Author: kono
Date: 2011-01-21 12:45:24 -0800 (Fri, 21 Jan 2011)
New Revision: 23548
Added:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.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/BiomartAttrMappingPanel.java
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
Log:
executeAndWait() method calls are removed.
Modified:
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
===================================================================
---
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
2011-01-21 20:42:37 UTC (rev 23547)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/LoadRepositoryTask.java
2011-01-21 20:45:24 UTC (rev 23548)
@@ -8,12 +8,13 @@
import java.util.Map;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
+import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.ValuedTask;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class LoadRepositoryTask implements ValuedTask<LoadRepositoryResult> {
+public class LoadRepositoryTask extends AbstractTask {
private static final Logger logger = LoggerFactory
.getLogger(LoadRepositoryTask.class);
@@ -22,9 +23,9 @@
private Map<String, Map<String, String>> reg;
- private boolean cancel = false;
-
+ private LoadRepositoryResult result;
+
// These databases are not compatible with this UI.
private static final List<String> databaseFilter = new
ArrayList<String>();
@@ -45,7 +46,7 @@
@Override
- public LoadRepositoryResult run(TaskMonitor taskMonitor) {
+ public void run(TaskMonitor taskMonitor) {
taskMonitor.setProgress(0.1);
taskMonitor.setStatusMessage("Loading list of available
marts...");
@@ -100,13 +101,10 @@
taskMonitor.setStatusMessage("Finished: " + dsList.size());
taskMonitor.setProgress(1.0);
- return new LoadRepositoryResult(this.datasourceMap,
this.dsList);
+ result = new LoadRepositoryResult(this.datasourceMap,
this.dsList);
}
-
- @Override
- public void cancel() {
- //TODO: implement this
- boolean cancel = true;
+
+ public LoadRepositoryResult getResult() {
+ return result;
}
-
}
Added:
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
(rev 0)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartDialogTask.java
2011-01-21 20:45:24 UTC (rev 23548)
@@ -0,0 +1,57 @@
+package org.cytoscape.io.webservice.biomart.task;
+
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.io.webservice.biomart.BiomartClient;
+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;
+
+public class ShowBiomartDialogTask extends AbstractTask {
+
+ private static final Logger logger =
LoggerFactory.getLogger(ShowBiomartDialogTask.class);
+
+ 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 LoadRepositoryTask loadTask;
+
+ public ShowBiomartDialogTask(final BiomartClient client,
+ final TaskManager taskManager,
+ final CyApplicationManager appManager,
+ final CyTableManager tblManager, final
CySwingApplication app, final LoadRepositoryTask loadTask) {
+
+ this.app = app;
+ this.client = client;
+ this.taskManager = (GUITaskManager) taskManager;
+ this.appManager = appManager;
+ this.tblManager = tblManager;
+ this.loadTask = loadTask;
+ }
+
+ @Override
+ 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.setLocationRelativeTo(app.getJFrame());
+ dialog.setVisible(true);
+
+ logger.info("BioMart Client initialized.");
+ }
+ }
+
+ public BiomartMainDialog getDialog() {
+ return dialog;
+ }
+}
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
2011-01-21 20:42:37 UTC (rev 23547)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2011-01-21 20:45:24 UTC (rev 23548)
@@ -1,21 +1,13 @@
package org.cytoscape.io.webservice.biomart.task;
import java.awt.event.ActionEvent;
-import java.util.List;
-import java.util.concurrent.CancellationException;
-import java.util.concurrent.ExecutionException;
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.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.ValuedTask;
-import org.cytoscape.work.ValuedTaskExecutor;
import org.cytoscape.work.swing.GUITaskManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -28,16 +20,17 @@
private static final long serialVersionUID = -1329132199540543764L;
- private static final Logger logger = LoggerFactory
- .getLogger(ShowBiomartGUIAction.class);
+ private static final Logger logger =
LoggerFactory.getLogger(ShowBiomartGUIAction.class);
- private BiomartMainDialog dialog;
-
private final BiomartClient client;
- private final GUITaskManager taskManager;
private final CyApplicationManager appManager;
private final CyTableManager tblManager;
+ private final GUITaskManager taskManager;
private final CySwingApplication app;
+
+ private ShowBiomartDialogTask showDialogTask;
+
+ private final LoadRepositoryTask firstTask;
public ShowBiomartGUIAction(final BiomartClient client,
final TaskManager taskManager,
@@ -46,25 +39,34 @@
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.appManager = appManager;
- this.tblManager = tblManager;
+
+ this.firstTask = new LoadRepositoryTask(client.getRestClient());
+ this.showDialogTask = new ShowBiomartDialogTask(client,
taskManager, appManager, tblManager, app, firstTask);
}
@Override
public void actionPerformed(ActionEvent ae) {
// Lazy instantiation. This process depends on network
connection.
