Author: jm
Date: 2012-02-14 12:50:53 -0800 (Tue, 14 Feb 2012)
New Revision: 28268
Removed:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/BioMartTaskFactory.java
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/api/webservice-api/src/main/java/org/cytoscape/io/webservice/WebServiceClient.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTaskFactory.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportFilterTaskFactory.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceEdgeContextMenuTaskFactory.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceNodeContextMenuTaskFactory.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ui/NCBIGenePanel.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/PSICQUICSearchUI.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
Log:
Refactored web services
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/api/webservice-api/src/main/java/org/cytoscape/io/webservice/WebServiceClient.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/api/webservice-api/src/main/java/org/cytoscape/io/webservice/WebServiceClient.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/api/webservice-api/src/main/java/org/cytoscape/io/webservice/WebServiceClient.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -34,6 +34,7 @@
*/
package org.cytoscape.io.webservice;
+import java.awt.Container;
import java.net.URI;
import org.cytoscape.work.TaskFactory;
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -86,7 +86,7 @@
@Override
public WebServiceClientContext createTaskContext() {
- WebServiceClientContextImpl context = new WebServiceClientContextImpl();
+ WebServiceClientContext context = super.createTaskContext();
context.setQueryBuilderGUI(mainPanel);
return context;
}
@@ -128,6 +128,5 @@
desc = desc.replaceAll("</span>", "</B>");
return "<html><body>" + desc + "</body></html>";
}
-
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -36,6 +36,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.io.webservice.TableImportWebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
import org.cytoscape.io.webservice.biomart.task.ImportTableTask;
import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
@@ -46,6 +47,7 @@
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.TaskIterator;
+import org.osgi.framework.ServiceException;
/**
@@ -55,13 +57,13 @@
public class BiomartClient extends AbstractWebServiceClient implements
TableImportWebServiceClient {
private final CyTableFactory tableFactory;
private final BiomartRestClient restClient;
- private BiomartAttrMappingPanel gui;
private ImportTableTask importTask;
private final CyNetworkManager networkManager;
private final CyApplicationManager applicationManager;
private final CySwingApplication app;
private final CyTableManager tableManager;
private final CyRootNetworkManager cyRootNetworkFactory;
+ private BiomartAttrMappingPanel gui;
/**
* Creates a new Biomart Client object.
@@ -89,10 +91,6 @@
// TODO: set optional parameters (Tunables?)
}
- public void setGUI(final BiomartAttrMappingPanel gui) {
- this.gui = gui;
- }
-
public BiomartRestClient getRestClient() {
return this.restClient;
}
@@ -107,12 +105,20 @@
}
@Override
- public TaskIterator createTaskIterator() {
+ public WebServiceClientContext createTaskContext() {
+ WebServiceClientContext context = super.createTaskContext();
+ context.setQueryBuilderGUI(gui);
+ return context;
+ }
+
+ @Override
+ public TaskIterator createTaskIterator(WebServiceClientContext context)
{
+ BiomartAttrMappingPanel gui = (BiomartAttrMappingPanel)
context.getQueryBuilderGUI();
if (gui == null)
throw new IllegalStateException(
"Could not build query because Query
Builder GUI is null.");
- final BiomartQuery query = this.gui.getTableImportQuery();
+ final BiomartQuery query = gui.getTableImportQuery();
importTask = new ImportTableTask(restClient, query,
tableFactory, networkManager,
applicationManager,
app.getJFrame(), tableManager,
@@ -120,4 +126,9 @@
return new TaskIterator(importTask);
}
+
+ // TODO: This still needs refactoring
+ public void setGUI(BiomartAttrMappingPanel gui) {
+ this.gui = gui;
+ }
}
Deleted:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/BioMartTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/BioMartTaskFactory.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/BioMartTaskFactory.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,23 +0,0 @@
