Author: kono
Date: 2012-04-13 13:10:54 -0700 (Fri, 13 Apr 2012)
New Revision: 28828
Modified:
core3/api/trunk/webservice-api/pom.xml
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/NetworkImportWebServiceClient.java
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/SearchWebServiceClient.java
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/TableImportWebServiceClient.java
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/events/SearchFinishedListener.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
core3/impl/trunk/webservice-biomart-client-impl/pom.xml
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
Log:
fixes #855 some of the web service clients interfaces are now marker interface.
Modified: core3/api/trunk/webservice-api/pom.xml
===================================================================
--- core3/api/trunk/webservice-api/pom.xml 2012-04-13 20:08:01 UTC (rev
28827)
+++ core3/api/trunk/webservice-api/pom.xml 2012-04-13 20:10:54 UTC (rev
28828)
@@ -13,7 +13,6 @@
</properties>
<modelVersion>4.0.0</modelVersion>
- <groupId>org.cytoscape</groupId>
<artifactId>webservice-api</artifactId>
<name>Cytoscape Webservice API (${project.artifactId})</name>
Modified:
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/NetworkImportWebServiceClient.java
===================================================================
---
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/NetworkImportWebServiceClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/NetworkImportWebServiceClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -1,18 +1,10 @@
package org.cytoscape.io.webservice;
-import java.util.Set;
-import org.cytoscape.model.CyNetwork;
-
/**
- * An interface that defines a web service client that will
- * return a set of networks.
+ * Marker interface for web service clients that have ability to import
network data.
+ *
* @CyAPI.Spi.Interface
*/
public interface NetworkImportWebServiceClient {
- /**
- * Returns the set of networks returned from the webservice.
- * @return The set of networks returned from the webservice.
- */
- Set<CyNetwork> getNetworks();
}
Modified:
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/SearchWebServiceClient.java
===================================================================
---
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/SearchWebServiceClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/SearchWebServiceClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -1,16 +1,10 @@
package org.cytoscape.io.webservice;
/**
- * An interface that defines a queryable web service
- * that returns a search result.
- * @param <T> The type of the search result.
+ * Marker interface for web service clients sending search query
+ * and getting arbitrary search result.
+ *
* @CyAPI.Spi.Interface
*/
-public interface SearchWebServiceClient<T> {
-
- /**
- * Returns the search result object.
- * @return the search result object.
- */
- T getSearchResult();
+public interface SearchWebServiceClient {
}
Modified:
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/TableImportWebServiceClient.java
===================================================================
---
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/TableImportWebServiceClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/TableImportWebServiceClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -1,19 +1,10 @@
package org.cytoscape.io.webservice;
-import java.util.Set;
-import org.cytoscape.model.CyTable;
-
/**
- * An interface that defines a web service client that will
- * return a set of tables.
+ * Maker interface for web service clients that have ability to import table
data.
+ *
* @CyAPI.Spi.Interface
*/
public interface TableImportWebServiceClient {
-
- /**
- * Returns a set of tables from the web service.
- * @return a set of tables from the web service.
- */
- Set<CyTable> getTables();
}
Modified:
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/events/SearchFinishedListener.java
===================================================================
---
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/events/SearchFinishedListener.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/api/trunk/webservice-api/src/main/java/org/cytoscape/io/webservice/events/SearchFinishedListener.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -9,5 +9,5 @@
* The method that should handle the specified event.
* @param evt The event to be handled.
*/
- void handleEvent(final SearchFinishedEvent evt);
+ void handleEvent(final SearchFinishedEvent<?> evt);
}
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/web_service/CytoscapeCPathWebService.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -28,7 +28,7 @@
* CPath Web Service, integrated into the Cytoscape Web Services Framework.
