkManager,
- final CyApplicationManager applicationManager) {
-
+ final CyApplicationManager applicationManager, final
Window parent) {
+
this.client = client;
this.query = query;
this.tableFactory = tableFactory;
-
+ this.parent = parent;
+
this.networkManager = networkManager;
this.applicationManager = applicationManager;
-
+
this.tables = new HashSet<CyTable>();
}
@@ -58,39 +61,42 @@
if (query == null)
throw new NullPointerException("Query is null");
+ taskMonitor.setProgress(0.0);
+ taskMonitor.setTitle("Loading data table from BioMart...");
+ taskMonitor.setStatusMessage("Loading data...");
+
final BufferedReader result =
client.sendQuery(query.getQueryString());
if (result.ready() == false)
throw new IOException("Could not get result.");
- final CyTable newTable = mapping(result,
query.getKeyColumnName());
+ taskMonitor.setStatusMessage("Creating global table...");
+ final CyTable newTable = createGlobalTable(result,
+ query.getKeyColumnName());
+
tables.add(newTable);
-
+
final MapNetworkAttrTask localMappingTask = new
MapNetworkAttrTask(
- CyNode.class, newTable,
- networkManager, applicationManager);
-
- this.insertTasksAfterCurrentTask(localMappingTask);
+ CyNode.class, newTable, networkManager,
applicationManager);
+ final ShowResultTask messageTask = new ShowResultTask();
+ this.insertTasksAfterCurrentTask(localMappingTask, messageTask);
}
- private CyTable mapping(BufferedReader reader, String key)
+ private CyTable createGlobalTable(BufferedReader reader, String key)
throws IOException {
-
- System.out.println("Key name = " + key);
- final CyTable globalTable =
tableFactory.createTable(query.getTableName(), key,
- String.class, true);
-
-
// Read result from reader
String line = reader.readLine();
System.out.println("Table Header: " + line);
final String[] columnNames = line.split("\\t");
if (columnNames[0].contains("Query ERROR"))
- throw new IOException("Biomart service returns Querry
ERROR. ");
+ throw new IOException("BioMart service returns error:
\n" + line);
+ final CyTable globalTable = tableFactory.createTable(
+ query.getTableName(), key, String.class, true);
+
// For status report
int recordCount = 0;
List<String> report = new ArrayList<String>();
@@ -106,7 +112,6 @@
if (columnNames[i].equals(key))
keyIdx = i;
}
-
String[] row;
String val;
@@ -140,77 +145,96 @@
if ((val != null) && (val.length() != 0)) {
- if(j == keyIdx) {
+ if (j == keyIdx) {
cyRow.set(key, val);
}
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++;
-// }
+ // 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++;
+ // }
}
}
}
reader.close();
reader = null;
-
+
// Dump table
-// final List<CyRow> rows = globalTable.getAllRows();
-// for(CyRow r: rows) {
-// Map<String, Object> rowVals = r.getAllValues();
-// for(String k :rowVals.keySet()) {
-// System.out.print(k + ":" + rowVals.get(k) + "
");
-// }
-// System.out.println();
-// }
-
+ // final List<CyRow> rows = globalTable.getAllRows();
+ // for(CyRow r: rows) {
+ // Map<String, Object> rowVals = r.getAllValues();
+ // for(String k :rowVals.keySet()) {
+ // System.out.print(k + ":" + rowVals.get(k) + " ");
+ // }
+ // System.out.println();
+ // }
+
return globalTable;
}
public Set<CyTable> getCyTables() {
return tables;
}
+
+
+ // Show result.
+ private final class ShowResultTask extends AbstractTask {
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ final CyTable table = tables.iterator().next();
+ if (table != null) {
+ JOptionPane.showMessageDialog(parent,
+ "New table loaded.\n" +
table.getTitle() + " contains "
+ +
table.getRowCount() + " rows.",
+ "Table Loaded from BioMart",
+
JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+ }
+
}
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -4,12 +4,8 @@
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;
import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskManager;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.swing.GUITaskManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -2,10 +2,13 @@
import java.awt.event.ActionEvent;
+import javax.swing.JOptionPane;
+
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.session.CyApplicationManager;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.swing.GUITaskManager;
@@ -26,6 +29,7 @@
private final CySwingApplication app;
private ShowBiomartDialogTask showDialogTask;
+ private final CyApplicationManager appManager;
private final LoadRepositoryTask firstTask;
@@ -36,6 +40,7 @@
super("from Biomart...", appManager);
setPreferredMenu("File.Import.Table.WebService");
+ this.appManager = appManager;
this.app = app;
this.taskManager = (GUITaskManager) taskManager;
@@ -45,6 +50,14 @@
@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();
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -73,7 +73,7 @@
private static final long serialVersionUID = 8665197023334496167L;
- protected static final String TABLE_PREFIX = "BioMart Table ";
+ protected static final String TABLE_PREFIX = "BioMart Global Table ";
/**
* Will be caught by parent object (usually a dialog.)
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-01-26 00:45:16 UTC (rev 23621)
@@ -321,6 +321,7 @@
@Override
protected void importAttributes() {
+ taskManager.setParent(parent);
taskManager.execute(client);
}
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
2011-01-26 00:01:44 UTC (rev 23620)
+++
core3/webservice-biomart-client/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-26 00:45:16 UTC (rev 23621)
@@ -33,6 +33,7 @@
<constructor-arg ref="cyTableFactoryServiceRef" />
<constructor-arg ref="cyNetworkManagerServiceRef" />
<constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
</bean>
<bean id="biomartAttrMappingPanel"
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