-package org.cytoscape.io.webservice.biomart.task;
-
-import org.cytoscape.work.Task;
-import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.TaskIterator;
-
-public class BioMartTaskFactory implements TaskFactory{
-
- private TaskIterator itr;
-
- public BioMartTaskFactory(final Task firstTask) {
- if(firstTask == null)
- throw new NullPointerException("First task is null.");
-
- this.itr = new TaskIterator(firstTask);
- }
-
- @Override
- public TaskIterator createTaskIterator() {
- return itr;
- }
-
-}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTaskFactory.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportAttributeListTaskFactory.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,20 +1,22 @@
package org.cytoscape.io.webservice.biomart.task;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class ImportAttributeListTaskFactory implements TaskFactory {
+public class ImportAttributeListTaskFactory extends AbstractTaskFactory {
- final ImportAttributeListTask task;
+ private String datasourceName;
+ private BiomartRestClient client;
public ImportAttributeListTaskFactory(final String datasourceName,
final BiomartRestClient client) {
- task = new ImportAttributeListTask(datasourceName, client);
+ this.datasourceName = datasourceName;
+ this.client = client;
}
@Override
- public TaskIterator createTaskIterator() {
- return new TaskIterator(task);
+ public TaskIterator createTaskIterator(Object context) {
+ return new TaskIterator(new
ImportAttributeListTask(datasourceName, client));
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportFilterTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportFilterTaskFactory.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportFilterTaskFactory.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,33 +1,21 @@
package org.cytoscape.io.webservice.biomart.task;
import org.cytoscape.io.webservice.biomart.rest.BiomartRestClient;
-import org.cytoscape.work.Task;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class ImportFilterTaskFactory implements TaskFactory {
+public class ImportFilterTaskFactory extends AbstractTaskFactory {
private final BiomartRestClient client;
private final String datasourceName;
-
- private Task task;
public ImportFilterTaskFactory(final String datasourceName, final
BiomartRestClient client) {
this.client = client;
this.datasourceName = datasourceName;
- task = null;
}
@Override
- public TaskIterator createTaskIterator() {
- if(task == null)
- return new TaskIterator(new
ImportFilterTask(datasourceName, client));
- else
- return new TaskIterator(task);
+ public TaskIterator createTaskIterator(Object context) {
+ return new TaskIterator(new ImportFilterTask(datasourceName,
client));
}
-
- public void setTask(Task task) {
- this.task = task;
- }
-
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/task/ShowBiomartGUIAction.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -10,6 +10,9 @@
import org.cytoscape.io.webservice.biomart.BiomartClient;
import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.work.AbstractTaskFactory;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.swing.DialogTaskManager;
import org.slf4j.Logger;
@@ -69,11 +72,13 @@
private void initDialog() {
-
- final BioMartTaskFactory tf = new BioMartTaskFactory(firstTask);
- tf.createTaskIterator().insertTasksAfter(firstTask,
showDialogTask);
-
+ final TaskFactory<Object> tf = new AbstractTaskFactory() {
+ @Override
+ public TaskIterator createTaskIterator(Object context) {
+ return new TaskIterator(firstTask,
showDialogTask);
+ }
+ };
taskManager.setExecutionContext(app.getJFrame());
- taskManager.execute(tf);
+ taskManager.execute(tf, tf.createTaskContext());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -53,7 +53,6 @@
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.ImportFilterTask;
import org.cytoscape.io.webservice.biomart.task.LoadRepositoryResult;
@@ -65,7 +64,9 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.AbstractTaskFactory;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.swing.DialogTaskManager;
@@ -200,19 +201,27 @@
taskManager.setExecutionContext(parent);
if (type.equals(SourceType.ATTRIBUTE)) {