*/
public class CytoscapeCPathWebService extends AbstractWebServiceGUIClient
- implements NetworkImportWebServiceClient,
SearchWebServiceClient<Object>
+ implements NetworkImportWebServiceClient, SearchWebServiceClient
{
// Display name of this client.
private static final String DISPLAY_NAME =
CPathProperties.getInstance().getCPathServerName() +
@@ -75,19 +75,8 @@
return mainPanel;
}
- @Override
- public Set<CyNetwork> getNetworks() {
- // TODO Auto-generated method stub
- return null;
- }
@Override
- public Object getSearchResult() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public TaskIterator createTaskIterator(Object query) {
CPathResponseFormat format = CPathResponseFormat.BINARY_SIF;
CPathNetworkImportTask task =
factory.createCPathNetworkImportTask((String) query, webApi, format);
Modified: core3/impl/trunk/webservice-biomart-client-impl/pom.xml
===================================================================
--- core3/impl/trunk/webservice-biomart-client-impl/pom.xml 2012-04-13
20:08:01 UTC (rev 28827)
+++ core3/impl/trunk/webservice-biomart-client-impl/pom.xml 2012-04-13
20:10:54 UTC (rev 28828)
@@ -14,7 +14,6 @@
</properties>
<modelVersion>4.0.0</modelVersion>
- <groupId>org.cytoscape</groupId>
<artifactId>webservice-biomart-client-impl</artifactId>
<name>Cytoscape Biomart Webservice Impl (${project.artifactId})</name>
Modified:
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
===================================================================
---
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-biomart-client-impl/src/main/java/org/cytoscape/io/webservice/biomart/BiomartClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -35,7 +35,6 @@
import org.cytoscape.application.CyApplicationManager;
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;
import org.cytoscape.io.webservice.biomart.ui.BiomartAttrMappingPanel;
@@ -53,7 +52,8 @@
* Biomart Web Service Client.
*
*/
-public class BiomartClient extends AbstractWebServiceGUIClient implements
TableImportWebServiceClient {
+public class BiomartClient extends AbstractWebServiceGUIClient {
+
private final CyTableFactory tableFactory;
private final BiomartRestClient restClient;
private ImportTableTask importTask;
@@ -95,14 +95,6 @@
return this.restClient;
}
- @Override
- public Set<CyTable> getTables() {
- // Return empty task if not executed yet.
- if (importTask == null)
- return new HashSet<CyTable>();
- else
- return importTask.getCyTables();
- }
@Override
public TaskIterator createTaskIterator(Object query) {
Modified:
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
===================================================================
---
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-impl/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceImportDialog.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -43,8 +43,6 @@
private static final Icon DEF_ICON = new ImageIcon(
WebServiceImportDialog.class.getResource("/images/stock_internet-32.png"));
-// private static final Icon NETWORK_IMPORT_ICON = new ImageIcon(
-//
WebServiceImportDialog.class.getResource("/images/networkImportIcon.png"));
private static final String NO_CLIENT = "No Service Client";
private JButton cancelButton;
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBITableImportClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -47,9 +47,4 @@
networkManager,
applicationManager, tableManager,
cyRootNetworkFactory));
}
-
- @Override
- public Set<CyTable> getTables() {
- return null;
- }
}
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/NCBIWebServiceClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -1,6 +1,5 @@
package org.cytoscape.webservice.ncbi;
-
import java.util.HashSet;
import java.util.Set;
@@ -15,10 +14,8 @@
import org.cytoscape.webservice.ncbi.task.ImportNetworkFromGeneTask;
import org.cytoscape.work.TaskIterator;
-
-public class NCBIWebServiceClient extends AbstractWebServiceClient
- implements NetworkImportWebServiceClient,
SearchWebServiceClient<Set<String>>
-{
+public class NCBIWebServiceClient extends AbstractWebServiceClient implements
NetworkImportWebServiceClient,
+ SearchWebServiceClient {
private final CyNetworkFactory networkFactory;
