Author: kono
Date: 2011-03-08 11:54:12 -0800 (Tue, 08 Mar 2011)
New Revision: 24334
Added:
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
Removed:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/MajorIDSets.java
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/QuickStartState.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/QuickStartTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNetworkIdTypeTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectTableMappingKeyTask.java
Log:
Network load work flow is mostly done.
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
(from rev 24332,
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/MajorIDSets.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/IDType.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -0,0 +1,21 @@
+package org.cytoscape.task.internal.quickstart;
+
+/**
+ * List of major ID types.
+ */
+public enum IDType {
+ ENSEMBL("Ensembl Gene ID"), ENTREZ_GENE("Entrez Gene ID"),
UNIPROT("UniProt ID");
+
+ 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/ImportTaskUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -0,0 +1,53 @@
+package org.cytoscape.task.internal.quickstart;
+
+import java.util.Properties;
+
+import org.cytoscape.io.read.CyNetworkViewReaderManager;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.task.internal.loadnetwork.LoadNetworkFileTask;
+import org.cytoscape.task.internal.loadnetwork.LoadNetworkURLTask;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.work.Task;
+
+public class ImportTaskUtil {
+
+ private CyNetworkViewReaderManager mgr;
+ private CyNetworkManager netmgr;
+ private final CyNetworkViewManager networkViewManager;
+ private Properties props;
+ private StreamUtil streamUtil;
+
+ private CyNetworkNaming cyNetworkNaming;
+
+ public ImportTaskUtil(
+ CyNetworkViewReaderManager mgr,
+ CyNetworkManager netmgr,
+ final CyNetworkViewManager networkViewManager,
+ CyProperty<Properties> cyProps, CyNetworkNaming
cyNetworkNaming,
+ StreamUtil streamUtil) {
+ this.mgr = mgr;
+ this.netmgr = netmgr;
+ this.networkViewManager = networkViewManager;
+ this.props = cyProps.getProperties();
+ this.cyNetworkNaming = cyNetworkNaming;
+ this.streamUtil = streamUtil;
+
+ }
+
+ public Task getURLImportTask() {
+ return new LoadNetworkURLTask(mgr, netmgr, networkViewManager,
props, cyNetworkNaming, streamUtil);
+ }
+
+ public Task getFileImportTask() {
+ return new LoadNetworkFileTask(mgr, netmgr, networkViewManager,
props, cyNetworkNaming);
+ }
+
+ public Task getWebServiceImportTask() {
+ // TODO: what should I return?
+ return null;
+ }
+
+}
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 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -35,8 +35,8 @@
package org.cytoscape.task.internal.quickstart;
+import org.cytoscape.task.internal.quickstart.QuickStartState.Job;
import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.util.ListSingleSelection;
@@ -53,22 +53,28 @@
FROM_FILE, FROM_URL, FROM_SERVICE);
private QuickStartState state;
+ private final ImportTaskUtil util;
- public LoadNetworkTask(QuickStartState state) {
+ 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));
+
final String selected = dataSource.getSelectedValue();
if(selected == FROM_FILE) {
// Load file task
+ insertTasksAfterCurrentTask(util.getFileImportTask());
} else if(selected == FROM_URL) {
// Load URL task
+ insertTasksAfterCurrentTask(util.getURLImportTask());
} else if(selected == FROM_SERVICE) {
// TODO create new task
}
- // Next, specify ID type
- insertTasksAfterCurrentTask(new SelectNetworkIdTypeTask(state));
+ state.finished(Job.LOAD_NETWORK);
}
}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/MajorIDSets.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/MajorIDSets.java
2011-03-08 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/MajorIDSets.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -1,21 +0,0 @@
-package org.cytoscape.task.internal.quickstart;
-
-/**
- * List of major ID types.