- final ImportAttributeListTask firstTask = new
ImportAttributeListTask(
- datasourceName, client.getRestClient());
- final SetAttributeTask setAttrTask = new
SetAttributeTask(firstTask);
- final BioMartTaskFactory tf = new
BioMartTaskFactory(firstTask);
- tf.createTaskIterator().insertTasksAfter(firstTask,
setAttrTask);
- taskManager.execute(tf);
+ TaskFactory<Object> tf = new AbstractTaskFactory() {
+ @Override
+ public TaskIterator createTaskIterator(Object
context) {
+ final ImportAttributeListTask firstTask
= new ImportAttributeListTask(
+ datasourceName,
client.getRestClient());
+ final SetAttributeTask setAttrTask =
new SetAttributeTask(firstTask);
+ return new TaskIterator(firstTask,
setAttrTask);
+ }
+ };
+ taskManager.execute(tf, tf.createTaskContext());
} else if (type.equals(SourceType.FILTER)) {
- final ImportFilterTask firstTask = new ImportFilterTask(
- datasourceName, client.getRestClient());
- final SetFilterTask setFilterTask = new
SetFilterTask(firstTask);
- final BioMartTaskFactory tf = new
BioMartTaskFactory(firstTask);
- tf.createTaskIterator().insertTasksAfter(firstTask,
setFilterTask);
- taskManager.execute(tf);
+ TaskFactory<Object> tf = new AbstractTaskFactory() {
+ @Override
+ public TaskIterator createTaskIterator(Object
context) {
+ final ImportFilterTask firstTask = new
ImportFilterTask(
+ datasourceName,
client.getRestClient());
+ final SetFilterTask setFilterTask = new
SetFilterTask(firstTask);
+ return new TaskIterator(firstTask,
setFilterTask);
+ }
+ };
+ taskManager.execute(tf, tf.createTaskContext());
}
}
@@ -323,7 +332,7 @@
@Override
protected void importAttributes() {
//taskManager.setParent(parent);
- taskManager.execute(client);
+ taskManager.execute(client, client.createTaskContext());
}
public BiomartQuery getTableImportQuery() {
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceEdgeContextMenuTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceEdgeContextMenuTaskFactory.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceEdgeContextMenuTaskFactory.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -2,6 +2,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.task.AbstractEdgeViewTaskFactory;
+import org.cytoscape.task.EdgeViewTaskContext;
import org.cytoscape.work.TaskIterator;
public class WebServiceEdgeContextMenuTaskFactory extends
AbstractEdgeViewTaskFactory {
@@ -11,8 +12,8 @@
}
@Override
- public TaskIterator createTaskIterator() {
- return new TaskIterator(new
WebServiceContextMenuTask<CyEdge>(edgeView));
+ public TaskIterator createTaskIterator(EdgeViewTaskContext context) {
+ return new TaskIterator(new
WebServiceContextMenuTask<CyEdge>(context.getEdgeView()));
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceNodeContextMenuTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceNodeContextMenuTaskFactory.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/task/WebServiceNodeContextMenuTaskFactory.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -2,6 +2,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNodeViewTaskFactory;
+import org.cytoscape.task.NodeViewTaskContext;
import org.cytoscape.work.TaskIterator;
public class WebServiceNodeContextMenuTaskFactory extends
AbstractNodeViewTaskFactory {
@@ -11,8 +12,8 @@
}
@Override
- public TaskIterator createTaskIterator() {
- return new TaskIterator(new
WebServiceContextMenuTask<CyNode>(nodeView));
+ public TaskIterator createTaskIterator(NodeViewTaskContext context) {
+ return new TaskIterator(new
WebServiceContextMenuTask<CyNode>(context.getNodeView()));
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -54,9 +54,10 @@
import javax.swing.LayoutStyle;
import org.cytoscape.io.webservice.NetworkImportWebServiceClient;
-import org.cytoscape.io.webservice.SearchWebServiceClient;
import org.cytoscape.io.webservice.WebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskManager;
@@ -134,7 +135,8 @@
if (client instanceof WebServiceClient) {
WebServiceClient service = (WebServiceClient) client;
- Container container = service.getQueryBuilderGUI();
+ WebServiceClientContext context =
service.createTaskContext();
+ Container container = context.getQueryBuilderGUI();
if (container != null) {
serviceUIPanels.put(client, container);
}
@@ -440,8 +442,9 @@
}
// Set query. Just pass the text in the panel.