private final CyTableFactory tableFactory;
private final CyNetworkManager manager;
@@ -26,17 +23,15 @@
private ImportNetworkFromGeneTask networkTask;
- public NCBIWebServiceClient(final String uri, final String displayName,
- final String description, final
CyNetworkFactory networkFactory,
- final CyTableFactory tableFactory,
- final CyNetworkManager manager, final
CyTableManager tableManager)
- {
+ public NCBIWebServiceClient(final String uri, final String displayName,
final String description,
+ final CyNetworkFactory networkFactory, final
CyTableFactory tableFactory, final CyNetworkManager manager,
+ final CyTableManager tableManager) {
super(uri, displayName, description);
this.networkFactory = networkFactory;
- this.manager = manager;
- this.tableFactory = tableFactory;
- this.tableManager = tableManager;
+ this.manager = manager;
+ this.tableFactory = tableFactory;
+ this.tableManager = tableManager;
}
@Override
@@ -44,27 +39,9 @@
if (query == null)
throw new NullPointerException("Query object is null.");
else {
- networkTask = new
ImportNetworkFromGeneTask(query.toString(),
-
networkFactory, tableFactory,
- manager,
tableManager);
+ networkTask = new
ImportNetworkFromGeneTask(query.toString(), networkFactory, tableFactory,
manager,
+ tableManager);
return new TaskIterator(networkTask);
}
}
-
- @Override
- public Set<CyNetwork> getNetworks() {
- final Set<CyNetwork> result = new HashSet<CyNetwork>();
- if (networkTask != null) {
- final CyNetwork network = networkTask.getNetwork();
- if (network != null)
- result.add(network);
- }
- return result;
- }
-
- @Override
- public Set<String> getSearchResult() {
- // TODO Auto-generated method stub
- return null;
- }
}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICWebServiceClient.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -32,7 +32,7 @@
import org.slf4j.LoggerFactory;
public class PSICQUICWebServiceClient extends AbstractWebServiceGUIClient
implements NetworkImportWebServiceClient,
- SearchWebServiceClient<Set<String>> {
+ SearchWebServiceClient {
private static final Logger logger =
LoggerFactory.getLogger(PSICQUICWebServiceClient.class);
@@ -43,7 +43,7 @@
private RegistryManager regManager;
private final CyNetworkManager networkManager;
- private final TaskManager tManager;
+ private final TaskManager<?, ?> tManager;
private ImportNetworkFromPSICQUICTask networkTask;
private final NetworkTaskFactory createViewTaskFactory;
@@ -53,7 +53,7 @@
private final OpenBrowser openBrowser;
public PSICQUICWebServiceClient(final String uri, final String
displayName, final String description,
- final CyNetworkFactory networkFactory, final
CyNetworkManager networkManager, final TaskManager tManager,
+ final CyNetworkFactory networkFactory, final
CyNetworkManager networkManager, final TaskManager<?, ?> tManager,
final NetworkTaskFactory createViewTaskFactory, final
OpenBrowser openBrowser) {
super(uri, displayName, description);
@@ -124,17 +124,7 @@
}
}
- public Set<CyNetwork> getNetworks() {
- if (networkTask != null)
- return networkTask.getNetworks();
- else
- return new HashSet<CyNetwork>();
- }
- public Set<String> getSearchResult() {
- return null;
- }
-
private static final class InitRegistryManagerTask implements
Callable<RegistryManager> {
@Override
public RegistryManager call() throws Exception {
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-04-13 20:08:01 UTC (rev 28827)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/task/ImportNetworkFromPSICQUICTask.java
2012-04-13 20:10:54 UTC (rev 28828)
@@ -8,6 +8,7 @@
import java.util.Set;
import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
@@ -113,15 +114,9 @@
networks.add(network);
}
- if (!canceled) {
- int retValue = JOptionPane.showConfirmDialog(null, "Do
you want to create views?");
- if (retValue == JOptionPane.YES_OPTION) {
- // Create View
- for (final CyNetwork network : networks) {
-
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator(network));
- }
- }
- }
+ if (!canceled)
+ for (final CyNetwork network : networks)
+
insertTasksAfterCurrentTask(createViewTaskFactory.createTaskIterator(network));
}
@Override
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