Author: kono
Date: 2011-03-08 15:45:51 -0800 (Tue, 08 Mar 2011)
New Revision: 24345
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromWebServiceTask.java
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartState.java
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Some new tasks are added.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -30,22 +30,19 @@
package org.cytoscape.task.internal.loadnetwork;
-import java.net.URL;
import java.io.IOException;
+import java.net.URL;
import java.util.Properties;
-import org.cytoscape.io.DataCategory;
import org.cytoscape.io.read.CyNetworkViewReaderManager;
import org.cytoscape.io.util.StreamUtil;
-import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkViewManager;
-import org.cytoscape.session.CyNetworkNaming;
-
/**
* Specific instance of AbstractLoadNetworkTask that loads a URL.
*/
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -4,18 +4,18 @@
* List of major ID types.
*/
public enum IDType {
- ENSEMBL("Ensembl Gene ID"), ENTREZ_GENE("Entrez Gene ID"),
UNIPROT("UniProt ID");
-
+ ENSEMBL("Ensembl Gene ID"), ENTREZ_GENE("Entrez Gene ID"),
+ UNIPROT("UniProt ID"), REFSEQ("RefSeq ID"),
+ EMBL("EMBL (Genbank) ID"), GENE_SYMBOL("Gene Symbol");
+
private final String displayName;
-
+
private IDType(final String displayName) {
this.displayName = displayName;
}
-
-
+
public String getDisplayName() {
return this.displayName;
}
-
-
+
}
\ No newline at end of file
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromWebServiceTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromWebServiceTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromWebServiceTask.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -0,0 +1,26 @@
+package org.cytoscape.task.internal.quickstart;
+
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.util.ListSingleSelection;
+
+public class ImportNetworkFromWebServiceTask extends AbstractTask {
+
+ @Tunable(description = "Select Species")
+ public final ListSingleSelection<String> species;
+
+ ImportNetworkFromWebServiceTask() {
+ super();
+
+ // TODO: Load list of species from property file.
+ this.species = new ListSingleSelection<String>("Human",
"Mouse", "Fly", "Yeast");
+
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ System.out.println("This function is not implemented yet.");
+ }
+
+}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -46,8 +46,7 @@
}
public Task getWebServiceImportTask() {
- // TODO: what should I return?
- return null;
+ return new ImportNetworkFromWebServiceTask();
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -31,7 +31,7 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
package org.cytoscape.task.internal.quickstart;
@@ -42,39 +42,42 @@
import org.cytoscape.work.util.ListSingleSelection;
public class LoadNetworkTask extends AbstractTask {
-
+
private static final String FROM_FILE = "File";
private static final String FROM_URL = "URL";
private static final String FROM_SERVICE = "Public Database";
-
-
+
@Tunable(description = "Select Data Source Type")
public ListSingleSelection<String> dataSource = new
ListSingleSelection<String>(
FROM_FILE, FROM_URL, FROM_SERVICE);
-
+
private QuickStartState state;
private final ImportTaskUtil util;
-
+
public LoadNetworkTask(QuickStartState state, ImportTaskUtil util) {
this.state = state;
this.util = util;
}
- public void run(TaskMonitor e) {
- // This is for next step: specify ID type
- insertTasksAfterCurrentTask(new SelectNetworkIdTypeTask(state));
-
+ public void run(TaskMonitor monitor) {
+
+ if (state.getIDType() == null) {
+ // This is for next step: specify ID type
+ insertTasksAfterCurrentTask(new
SelectNetworkIdTypeTask(state));
+ }
+
final String selected = dataSource.getSelectedValue();
- if(selected == FROM_FILE) {
+ if (selected == FROM_FILE) {
// Load file task
insertTasksAfterCurrentTask(util.getFileImportTask());
- } else if(selected == FROM_URL) {
+ } else if (selected == FROM_URL) {
// Load URL task
insertTasksAfterCurrentTask(util.getURLImportTask());
- } else if(selected == FROM_SERVICE) {
- // TODO create new task
+ } else if (selected == FROM_SERVICE) {
+
insertTasksAfterCurrentTask(util.getWebServiceImportTask());
}
-
+
state.finished(Job.LOAD_NETWORK);
+
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartState.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartState.java
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartState.java
2011-03-08 23:45:51 UTC (rev 24345)
@@ -47,6 +47,8 @@
SELECT_NETWORK_ID_TYPE,
SELECT_TABLE_ID_TYPE;
}
+
+ private IDType idType;
private final Set<Job> completedSoFar =
Collections.synchronizedSet(EnumSet.noneOf(Job.class));
@@ -57,4 +59,12 @@
synchronized boolean isFinished() {
return (completedSoFar.size() == Job.values().length);
}
+
+ public IDType getIDType() {
+ return this.idType;
+ }
+
+ public void setIDType(IDType idType) {
+ this.idType = idType;
+ }
}
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-03-08 23:27:07 UTC (rev 24344)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-03-08 23:45:51 UTC (rev 24345)
@@ -315,5 +315,15 @@
<bean id="quickStartTaskFactory"
class="org.cytoscape.task.internal.quickstart.QuickStartTaskFactory">
+ <constructor-arg ref="importTaskUtil" />
</bean>
+
+ <bean id="importTaskUtil"
class="org.cytoscape.task.internal.quickstart.ImportTaskUtil">
+ <constructor-arg ref="cyNetworkViewReaderManagerServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="cyNetworkViewManagerServiceRef" />
+ <constructor-arg ref="cyPropertyServiceRef" />
+ <constructor-arg ref="cyNetworkNamingServiceRef" />
+ <constructor-arg ref="streamUtilRef" />
+ </bean>
</beans>
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