Author: kono
Date: 2012-07-24 10:41:07 -0700 (Tue, 24 Jul 2012)
New Revision: 29974
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
Log:
Add code to close the stream to avoid resource leak.
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2012-07-24 16:32:05 UTC (rev 29973)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2012-07-24 17:41:07 UTC (rev 29974)
@@ -27,16 +27,15 @@
*/
package org.cytoscape.task.internal.layout;
+import java.util.Collection;
+import java.util.Properties;
+
import org.cytoscape.task.AbstractNetworkViewCollectionTask;
-import org.cytoscape.task.AbstractNetworkViewTask;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
-import java.util.Collection;
-import java.util.Properties;
-
public class ApplyPreferredLayoutTask extends
AbstractNetworkViewCollectionTask {
private static final String DEF_LAYOUT = "force-directed";
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
2012-07-24 16:32:05 UTC (rev 29973)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
2012-07-24 17:41:07 UTC (rev 29974)
@@ -12,6 +12,7 @@
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
+
import org.cytoscape.io.read.VizmapReaderManager;
import org.cytoscape.task.read.LoadVizmapFileTaskFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -20,20 +21,23 @@
import org.cytoscape.work.SynchronousTaskManager;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TunableSetter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
-
public class LoadVizmapFileTaskFactoryImpl extends AbstractTaskFactory
implements LoadVizmapFileTaskFactory {
+ private static final Logger logger =
LoggerFactory.getLogger(LoadVizmapFileTaskFactoryImpl.class);
+
private final VizmapReaderManager vizmapReaderMgr;
private final VisualMappingManager vmMgr;
private final SynchronousTaskManager<?> syncTaskManager;
- private LoadVizmapFileTask task;
+ private LoadVizmapFileTask task;
- private final TunableSetter tunableSetter;
+ private final TunableSetter tunableSetter;
-
- public LoadVizmapFileTaskFactoryImpl(VizmapReaderManager
vizmapReaderMgr, VisualMappingManager vmMgr, SynchronousTaskManager<?>
syncTaskManager, TunableSetter tunableSetter) {
+ public LoadVizmapFileTaskFactoryImpl(VizmapReaderManager
vizmapReaderMgr, VisualMappingManager vmMgr,
+ SynchronousTaskManager<?> syncTaskManager,
TunableSetter tunableSetter) {
this.vizmapReaderMgr = vizmapReaderMgr;
this.vmMgr = vmMgr;
this.syncTaskManager = syncTaskManager;
@@ -43,14 +47,15 @@
@Override
public TaskIterator createTaskIterator() {
task = new LoadVizmapFileTask(vizmapReaderMgr, vmMgr);
- return new TaskIterator(2,task);
+ return new TaskIterator(2, task);
}
public Set<VisualStyle> loadStyles(File f) {
// Set up map containing values to be assigned to tunables.
- // The name "file" is the name of the tunable field in
LoadVizmapFileTask.
- Map<String,Object> m = new HashMap<String,Object>();
- m.put("file",f);
+ // The name "file" is the name of the tunable field in
+ // LoadVizmapFileTask.
+ Map<String, Object> m = new HashMap<String, Object>();
+ m.put("file", f);
syncTaskManager.setExecutionContext(m);
syncTaskManager.execute(createTaskIterator());
@@ -59,7 +64,7 @@
}
public Set<VisualStyle> loadStyles(InputStream is) {
- //Save the contents of inputStream in a tmp file
+ // Save the contents of inputStream in a tmp file
File f = this.getFileFromStream(is);
return this.loadStyles(f);
}
@@ -70,14 +75,14 @@
final Map<String, Object> m = new HashMap<String, Object>();
m.put("file", file);
- return
tunableSetter.createTaskIterator(this.createTaskIterator(), m);
+ return
tunableSetter.createTaskIterator(this.createTaskIterator(), m);
}
-
+
// Read the inputStream and save the content in a tmp file
- private File getFileFromStream(InputStream is){
+ private File getFileFromStream(InputStream is) {
File returnFile = null;
-
+
// Get the contents from inputStream
ArrayList<String> list = new ArrayList<String>();
@@ -85,44 +90,51 @@
String line;
try {
- bf = new BufferedReader(new InputStreamReader(is));
+ bf = new BufferedReader(new InputStreamReader(is));
while (null != (line = bf.readLine())) {
list.add(line);
}
- }
- catch (IOException e){
- }
- finally {
+ } catch (IOException e) {
+ logger.error("Could not read the VizMap file.", e);
+ } finally {
try {
- if (bf != null) bf.close();
+ if (bf != null)
+ bf.close();
+ } catch (IOException e) {
+ logger.error("Could not Close the stream.", e);
+ bf = null;
}
- catch (IOException e) {
- }
}
- if (list.size()==0){
+ if (list.size() == 0)
return null;
- }
// Save the content to a tmp file
- Writer output;
+ Writer output = null;
try {
returnFile = File.createTempFile("visualStyles",
".props", new File(System.getProperty("java.io.tmpdir")));
returnFile.deleteOnExit();
-
- //use buffering
+
+ // use buffering
output = new BufferedWriter(new FileWriter(returnFile));
- //FileWriter always assumes default encoding is OK!
- for (int i=0; i< list.size(); i++){
- output.write( list.get(i)+ "\n");
+ // FileWriter always assumes default encoding is OK!
+ for (int i = 0; i < list.size(); i++) {
+ output.write(list.get(i) + "\n");
}
- output.close();
- }
- catch(IOException ioe){
+ } catch (IOException ioe) {
ioe.printStackTrace();
+ } finally {
+ if (output != null) {
+ try {
+ output.close();
+ output = null;
+ } catch (IOException e) {
+ logger.error("Could not close stream.",
e);
+ output = null;
+ }
+
+ }
}
-
return returnFile;
}
-
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