- client.setQuery(this.queryTextPane.getText());
- taskManager.execute(client);
+ WebServiceClientContext context = client.createTaskContext();
+ context.setQuery(this.queryTextPane.getText());
+ taskManager.execute(client, context);
}
@@ -460,7 +463,7 @@
//AboutDialog.showDialog(clientName, icon, description);
}
- private final class ImportNetworkTaskFactory implements TaskFactory {
+ private final class ImportNetworkTaskFactory extends
AbstractTaskFactory {
private final TaskFactory tFactory;
@@ -469,9 +472,9 @@
}
@Override
- public TaskIterator createTaskIterator() {
+ public TaskIterator createTaskIterator(Object context) {
final TaskIterator itr = new TaskIterator();
- itr.insertTasksAfter(new RegisterNetworkTask(),
tFactory.createTaskIterator().next());
+ itr.insertTasksAfter(new RegisterNetworkTask(),
tFactory.createTaskIterator(tFactory.createTaskContext()).next());
return itr;
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,16 +1,18 @@
package org.cytoscape.webservice.ncbi;
+import java.awt.Container;
import java.util.Set;
-import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.io.webservice.TableImportWebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.io.webservice.client.AbstractWebServiceClient;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.webservice.ncbi.task.ImportTableFromNCBITask;
import org.cytoscape.work.TaskIterator;
@@ -40,10 +42,10 @@
}
@Override
- public TaskIterator createTaskIterator() {
+ public TaskIterator createTaskIterator(WebServiceClientContext context)
{
return new TaskIterator(
- new ImportTableFromNCBITask(tableFactory, ((NCBIQuery)
this.currentQuery).getIds(),
- ((NCBIQuery)
this.currentQuery).getCategory(),
+ new ImportTableFromNCBITask(tableFactory, ((NCBIQuery)
context.getQuery()).getIds(),
+ ((NCBIQuery)
context.getQuery()).getCategory(),
networkManager,
applicationManager, tableManager,
cyRootNetworkFactory));
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,11 +1,13 @@
package org.cytoscape.webservice.ncbi;
+import java.awt.Container;
import java.util.HashSet;
import java.util.Set;
import org.cytoscape.io.webservice.NetworkImportWebServiceClient;
import org.cytoscape.io.webservice.SearchWebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.io.webservice.client.AbstractWebServiceClient;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
@@ -40,11 +42,11 @@
}
@Override
- public TaskIterator createTaskIterator() {
- if (currentQuery == null)
+ public TaskIterator createTaskIterator(WebServiceClientContext context)
{
+ if (context.getQuery() == null)
throw new NullPointerException("Query object is null.");
else {
- networkTask = new
ImportNetworkFromGeneTask(this.currentQuery.toString(),
+ networkTask = new
ImportNetworkFromGeneTask(context.getQuery().toString(),
networkFactory, tableFactory,
manager,
tableManager);
return new TaskIterator(networkTask);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ui/NCBIGenePanel.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ui/NCBIGenePanel.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/ui/NCBIGenePanel.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -44,6 +44,7 @@
import javax.swing.Icon;
import javax.swing.ImageIcon;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
@@ -112,8 +113,9 @@
@Override
protected void importAttributes() {
logger.debug("Import start.");
- client.setQuery(new NCBIQuery(getCategory(), createIDSet()));
- taskManager.execute(client);
+ WebServiceClientContext context = client.createTaskContext();
+ context.setQuery(new NCBIQuery(getCategory(), createIDSet()));
+ taskManager.execute(client, context);
}
private Set<AnnotationCategory> getCategory() {
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -1,6 +1,5 @@
package org.cytoscape.webservice.psicquic;
-import java.awt.Container;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
@@ -16,6 +15,7 @@
import org.cytoscape.io.webservice.NetworkImportWebServiceClient;
import org.cytoscape.io.webservice.SearchWebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClientContext;
import org.cytoscape.io.webservice.client.AbstractWebServiceClient;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
@@ -104,7 +104,16 @@
logger.info("RegistryManager initialized in " + sec + " sec.");
}
- public TaskIterator createTaskIterator() {
+ @Override
+ public WebServiceClientContext createTaskContext() {
+ WebServiceClientContext context = super.createTaskContext();
+ context.setQueryBuilderGUI(new PSICQUICSearchUI(networkManager,