- if (dialog == null) {
- logger.debug("BioMart Dialog initialization process
start.");
- dialog = new BiomartMainDialog(client, taskManager,
appManager, tblManager, app);
- logger.info("BioMart Client dialog initialized.");
+ if (showDialogTask.getDialog() == null) {
+ initDialog();
+ } else {
+
showDialogTask.getDialog().setLocationRelativeTo(app.getJFrame());
+ showDialogTask.getDialog().setVisible(true);
}
+ }
+
+
+ private void initDialog() {
- dialog.setLocationRelativeTo(app.getJFrame());
- dialog.setVisible(true);
+ final BioMartTaskFactory tf = new BioMartTaskFactory(firstTask);
+ tf.getTaskIterator().insertTasksAfter(firstTask,
showDialogTask);
+ ((GUITaskManager) taskManager).setParent(app.getJFrame());
- logger.info("BioMart Client initialized.");
+ taskManager.execute(tf);
}
}
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
2011-01-21 20:42:37 UTC (rev 23547)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-01-21 20:45:24 UTC (rev 23548)
@@ -41,8 +41,6 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.concurrent.CancellationException;
-import java.util.concurrent.ExecutionException;
import javax.swing.DefaultListModel;
import javax.swing.Icon;
@@ -51,36 +49,30 @@
import org.cytoscape.io.webservice.biomart.BiomartClient;
import org.cytoscape.io.webservice.biomart.BiomartQuery;
import org.cytoscape.io.webservice.biomart.rest.Attribute;
-import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
import org.cytoscape.io.webservice.biomart.rest.Dataset;
import org.cytoscape.io.webservice.biomart.rest.Filter;
import org.cytoscape.io.webservice.biomart.rest.XMLQueryBuilder;
import org.cytoscape.io.webservice.biomart.task.BioMartTaskFactory;
import org.cytoscape.io.webservice.biomart.task.ImportAttributeListTask;
-import org.cytoscape.io.webservice.biomart.task.ImportAttributeListTaskFactory;
import org.cytoscape.io.webservice.biomart.task.ImportFilterTask;
-import org.cytoscape.io.webservice.biomart.task.ImportFilterTaskFactory;
import org.cytoscape.io.webservice.biomart.task.LoadRepositoryResult;
-import org.cytoscape.io.webservice.biomart.task.LoadRepositoryTask;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.ValuedTask;
-import org.cytoscape.work.ValuedTaskExecutor;
+import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.swing.GUITaskManager;
-
public class BiomartAttrMappingPanel extends AttributeImportPanel {
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;
@@ -99,12 +91,12 @@
// These databases are not compatible with this UI.
private static final List<String> databaseFilter = new
ArrayList<String>();
- private final TaskManager taskManager;
+ private final GUITaskManager taskManager;
private final CyApplicationManager appManager;
private final CyTableManager tblManager;
private final Window parent;
-
+
private final BiomartClient client;
/**
@@ -116,20 +108,20 @@
* DOCUMENT ME!
* @throws Exception
*/
- public BiomartAttrMappingPanel(final BiomartClient client,
+ public BiomartAttrMappingPanel(final LoadRepositoryResult res, final
BiomartClient client,
final TaskManager taskManager,
final CyApplicationManager appManager,
final CyTableManager tblManager, final Window parent) {
super(LOGO, "Biomart", "Import Settings");
this.client = client;
- this.taskManager = taskManager;
+ this.taskManager = (GUITaskManager) taskManager;
this.appManager = appManager;
this.tblManager = tblManager;
this.parent = parent;
// Access the MartService and get the available services.
