Author: kono
Date: 2011-06-24 15:19:47 -0700 (Fri, 24 Jun 2011)
New Revision: 25929
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
Removed:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SelectNetworkTask.java
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask2.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
Log:
QuickStart task had been replaced by a simplified version. This may be
revisited in the future.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -15,14 +15,24 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.loadnetwork.AbstractLoadNetworkTask;
import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SearchRelatedGenesTask;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.util.ListSingleSelection;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
public class ImportNetworkFromPublicDataSetTask extends
AbstractLoadNetworkTask {
+
+ private static final Logger logger =
LoggerFactory.getLogger(ImportNetworkFromPublicDataSetTask.class);
+
+ private static final String quickStartPropertyKey =
"showQuickStartAtStartup";
+
+ @Tunable(description="Show this dialog at Cytoscape start-up")
+ public boolean showQuickStartAtStartup; // get this value from system
property
- @Tunable(description = "Select Data Source")
+ @Tunable(description = "What kind of network do you need?")
public ListSingleSelection<String> dataSource;
private final Map<String, URL> sourceMap;
@@ -61,6 +71,8 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+
+ props.setProperty(quickStartPropertyKey, new
Boolean(showQuickStartAtStartup).toString());
taskMonitor.setStatusMessage("Update is done.");
final String selected = this.dataSource.getSelectedValue();
@@ -93,10 +105,11 @@
if (reader == null)
throw new NullPointerException("Failed to find reader
for specified URL: " + name);
+
insertTasksAfterCurrentTask(new SetNetworkNameTask(reader,
selected));
-
taskMonitor.setStatusMessage("Loading network...");
loadNetwork(reader);
+
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -50,9 +50,8 @@
protected static final String LOAD_SUBNETWORK = "Create subnetwork from
interactome";
// @Tunable(description="What would you like to do today?\nCytoscape
requires at the minimum a network to do anything. A network and attributes
makes life much better. If you don't have a network, that's OK, we'll help you
find one.")
- @Tunable(description = "What would you like to do today?")
- public ListSingleSelection<String> selection = new
ListSingleSelection<String>(
- LOAD_NETWORK, LOAD_TABLE, LOAD_SUBNETWORK);
+ //@Tunable(description = "What would you like to do today?")
+ //public ListSingleSelection<String> selection = new
ListSingleSelection<String>(LOAD_NETWORK, LOAD_TABLE, LOAD_SUBNETWORK);
protected final QuickStartState state;
protected final ImportTaskUtil importTaskUtil;
@@ -74,13 +73,15 @@
}
protected void doLoading(){
- String selected = selection.getSelectedValue();
- if (selected == LOAD_NETWORK) {
- insertTasksAfterCurrentTask(new LoadNetworkTask(state,
importTaskUtil));
- } else if (selected == LOAD_TABLE)
- insertTasksAfterCurrentTask(new LoadTableTask(state,
importTaskUtil));
- else if (selected == LOAD_SUBNETWORK) {
- insertTasksAfterCurrentTask(new
SubnetworkBuilderTask(networkManager, subnetworkUtil));
- }
+
insertTasksAfterCurrentTask(importTaskUtil.getWebServiceImportTask());
+ // Old Tasks
+// String selected = selection.getSelectedValue();
+// if (selected == LOAD_NETWORK) {
+// insertTasksAfterCurrentTask(new LoadNetworkTask(state,
importTaskUtil));
+// } else if (selected == LOAD_TABLE)
+// insertTasksAfterCurrentTask(new LoadTableTask(state,
importTaskUtil));
+// else if (selected == LOAD_SUBNETWORK) {
+// insertTasksAfterCurrentTask(new
SubnetworkBuilderTask(networkManager, subnetworkUtil));
+// }
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask2.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask2.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask2.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -1,7 +1,6 @@
package org.cytoscape.task.internal.quickstart;
import org.cytoscape.model.CyNetworkManager;
-import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderTask;
import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -24,7 +23,6 @@
public void run(TaskMonitor e) {
// Save the property value of showQuickStartAtStartup
- System.out.println("showQuickStartAtStartup = "+
showQuickStartAtStartup);
importTaskUtil.getCyProperty().getProperties().setProperty(quickStartPropertyKey,
new Boolean(showQuickStartAtStartup).toString());
doLoading();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -12,6 +12,7 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new QuickStartTask2(new
QuickStartState(), util, networkManager, subnetworkUtil));
+ return new TaskIterator(new
SimplifiedQuickStartTask(subnetworkUtil));
+// return new TaskIterator(new QuickStartTask2(new
QuickStartState(), util, networkManager, subnetworkUtil));
}
}
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -0,0 +1,33 @@
+package org.cytoscape.task.internal.quickstart;
+
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SearchRelatedGenesTask;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderState;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.util.ListSingleSelection;
+
+public class SelectNextTask extends AbstractTask {
+
+ private static final String SEARCH_OPTION = "Search this network and
create subnetwork";
+ private static final String FINISH_OPTION = "Finished";
+
+ @Tunable(description = "What would you like to do next?")
+ public ListSingleSelection<String> selection = new
ListSingleSelection<String>(SEARCH_OPTION, FINISH_OPTION);
+
+ private final SubnetworkBuilderUtil subnetworkUtil;
+
+
+ SelectNextTask(final SubnetworkBuilderUtil subnetworkUtil) {
+ this.subnetworkUtil = subnetworkUtil;
+ }
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ final String selected = selection.getSelectedValue();
+
+ if(selected == SEARCH_OPTION)
+ insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState()));
+ }
+
+}
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -0,0 +1,21 @@
+package org.cytoscape.task.internal.quickstart;
+
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+
+public class SimplifiedQuickStartTask extends AbstractTask {
+
+ private final SubnetworkBuilderUtil subnetworkUtil;
+
+ SimplifiedQuickStartTask(final SubnetworkBuilderUtil subnetworkUtil) {
+ this.subnetworkUtil = subnetworkUtil;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ insertTasksAfterCurrentTask(new SelectNextTask(subnetworkUtil));
+
insertTasksAfterCurrentTask(subnetworkUtil.getWebServiceImportTask());
+ }
+
+}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -21,7 +21,7 @@
private final SubnetworkBuilderState state;
private final SubnetworkBuilderUtil util;
- SearchRelatedGenesTask(final SubnetworkBuilderUtil util, final
SubnetworkBuilderState state) {
+ public SearchRelatedGenesTask(final SubnetworkBuilderUtil util, final
SubnetworkBuilderState state) {
this.state = state;
this.util = util;
}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SelectNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SelectNetworkTask.java
2011-06-24 22:15:32 UTC (rev 25928)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SelectNetworkTask.java
2011-06-24 22:19:47 UTC (rev 25929)
@@ -1,13 +0,0 @@
-package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
-
-import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskMonitor;
-
-public class SelectNetworkTask extends AbstractTask {
-
- @Override
- public void run(TaskMonitor monitor) throws Exception {
-
- }
-
-}
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