regManager, client, tManager, createViewTaskFactory, openBrowser));
+ return context;
+ }
+
+ public TaskIterator createTaskIterator(WebServiceClientContext context)
{
+ Object currentQuery = context.getQuery();
+
if (regManager == null)
throw new NullPointerException("RegistryManager is
null");
@@ -141,9 +150,4 @@
return new RegistryManager();
}
}
-
- @Override
- public Container getQueryBuilderGUI() {
- return new PSICQUICSearchUI(networkManager, regManager, client,
tManager, createViewTaskFactory, openBrowser);
- }
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -12,14 +12,13 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.task.NetworkTaskContext;
import org.cytoscape.task.NetworkTaskFactory;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient;
import org.cytoscape.webservice.psicquic.PSICQUICRestClient.SearchMode;
import org.cytoscape.webservice.psicquic.RegistryManager;
import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskMonitor;
-import org.omg.CORBA.PRIVATE_MEMBER;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -31,7 +30,7 @@
private final RegistryManager registryManager;
// TaskFactory for creating view
- private final NetworkTaskFactory createViewTaskFactory;
+ private final NetworkTaskFactory<NetworkTaskContext>
createViewTaskFactory;
private String query;
@@ -47,7 +46,7 @@
private volatile boolean canceled = false;
public ImportNetworkFromPSICQUICTask(final String query, final
PSICQUICRestClient client, final CyNetworkManager manager,
- final RegistryManager registryManager, final
Set<String> searchResult, final SearchMode mode, final NetworkTaskFactory
createViewTaskFactory) {
+ final RegistryManager registryManager, final
Set<String> searchResult, final SearchMode mode, final
NetworkTaskFactory<NetworkTaskContext> createViewTaskFactory) {
this.client = client;
this.manager = manager;
this.registryManager = registryManager;
@@ -118,8 +117,9 @@
if (retValue == JOptionPane.YES_OPTION) {
// Create View
for (final CyNetwork network : networks) {
-
createViewTaskFactory.setNetwork(network);
-
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator());
+ NetworkTaskContext context =
createViewTaskFactory.createTaskContext();
+ context.setNetwork(network);
+
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator(context));
}
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/PSICQUICSearchUI.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/PSICQUICSearchUI.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/PSICQUICSearchUI.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -34,6 +34,7 @@
import org.cytoscape.webservice.psicquic.task.SearchRecoredsTask;
import org.cytoscape.webservice.psicquic.ui.SelectorBuilder.Species;
import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskManager;
@@ -247,12 +248,13 @@
searchTask.setQuery(query);
searchTask.setTargets(activeSource.values());
- taskManager.execute(new TaskFactory() {
+ TaskFactory<?> factory = new AbstractTaskFactory() {
@Override
- public TaskIterator createTaskIterator() {
+ public TaskIterator createTaskIterator(Object context) {
return new TaskIterator(searchTask, new
SetTableTask(searchTask));
}
- });
+ };
+ taskManager.execute(factory, factory.createTaskContext());
}
private final class SetTableTask extends AbstractTask {
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
2012-02-14 20:13:46 UTC (rev 28267)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory/impl/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/ui/SourceStatusPanel.java
2012-02-14 20:50:53 UTC (rev 28268)
@@ -25,7 +25,7 @@
import org.cytoscape.webservice.psicquic.PSICQUICRestClient.SearchMode;
import org.cytoscape.webservice.psicquic.RegistryManager;
import org.cytoscape.webservice.psicquic.task.ImportNetworkFromPSICQUICTask;
-import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.AbstractTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskManager;
@@ -288,12 +288,13 @@
final ImportNetworkFromPSICQUICTask networkTask = new
ImportNetworkFromPSICQUICTask(query, client,
networkManager, manager, sourceURLs, mode,
createViewTaskFactory);
- taskManager.execute(new TaskFactory() {
+ AbstractTaskFactory factory = new AbstractTaskFactory() {
@Override
- public TaskIterator createTaskIterator() {
+ public TaskIterator createTaskIterator(Object context) {
return new TaskIterator(networkTask);
}
- });
+ };
+ taskManager.execute(factory, factory.createTaskContext());
Window parentWindow = ((Window) getRootPane().getParent());
parentWindow.pack();
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