- */
-public enum MajorIDSets {
- ENSEMBL("Ensembl Gene ID"), ENTREZ_GENE("Entrez Gene ID"),
UNIPROT("UniProt ID");
-
- private final String displayName;
-
- private MajorIDSets(final String displayName) {
- this.displayName = displayName;
- }
-
-
- public String getDisplayName() {
- return this.displayName;
- }
-
-
-}
\ No newline at end of file
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 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartState.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -35,15 +35,10 @@
package org.cytoscape.task.internal.quickstart;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-import java.util.EnumSet;
import java.util.Collections;
+import java.util.EnumSet;
+import java.util.Set;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTable;
-
class QuickStartState {
enum Job {
@@ -55,17 +50,6 @@
private final Set<Job> completedSoFar =
Collections.synchronizedSet(EnumSet.noneOf(Job.class));
- private final List<CyNetwork> networks = new ArrayList<CyNetwork>();
- private final List<CyTable> tables = new ArrayList<CyTable>();
-
- List<CyNetwork> getNetworks() {
- return networks;
- }
-
- List<CyTable> getTables() {
- return tables;
- }
-
synchronized void finished(Job j) {
completedSoFar.add(j);
}
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
2011-03-08 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -51,16 +51,18 @@
LOAD_NETWORK, LOAD_TABLE);
private final QuickStartState state;
+ private final ImportTaskUtil importTaskUtil;
- public QuickStartTask(final QuickStartState state) {
+ public QuickStartTask(final QuickStartState state, final ImportTaskUtil
importTaskUtil) {
super();
this.state = state;
+ this.importTaskUtil = importTaskUtil;
}
public void run(TaskMonitor e) {
String selected = selection.getSelectedValue();
if (selected == LOAD_NETWORK) {
- insertTasksAfterCurrentTask(new LoadNetworkTask(state));
+ insertTasksAfterCurrentTask(new LoadNetworkTask(state,
importTaskUtil));
} else if (selected == LOAD_TABLE)
insertTasksAfterCurrentTask(new LoadTableTask(state));
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory.java
2011-03-08 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -33,8 +33,14 @@
public class QuickStartTaskFactory implements TaskFactory {
+
+ private final ImportTaskUtil util;
+
+ public QuickStartTaskFactory(ImportTaskUtil util) {
+ this.util = util;
+ }
public TaskIterator getTaskIterator() {
- return new TaskIterator(new QuickStartTask(new
QuickStartState()));
+ return new TaskIterator(new QuickStartTask(new
QuickStartState(), util));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNetworkIdTypeTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNetworkIdTypeTask.java
2011-03-08 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNetworkIdTypeTask.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -3,6 +3,7 @@
import java.util.ArrayList;
import java.util.List;
+import org.cytoscape.task.internal.quickstart.QuickStartState.Job;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -18,15 +19,23 @@
public SelectNetworkIdTypeTask(final QuickStartState state) {
this.state = state;
final List<String> values = new ArrayList<String>();
- for(MajorIDSets val: MajorIDSets.values())
+ for(IDType val: IDType.values())
values.add(val.getDisplayName());
selection = new ListSingleSelection<String>(values);
}
@Override
- public void run(TaskMonitor arg0) throws Exception {
+ public void run(TaskMonitor monitor) throws Exception {
System.out.println("ID type selected for network. Selected
type = " + selection.getSelectedValue());
- insertTasksAfterCurrentTask(new LoadTableTask(state));
+ state.finished(Job.SELECT_NETWORK_ID_TYPE);
+
+ if(state.isFinished()) {
+ monitor.setStatusMessage("Finished!");
+ monitor.setProgress(1.0);
+ } else {
+ // Need to load table.
+ insertTasksAfterCurrentTask(new LoadTableTask(state));
+ }
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectTableMappingKeyTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectTableMappingKeyTask.java
2011-03-08 19:26:02 UTC (rev 24333)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectTableMappingKeyTask.java
2011-03-08 19:54:12 UTC (rev 24334)
@@ -12,7 +12,7 @@
@Tunable(description="Select Column ID Type")
- public ListSingleSelection<MajorIDSets> selection = new
ListSingleSelection<MajorIDSets>(MajorIDSets.ENSEMBL,MajorIDSets.ENTREZ_GENE,
MajorIDSets.UNIPROT);
+ public ListSingleSelection<IDType> selection = new
ListSingleSelection<IDType>(IDType.ENSEMBL,IDType.ENTREZ_GENE, IDType.UNIPROT);
private final QuickStartState state;
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