- initDataSources();
+ initDataSources(res);
}
/**
@@ -137,50 +129,24 @@
*
* @throws Exception
*/
- private void initDataSources() {
+ private void initDataSources(LoadRepositoryResult res) {
attributeMap = new HashMap<String, Map<String, String[]>>();
attributeListOrder = new HashMap<String, List<String>>();
filterMap = new HashMap<String, Map<String, String>>();
attrNameMap = new HashMap<String, Map<String, String>>();
// Import list of repositories.
- loadMartServiceList();
+ setMartServiceList(res);
// Load available filters for current source.
- loadFilter();
+ // loadFilter();
}
- public void loadMartServiceList() {
-
- final ValuedTask<LoadRepositoryResult> firstTask = new
LoadRepositoryTask(
- client.getRestClient());
- ValuedTaskExecutor<LoadRepositoryResult> ex = new
ValuedTaskExecutor<LoadRepositoryResult>(
- firstTask);
- final BioMartTaskFactory tf = new BioMartTaskFactory(ex);
- System.out.println("Current thread: " + Thread.currentThread());
- ((GUITaskManager) taskManager).setParent(parent);
- taskManager.execute(tf);
-
- LoadRepositoryResult result;
- try {
- result = ex.get();
-
- this.datasourceMap = result.getDatasourceMap();
- final List<String> dsList =
result.getSortedDataSourceList();
- // System.out.println("GOT datasource list from task: "
+ dsList);
- for (String ds : dsList)
- this.databaseComboBox.addItem(ds);
-
- } catch (CancellationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (ExecutionException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ public void setMartServiceList(LoadRepositoryResult res) {
+ this.datasourceMap = res.getDatasourceMap();
+ final List<String> dsList = res.getSortedDataSourceList();
+ for (String ds : dsList)
+ this.databaseComboBox.addItem(ds);
}
public void loadFilter() {
@@ -220,81 +186,22 @@
}
}
- private void fetchData(final String datasourceName, SourceType type) {
- Map<String, String> returnValMap = new HashMap<String,
String>();
- final List<String> order = new ArrayList<String>();
- final String selectedDB =
databaseComboBox.getSelectedItem().toString();
- final String selectedDBName = datasourceMap.get(selectedDB);
-
+ private void fetchData(final String datasourceName, final SourceType
type) {
+
+ taskManager.setParent(parent);
+
if (type.equals(SourceType.ATTRIBUTE)) {
-
- System.out.println("Calling attribute update task.");
-
- final ImportAttributeListTaskFactory tf = new
ImportAttributeListTaskFactory(
- datasourceName, client.getRestClient());
- final ImportAttributeListTask firstTask =
(ImportAttributeListTask) tf
- .getTaskIterator().next();
- taskManager.executeAndWait(tf);
- System.out.println("Calling attribute update task
done.");
-
- Map<String, String[]> attributeVals = firstTask
- .getAttributeValues();
- Map<String, String> names = new HashMap<String,
String>();
- attributeMap.put(selectedDBName, attributeVals);
- model.removeAllElements();
-
- String[] entry;
- String dispNameWithCategory;
-
- for (String attr : attributeVals.keySet()) {
- entry = attributeVals.get(attr);
-
- if ((entry != null) && (entry[0] != null)) {
- if ((entry.length > 2) && (entry[2] !=
null))
- dispNameWithCategory = entry[2]
+ ": \t" + entry[0]
- + "\t (" +
attr + ")";
- else
- dispNameWithCategory = " \t" +
entry[0] + "\t ("
- + attr + ")";
-
- names.put(dispNameWithCategory, attr);
- order.add(dispNameWithCategory);
- }
- }
-
-
- this.attrNameMap.put(selectedDBName, names);
- Collections.sort(order);
-
- for (String attrName : order) {
- model.addElement(attrName);
- }
-
- System.out.println("!!!!!!!!! attribute update task
2.");
- attributeListOrder.put(selectedDBName, order);
- // attrList.repaint();
-
- System.out.println("!!!!!!!!! attribute update task
done.");
-
+ 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 ImportFilterTaskFactory tf = new
ImportFilterTaskFactory(
- datasourceName, client.getRestClient());
- final ImportFilterTask firstTask = (ImportFilterTask) tf
- .getTaskIterator().next();
- tf.setTask(firstTask);
- taskManager.executeAndWait(tf);
- tf.setTask(null);
-
- returnValMap = firstTask.getFilters();
- filterMap.put(selectedDBName, returnValMap);
-
- List<String> filterNames = new ArrayList<String>(
- returnValMap.keySet());
- Collections.sort(filterNames);
-
- for (String filter : filterNames)
- attributeTypeComboBox.addItem(filter);
+ 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);
+ taskManager.execute(tf);
}
}
@@ -402,13 +309,11 @@
// return mappedKeys;
// }
-
-
@Override
protected void importAttributes() {
taskManager.execute(client);
}
-
+
public BiomartQuery getTableImportQuery() {
final String datasource = datasourceMap.get(databaseComboBox
.getSelectedItem());
@@ -471,18 +376,110 @@
}
// Create query
- return importAttributesFromService(dataset, attrs, filters,
keyInHeader,
- keyAttrName);
+ return importAttributesFromService(dataset, attrs, filters,
+ keyInHeader, keyAttrName);
}
-
+
private BiomartQuery importAttributesFromService(Dataset dataset,
Attribute[] attrs, Filter[] filters, String keyInHeader,
String keyAttrName) {
final String query = XMLQueryBuilder.getQueryString(dataset,
attrs,
filters);
-
+
return new BiomartQuery(query, keyAttrName);
}
+
+
+
+
+ ////////// Local tasks
+ private final class SetAttributeTask extends AbstractTask {
+
+ private final ImportAttributeListTask firstTask;
+
+ public SetAttributeTask(ImportAttributeListTask firstTask) {
+ this.firstTask = firstTask;
+ }
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ final List<String> order = new ArrayList<String>();
+ 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
+ .getAttributeValues();
+ Map<String, String> names = new HashMap<String,
String>();
+ attributeMap.put(selectedDBName, attributeVals);
+ model.removeAllElements();
+
+ String[] entry;
+ String dispNameWithCategory;
+
+ for (String attr : attributeVals.keySet()) {
+ entry = attributeVals.get(attr);
+
+ if ((entry != null) && (entry[0] != null)) {
+ if ((entry.length > 2) && (entry[2] !=
null))
+ dispNameWithCategory = entry[2]
+ ": \t" + entry[0]
+ + "\t (" +
attr + ")";
+ else
+ dispNameWithCategory = " \t" +
entry[0] + "\t ("
+ + attr + ")";
+
+ names.put(dispNameWithCategory, attr);
+ order.add(dispNameWithCategory);
+ }
+ }
+
+ attrNameMap.put(selectedDBName, names);
+ Collections.sort(order);
+
+ for (String attrName : order) {
+ model.addElement(attrName);
+ }
+
+ System.out.println("!!!!!!!!! attribute update task
2.");
+ attributeListOrder.put(selectedDBName, order);
+ // attrList.repaint();
+
+ System.out.println("!!!!!!!!! attribute update task
done.");
+ }
+
+ }
+
+ 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 selectedDBName =
datasourceMap.get(selectedDB);
+
+ returnValMap = firstTask.getFilters();
+ filterMap.put(selectedDBName, returnValMap);
+
+ List<String> filterNames = new ArrayList<String>(
+ returnValMap.keySet());
+ Collections.sort(filterNames);
+
+ for (String filter : filterNames)
+ attributeTypeComboBox.addItem(filter);
+ }
+
+ }
+
+
+
+
}
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
2011-01-21 20:42:37 UTC (rev 23547)
+++
core3/webservice-biomart-client/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartMainDialog.java
2011-01-21 20:45:24 UTC (rev 23548)
@@ -44,6 +44,7 @@
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;
@@ -67,7 +68,7 @@
*/
public BiomartMainDialog(final BiomartClient client, final TaskManager
taskManager,
final CyApplicationManager appManager,
- final CyTableManager tblManager, final
CySwingApplication app) {
+ final CyTableManager tblManager, final
CySwingApplication app, final LoadRepositoryResult result) {
super();
setTitle("BioMart Web Service Client");
@@ -87,7 +88,7 @@
tunablePanel.add(tPanel);
- panel = new BiomartAttrMappingPanel(client, taskManager,
appManager, tblManager, app.getJFrame());
+ panel = new BiomartAttrMappingPanel(result, client,
taskManager, appManager, tblManager, this);
client.setGUI(panel);
tabs.addTab("Query", panel);
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
